Allotrope Merged Ontology Suite
The AFO is an ontology suite that provides a standard vocabulary and semantic model for the representation of laboratory analytical processes. The AFO suite is aligned at the upper layer to the Basic Formal Ontology (BFO). The core domains modeled include: Equipment, Material, Process, and Results.
This version of Allotrope Foundation Ontology (AFO) has been prepared specifically for publication on the NCBO platform.
license: http://purl.allotrope.org/voc/creative-commons-attribution-license
rights: http://purl.allotrope.org/voc/copyright
Please get the latest version of AFO from http://purl.allotrope.org
' download_owl: http://aber-owl.net/media/ontologies/AFO/31/afo.owl homepage: http://purl.allotrope.org name: Allotrope Merged Ontology Suite prefix: AFO version: REC/2022/12 bioportal: contact: email: more.info@allotrope.org name: Allotrope Foundation description: 'Allotrope Merged Ontology Suite
The AFO is an ontology suite that provides a standard vocabulary and semantic model for the representation of laboratory analytical processes. The AFO suite is aligned at the upper layer to the Basic Formal Ontology (BFO). The core domains modeled include: Equipment, Material, Process, and Results.
This version of Allotrope Foundation Ontology (AFO) has been prepared specifically for publication on the NCBO platform.
license: http://purl.allotrope.org/voc/creative-commons-attribution-license
rights: http://purl.allotrope.org/voc/copyright
Please get the latest version of AFO from http://purl.allotrope.org
' homepage: http://purl.allotrope.org name: Allotrope Merged Ontology Suite prefix: AFO publication: http://www.allotrope.org version: REC/2022/12 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. homepage: https://seco.cs.aalto.fi/ontologies/afo/ license: CC-BY-4.0 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=$1 name: Assembling the Fungal Tree of Life - Taxonomy agilent.probe: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: 'This is the Agilent SurePrint G3 Human GE v2 8x60k Microarray, Agilent design ID 039494, GridName 039494_D_F_20120628. Probe layout is 1 x 1 x 384 rows x 164 cols, which is different from a similar ADF A-GEOD-16699 (1 x 1 x 328 rows x 192 cols). Version 2 of this array contains long intergenic non-coding RNA (lincRNA) probes designed to the human catalog of lincRNAs from the Broad Institute, along with an update of mRNA content when compared to version 1. Probes were designed using GRCh37 assembly of the human genome. Annotation of probes came from the following database: RefSeq Build 50, Ensembl Release 52, Unigene Build 216, GenBank (April 2009), Broad Institute Human lincRNA catalog (Nov 2011), Broad Institute TUCP transcripts catalog (Nov 2011). Probe annotation was taken from A-GEOD-16699.' example: A_24_P98555 homepage: https://www.ebi.ac.uk/arrayexpress/files/A-MEXP-2320/A-MEXP-2320.adf.txt keywords: - transcriptomics name: Agilent Probe pattern: ^A_\d+_.+$ 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/$1 contributor_extras: - email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 - email: cjmungall@lbl.gov github: cmungall name: Chris Mungall orcid: 0000-0002-6601-2165 go: homepage: http://agricola.nal.usda.gov/ name: AGRICultural OnLine Access prefix: AGRICOLA_ID mappings: biocontext: AGRICOLA go: AGRICOLA_ID miriam: agricola n2t: agricola uniprot: DB-0266 miriam: deprecated: false description: AGRICOLA (AGRICultural OnLine Access) serves as the catalog and index to the collections of the National Agricultural Library, as well as a primary public source for world-wide access to agricultural information. The database covers materials in all formats and periods, including printed works from as far back as the 15th century. homepage: http://agricola.nal.usda.gov/ id: 00000589 name: AGRICOLA namespaceEmbeddedInLui: false pattern: ^\d+$ 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 publications: - doi: 10.1093/nar/gkz813 pmc: PMC6943066 pubmed: '31552413' title: 'Alliance of Genome Resources Portal: unified model organism research platform.' year: 2020 synonyms: - AGR - AGRICOLA_ID uniprot: abbreviation: AGR category: Organism-specific databases homepage: https://alliancegenome.org/ name: The Alliance of Genome Resources prefix: DB-0266 publications: - doi: 10.1093/nar/gkz813 pubmed: '31552413' uri_format: https://alliancegenome.org/gene/$1 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/$1 contact: email: cjmungall@lbl.gov github: cmungall name: Chris Mungall orcid: 0000-0002-6601-2165 contributor: email: null github: sierra-moxon name: Sierra Moxon orcid: 0000-0002-8719-7760 description: 'The [Alliance of Genome Resources](https://www.alliancegenome.org/about-us) creates identifiers for several biological entity types including genes, other sequence features, constructs, morpholinos, TALENs, CRISPRs, variants, alleles, genotypes, strains, environments and experiments, phenotype annotations, expression annotations, disease annotations, interactions, and variant annotations. The Alliance of Genome Resources was founded by the following Model Organism databases and the Gene Ontology Consortium and distributes high-quality, curated knowledge about several model organisms in a single, unified location: - [ZFIN](https://zfin.org) - Zebrafish Information Network - [WormBase](https://wormbase.org) - [MGI](https://www.mgi.org) - Mouse Genome Informatics - [RGD](https://rgd.mcw.edu) - Rat Genome Database - [SGD](https://www.yeastgenome.org) - Saccharomyces Genome Database - [FlyBase](https://flybase.org) - [Xenbase](https://www.xenbase.org)' example: '100000000000001' github_request_issue: 359 homepage: https://www.alliancegenome.org keywords: - model organism database mappings: biolink: AGRKB name: Alliance of Genome Resources Knowledge Base pattern: ^[1-9][0-9]{14}$ 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/7/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. homepage: https://bigdata.cgiar.org/resources/agronomy-ontology/ license: CC-BY-4.0 name: Agronomy Ontology prefix: FAIRsharing.m40bhw publications: [] repository: https://github.com/AgriculturalSemantics/agro/issues/ 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 domain: agriculture download.owl: http://purl.obolibrary.org/obo/agro.owl homepage: https://github.com/AgriculturalSemantics/agro license: CC BY 4.0 license.url: https://creativecommons.org/licenses/by/4.0/ name: Agronomy Ontology preferredPrefix: AGRO prefix: agro publications: - id: http://ceur-ws.org/Vol-1747/IT205_ICBO2016.pdf title: 'Data-driven Agricultural Research for Development: A Need for Data Harmonization Via Semantics.' repository: https://github.com/AgriculturalSemantics/agro ols: description: AgrO is an ontlogy for representing agronomic practices, techniques, variables and related entities download: 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: An RDF vocabulary for describing the basic structure and content of concept schemes such as thesauri, classification schemes, subject heading lists, taxonomies, 'folksonomies', other types of controlled vocabulary, and also concept schemes embedded in glossaries and terminologies., An RDF vocabulary extending SKOS and allowing the description and linking of lexical entities. 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: 2022-09 banana: c_ bartoc: 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.\n\nAGROVOC consists\ \ of over 39,000 concepts available in up to 40 languages: Arabic, Chinese,\ \ Czech, English, French, German, Hindi, Hungarian, Italian, Japanese, Korean,\ \ Lao, Malay, Norwegian Bokm\xE5l, Persian, Polish, Portuguese, Russian, Slovak,\ \ Spanish, Swahili, Telugu, Thai, Turkish, Ukrainian and others.\n\nYou can\ \ use AGROVOC to look up the common name of a plant in a language that you do\ \ not master, or to find relations between a commodity and the crop from which\ \ it is produced. Your library can use AGROVOC to index its documents, or you\ \ can use it from inside your content management system (e.g., Drupal) to organize\ \ your documents or web site. You can also use AGROVOC as an hub to access many\ \ other vocabularies available on the web.\n\nTo date, AGROVOC is used by researchers,\ \ librarians and information managers for indexing, retrieving and organizing\ \ data in agricultural information systems and Web pages. Currently, AGROVOC\ \ is an SKOS-XL concept scheme and a Linked Open Data (LOD) set aligned with\ \ 16 other multilingual knowledge organization systems related to agriculture.\n\ \nYou may download AGROVOC, access its Web Services or SPARQL endpoint." homepage: http://www.fao.org/agrovoc/ license: CC BY-SA 3.0 name: AGROVOC prefix: '305' wikidata_database: Q292649 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. homepage: http://www.fao.org/agrovoc/ license: CC-BY-3.0-IGO 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 twitter: FAOAIMS homepage: https://data.apps.fao.org/catalog/organization/agrovoc mappings: agroportal: AGROVOC bartoc: '305' ecoportal: AGROVOC fairsharing: FAIRsharing.anpj91 wikidata: P8061 name: Agronomy Vocabulary pattern: ^[a-z0-9]+$ publications: - doi: 10.4060/cb2838en pmc: null pubmed: null title: AGROVOC year: 2021 - doi: 10.3390/engproc2021009017 pmc: null pubmed: null title: 'How Agricultural Digital Innovation Can Benefit from Semantics: The Case of the AGROVOC Multilingual Thesaurus' year: 2021 - doi: 10.1016/j.compag.2020.105965 pmc: null pubmed: null title: 'AGROVOC: The linked data concept hub for food and agriculture' year: 2022 - doi: 10.3390/engproc2021009017 pmc: null pubmed: null title: 'How Agricultural Digital Innovation Can Benefit from Semantics: The Case of the AGROVOC Multilingual Thesaurus' year: null - doi: 10.4060/cb2838en pmc: null pubmed: null title: "AGROVOC \u2013 Semantic data interoperability on food and agriculture" year: null - doi: 10.1016/j.compag.2020.105965 pmc: null pubmed: null title: 'AGROVOC: The linked data concept hub for food and agriculture' year: null references: - http://agrovoc.uniroma2.it/latestAgrovoc/agrovoc_core.nt.zip - http://agrovoc.uniroma2.it/latestAgrovoc/agrovoc_lod.nt.zip - https://en.wikipedia.org/wiki/AGROVOC uri_format: http://aims.fao.org/aos/agrovoc/c_$1 wikidata: database: Q292649 description: identifier for a subject in AGROVOC thesaurus example: - c_00824893 - c_10 - c_33507 name: AGROVOC ID prefix: P8061 uri_format: http://aims.fao.org/aos/agrovoc/$1 agsd: fairsharing: abbreviation: AGSD description: A comprehensive catalogue of animal genome size data where haploid DNA contents (C-values, in picograms) are currently available for 4972 species (3231 vertebrates and 1741 non-vertebrates) based on 6518 records from 669 published sources. homepage: http://www.genomesize.com name: Animal Genome Size Database prefix: FAIRsharing.efp5v2 publications: [] subjects: - Life Science mappings: fairsharing: FAIRsharing.efp5v2 prefixcommons: agsd re3data: r3d100012517 prefixcommons: description: The Animal Genome Size Database (AGSD) is a comprehensive catalogue of animal genome size data where haploid DNA contents (C-values, in picograms) are currently available for 4972 species (3231 vertebrates and 1741 non-vertebrates) based on 6518 records from 669 published sources. example: '4779' homepage: http://www.genomesize.com keywords: - DNA - genome name: Animal Genome Size Database pattern: ^\d+$ prefix: agsd uri_format: http://www.genomesize.com/result_species.php?id=$1 re3data: description: Welcome to the Animal Genome Size Database, Release 2.0, a comprehensive catalogue of animal genome size data. homepage: http://www.genomesize.com name: Animal Genome Size Database prefix: r3d100012517 xrefs: fairsharing: FAIRsharing.efp5v2 nif: 0000-02548 omics: '16749' scr: '007551' reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 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/11/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 publication: "Gir\xF3n, J. C., S. Tarasov, L. A. Gonz\xE1lez Monta\xF1a, N. Matentzoglu,\ \ A. D. Smith, M. Koch, B. E. Boudinot, P. Bouchard, R. Burks, L. Vogt, M. Yoder,\ \ D. Osumi-Sutherland, F. Friedrich, R. Beutel, I. Mik\xF3 (2022) Formalizing\ \ insect morphological data: a model-based, extensible insect anatomy ontology\ \ and its potential applications in biodiversity research and informatics. Preprints.\ \ https://doi.org/10.20944/preprints202201.0254.v1" version: '2023-01-22' 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. domain: anatomy and development download.json: http://purl.obolibrary.org/obo/aism.json download.obo: http://purl.obolibrary.org/obo/aism.obo download.owl: http://purl.obolibrary.org/obo/aism.owl homepage: https://github.com/insect-morphology/aism license: CC BY 4.0 license.url: https://creativecommons.org/licenses/by/4.0/ name: Ontology for the Anatomy of the Insect SkeletoMuscular system (AISM) preferredPrefix: AISM prefix: aism repository: https://github.com/insect-morphology/aism ols: description: The ontology for the Anatomy of the Insect SkeletoMuscular system (AISM) contains terms used to describe the cuticle - as a single anatomical structure - and the skeletal muscle system, to be used in insect biodiversity research. download: 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}$ alfred: comment: This resource doesn't exist on the web anymore deprecated: true mappings: prefixcommons: alfred prefixcommons: description: ALFRED has been designed to make allele frequency data on anthropologically defined human population samples readily available to the scientific community and to link these polymorphism data to the molecular genetics-human genome databases. example: LO362836C homepage: http://alfred.med.yale.edu keywords: - classification - genome name: The ALlele FREquency Database pattern: ^[A-Z]+\d+$ prefix: alfred pubmed_ids: - '12519999' uri_format: https://alfred.med.yale.edu/alfred/recordinfo.asp?UNID=$1 publications: - doi: 10.1093/nar/gkg043 pmc: PMC165490 pubmed: '12519999' title: 'ALFRED: the ALelle FREquency Database. Update.' year: 2003 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 allergome: biocontext: is_identifiers: true is_obo: false prefix: ALLERGOME uri_format: http://identifiers.org/allergome/$1 fairsharing: abbreviation: Allergome description: Allergome aims to supply information on Allergenic Molecules (Allergens) causing an IgE-mediated (allergic, atopic) disease (anaphylaxis, asthma, atopic dermatitis, conjunctivitis, rhinitis, urticaria). The resource is funded through the Allergen Data Laboratories via unrestricted grants from companies and institutions. homepage: http://www.allergome.org/ license: https://creativecommons.org/licenses/by-nc-sa/2.5 name: Allergome prefix: FAIRsharing.w6cxgb publications: - doi: null pubmed_id: 17393720 title: 'Allergome: a unifying platform.' - doi: 10.1016/j.cellimm.2007.02.012 pubmed_id: 17434469 title: 'Bioinformatics applied to allergy: allergen databases, from collecting sequence information to data integration. The Allergome platform as a model.' subjects: - Medicine - Health Science - Life Science - Biomedical Science mappings: biocontext: ALLERGOME fairsharing: FAIRsharing.w6cxgb miriam: allergome n2t: allergome prefixcommons: allergome uniprot: DB-0160 miriam: deprecated: false description: Allergome is a repository of data related to all IgE-binding compounds. Its purpose is to collect a list of allergenic sources and molecules by using the widest selection criteria and sources. homepage: http://www.allergome.org/ id: '00000334' name: Allergome namespaceEmbeddedInLui: false pattern: ^\d+$ 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: 10.1007/s11882-009-0055-9 pmc: null pubmed: '19671381' title: 'Allergen databases: current status and perspectives.' year: 2009 - doi: 10.1016/j.cellimm.2007.02.012 pmc: null pubmed: '17434469' title: 'Bioinformatics applied to allergy: allergen databases, from collecting sequence information to data integration. The Allergome platform as a model.' year: 2007 - doi: null pmc: null pubmed: '17393720' title: 'Allergome: a unifying platform.' year: 2006 uniprot: abbreviation: Allergome category: Protein family/group databases homepage: http://www.allergome.org/ name: Allergome; a platform for allergen knowledge prefix: DB-0160 publications: - doi: 10.1007/s11882-009-0055-9 pubmed: '19671381' uri_format: 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 keywords: - alzheimer's disease - genes - variants name: Alzforum Mutations synonyms: - Alzforum_mut uri_format: https://www.alzforum.org/mutations/$1 alzgene: mappings: prefixcommons: alzgene prefixcommons: description: "The AlzGene database provides a comprehensive, unbiased and regularly\ \ updated field synopsis of genetic association studies performed in Alzheimer\u2019\ s disease. In addition, hundreds of up-to-date meta-analyses are available for\ \ all eligible polymorphisms with sufficient data." example: '88' homepage: http://www.alzgene.org keywords: - gene name: Alzheimer Gene Database pattern: ^\d+$ prefix: alzgene pubmed_ids: - '17192785' uri_format: http://www.alzgene.org/geneoverview.asp?geneid=$1 publications: - doi: 10.1038/ng1934 pmc: null pubmed: '17192785' title: 'Systematic meta-analyses of Alzheimer disease genetic association studies: the AlzGene database.' year: 2007 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 amoebadb: biocontext: is_identifiers: true is_obo: false prefix: AMOEBADB uri_format: http://identifiers.org/amoebadb/$1 fairsharing: abbreviation: AmoebaDB description: AmoebaDB belongs to the EuPathDB family of databases and is an integrated genomic and functional genomic database for Entamoeba and Acanthamoeba parasites. In its first released, AmoebaDB contained the genomes of three Entamoeba species. AmoebaDB integrates whole genome sequence and annotation and will rapidly expand to include experimental data and environmental isolate sequences provided by community researchers . The database includes supplemental bioinformatics analyses and a web interface for data-mining. homepage: http://amoebadb.org name: AmoebaDB prefix: FAIRsharing.swbypy publications: - doi: 10.1093/nar/gkp941 pubmed_id: 19914931 title: 'EuPathDB: a portal to eukaryotic pathogen databases.' subjects: - Functional Genomics - Genomics twitter: eupathdb mappings: biocontext: AMOEBADB fairsharing: FAIRsharing.swbypy miriam: amoebadb n2t: amoebadb prefixcommons: amoebadb re3data: r3d100012457 miriam: deprecated: false description: AmoebaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. homepage: http://amoebadb.org/amoeba/ id: 00000148 name: AmoebaDB namespaceEmbeddedInLui: false pattern: ^EDI_\d+$ 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). domain: anatomy and development download.obo: http://purl.obolibrary.org/obo/amphx.obo download.owl: http://purl.obolibrary.org/obo/amphx.owl homepage: https://github.com/EBISPOT/amphx_ontology license: CC BY 3.0 license.url: http://creativecommons.org/licenses/by/3.0/ name: The Amphioxus Development and Anatomy Ontology preferredPrefix: AMPHX prefix: amphx repository: https://github.com/EBISPOT/amphx_ontology ols: description: An ontology for the development and anatomy of Amphioxus (Branchiostoma lanceolatum). download: 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/$1 fairsharing: abbreviation: AntWeb description: AntWeb is a website documenting the known species of ants, with records for each species linked to their geographical distribution, life history, and includes pictures. homepage: http://www.antweb.org license: CC-BY-4.0 name: AntWeb prefix: FAIRsharing.yk38tw publications: - doi: 10.1038/424242b pubmed_id: 12867945 title: Ants join online colony to boost conservation efforts. subjects: - Anatomy - Life Science mappings: biocontext: ANTWEB fairsharing: FAIRsharing.yk38tw miriam: antweb n2t: antweb ncbi: AntWeb prefixcommons: antweb wikidata: P5299 miriam: deprecated: false description: AntWeb is a website documenting the known species of ants, with records for each species linked to their geographical distribution, life history, and includes pictures. homepage: http://www.antweb.org/ id: '00000146' name: AntWeb namespaceEmbeddedInLui: false pattern: ^casent\d+(\-D\d+)?$ 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=$1 publications: - doi: 10.1038/424242b pmc: null pubmed: '12867945' title: Ants join online colony to boost conservation efforts. year: 2003 wikidata: database: Q2507304 description: identifier for a taxon in the AntWeb database example: - Haidomyrmex - Zatania electra homepage: https://www.antweb.org name: AntWeb ID pattern: ^[A-Z][a-z]+( [a-z]+){0,2}$ prefix: P5299 uri_format: https://www.antweb.org/description.do?taxonName=$1 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 homepage: http://bioportal.bioontology.org/ontologies/APAONTO name: Psychology Ontology prefix: FAIRsharing.gkw1w8 publications: [] subjects: - Psychology - Ontology and Terminology 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/$1 fairsharing: abbreviation: APD description: The Antimicrobial Peptide Database (APD) contains information on antimicrobial peptides from across a wide taxonomic range. It includes a glossary, nomenclature, classification, information search, prediction, design, and statistics of AMPs. The antimicrobial peptides in this database contain less than 100 amino acid residues, are in the mature and active form, and primarily from natural sources, ranging from bacteria, fungi, plants, to animals. homepage: https://wangapd3.com/main.php name: Antimicrobial Peptide Database prefix: FAIRsharing.ctwd7b publications: - doi: 10.1093/nar/gkn823 pubmed_id: 18957441 title: 'APD2: the updated antimicrobial peptide database and its application in peptide design.' - doi: 10.1093/nar/gkh025 pubmed_id: 14681488 title: 'APD: the Antimicrobial Peptide Database.' - doi: 10.1093/nar/gkv1278 pubmed_id: 26602694 title: 'APD3: the antimicrobial peptide database as a tool for research and education.' subjects: - Biology mappings: biocontext: APD fairsharing: FAIRsharing.ctwd7b miriam: apd n2t: apd prefixcommons: apd re3data: r3d100012901 miriam: deprecated: false description: The antimicrobial peptide database (APD) provides information on anticancer, antiviral, antifungal and antibacterial peptides. homepage: http://aps.unmc.edu/AP/ id: 00000278 name: APD namespaceEmbeddedInLui: false pattern: ^\d{5}$ 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 - doi: 10.1093/nar/gkn823 pmc: PMC2686604 pubmed: '18957441' title: 'APD2: the updated antimicrobial peptide database and its application in peptide design.' year: 2008 - doi: 10.1093/nar/gkh025 pmc: PMC308759 pubmed: '14681488' title: 'APD: the Antimicrobial Peptide Database.' year: 2004 re3data: description: The Antimicrobial Peptide Database (APD) was originally created by a graduate student, Zhe Wang, as his master's thesis in the laboratory of Dr. Guangshun Wang. The project was initiated in 2002 and the first version of the database was open to the public in August 2003. It contained 525 peptide entries, which can be searched in multiple ways, including APD ID, peptide name, amino acid sequence, original location, PDB ID, structure, methods for structural determination, peptide length, charge, hydrophobic content, antibacterial, antifungal, antiviral, anticancer, and hemolytic activity. Some results of this bioinformatics tool were reported in the 2004 database paper. The peptide data stored in the APD were gleaned from the literature (PubMed, PDB, Google, and Swiss-Prot) manually in over a decade. homepage: http://aps.unmc.edu/AP/main.php name: Antimicrobial Peptide Database prefix: r3d100012901 synonyms: - APD xrefs: fairsharing: FAIRsharing.ctwd7b nif: 0000-02553 omics: '05706' scr: '006606' aphidbase.transcript: biocontext: is_identifiers: true is_obo: false prefix: APHIDBASE.TRANSCRIPT uri_format: http://identifiers.org/aphidbase.transcript/$1 mappings: biocontext: APHIDBASE.TRANSCRIPT miriam: aphidbase.transcript n2t: aphidbase.transcript prefixcommons: aphidbase miriam: deprecated: false description: AphidBase is a centralized bioinformatic resource that was developed to facilitate community annotation of the pea aphid genome by the International Aphid Genomics Consortium (IAGC). The AphidBase Information System was designed to organize and distribute genomic data and annotations for a large international community. This collection references the transcript report, which describes genomic location, sequence and exon information. homepage: http://www.aphidbase.com/aphidbase id: 00000393 name: AphidBase Transcript namespaceEmbeddedInLui: false pattern: ^ACYPI\d{6}(-RA)?$ prefix: aphidbase.transcript sampleId: ACYPI000159 uri_format: http://bipaa.genouest.org/apps/grs-2.3/grs?reportID=aphidbase_transcript_report&objectID=$1 n2t: description: AphidBase is a centralized bioinformatic resource that was developed to facilitate community annotation of the pea aphid genome by the International Aphid Genomics Consortium (IAGC). The AphidBase Information System was designed to organize and distribute genomic data and annotations for a large international community. This collection references the transcript report, which describes genomic location, sequence and exon information. example: ACYPI000159 homepage: http://www.aphidbase.com/aphidbase name: AphidBase at INRA namespaceEmbeddedInLui: false pattern: ^ACYPI\d{6}(-RA)?$ prefix: aphidbase.transcript uri_format: http://bipaa.genouest.org/apps/grs-2.3/grs?reportID=aphidbase_transcript_report&objectID=$1 prefixcommons: description: The Aphid Genome Database's aim is to improve the current pea aphid genome assembly and annotation, and to provide new aphid genome sequences as well as tools for analysis of these genomes. example: ACYPI003698-RA homepage: http://www.aphidbase.com keywords: - genome miriam: aphidbase.transcript name: 'Aphidbase: an aphid genomics database' pattern: ^ACYPI\d+$ prefix: aphidbase pubmed_ids: - '20482635' publications: - doi: 10.1111/j.1365-2583.2009.00930.x pmc: PMC4372297 pubmed: '20482635' title: 'AphidBase: a centralized bioinformatic resource for annotation of the pea aphid genome.' year: 2010 apid.interactions: biocontext: 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/43/apo.owl homepage: http://www.yeastgenome.org/ name: Ascomycete phenotype ontology prefix: APO biocontext: is_identifiers: false is_obo: true prefix: APO uri_format: http://purl.obolibrary.org/obo/APO_$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 contact: email: cherry@stanford.edu name: J. Michael Cherry orcid: 0000-0001-9163-5180 description: Ascomycete Phenotype Ontology is a structured controlled vocabulary for the phenotypes of Ascomycete fungi. homepage: http://bioportal.bioontology.org/ontologies/APO?p=summary name: Ascomycete Phenotype Ontology prefix: FAIRsharing.dyqz3y publications: [] subjects: - Life Science - Cell Biology twitter: yeastgenome mappings: aberowl: APO biocontext: APO 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 domain: phenotype download.obo: http://purl.obolibrary.org/obo/apo.obo download.owl: http://purl.obolibrary.org/obo/apo.owl homepage: http://www.yeastgenome.org/ license: CC BY 4.0 license.url: https://creativecommons.org/licenses/by/4.0/ name: Ascomycete phenotype ontology preferredPrefix: APO prefix: apo publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/20157474 title: New mutant phenotype data curation system in the Saccharomyces Genome Database repository: https://github.com/obophenotype/ascomycete-phenotype-ontology ols: description: A structured controlled vocabulary for the phenotypes of Ascomycete fungi. download: 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/20/apollo_sv.owl homepage: https://github.com/ApolloDev/apollo-sv name: Apollo Structured Vocabulary prefix: APOLLO_SV bioportal: contact: email: diller17@ufl.edu name: Matthew Diller description: Apollo-SV, developed as an OWL specification, defines the terms and relations necessary for interoperation between epidemic simulators and public health application software that interface with these simulators. homepage: https://github.com/ApolloDev/apollo-sv name: Apollo Structured Vocabulary prefix: APOLLO-SV version: '2023-01-10' example: '00000443' fairsharing: abbreviation: Apollo-SV contact: email: hoganwr@gmail.com name: William Hogan orcid: 0000-0002-9881-1017 description: An ontology of infectious disease epidemiology and ecology (a.k.a. population biology). homepage: http://purl.obolibrary.org/obo/apollo_sv.owl license: CC-BY-3.0 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.' repository: https://github.com/ApolloDev/apollo-sv 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 domain: health download.owl: http://purl.obolibrary.org/obo/apollo_sv.owl homepage: https://github.com/ApolloDev/apollo-sv license: CC BY 4.0 license.url: https://creativecommons.org/licenses/by/4.0/ name: Apollo Structured Vocabulary preferredPrefix: APOLLO_SV prefix: apollo_sv publications: - id: https://doi.org/10.1186/s13326-016-0092-y title: 'The Apollo Structured Vocabulary: an OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation' repository: https://github.com/ApolloDev/apollo-sv ols: description: 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}$ providers: - code: conflated description: This might be resulting from properties in Apollo SV actually trying to use appropriate identifiers homepage: http://purl.obolibrary.org name: OBO PURL in Parts uri_format: http://purl.obolibrary.org/obo/apollo_sv/dev/apollo_sv.owl#APOLLO_SV_$1 publications: - doi: 10.1186/s13326-016-0092-y pmc: PMC4989460 pubmed: '27538448' title: 'The Apollo Structured Vocabulary: an OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation.' year: 2016 - doi: null pmc: PMC3900155 pubmed: '24551417' title: 'Apollo: giving application developers a single point of access to public health models using structured vocabularies and Web services.' year: 2013 arachnoserver: biocontext: is_identifiers: true is_obo: false prefix: ARACHNOSERVER uri_format: http://identifiers.org/arachnoserver/$1 edam: description: Unique identifier of a toxin from the ArachnoServer database. name: ArachnoServer obsolete: false prefix: '2578' fairsharing: abbreviation: ArachnoServer description: ArachnoServer is a manually curated database containing information on the sequence, three-dimensional structure, and biological activity of protein toxins derived from spider venom. homepage: http://www.arachnoserver.org name: 'ArachnoServer: Spider toxin database' prefix: FAIRsharing.c54ywe publications: - doi: 10.1093/nar/gkq1058 pubmed_id: 21036864 title: ArachnoServer 2.0, an updated online resource for spider toxin sequences and structures. subjects: - Life Science mappings: biocontext: ARACHNOSERVER edam: '2578' fairsharing: FAIRsharing.c54ywe miriam: arachnoserver n2t: arachnoserver prefixcommons: arachnoserver re3data: r3d100012902 uniprot: DB-0145 miriam: deprecated: false description: ArachnoServer (www.arachnoserver.org) is a manually curated database providing information on the sequence, structure and biological activity of protein toxins from spider venoms. It include a molecular target ontology designed specifically for venom toxins, as well as current and historic taxonomic information. homepage: http://www.arachnoserver.org/ id: 00000193 name: ArachnoServer namespaceEmbeddedInLui: false pattern: ^AS\d{6}$ 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/bioinformatics/btx661 pmc: null pubmed: '29069336' title: 'ArachnoServer 3.0: an online resource for automated discovery, analysis and annotation of spider toxins.' year: 2018 - doi: 10.1093/nar/gkq1058 pmc: PMC3013666 pubmed: '21036864' title: ArachnoServer 2.0, an updated online resource for spider toxin sequences and structures. year: 2010 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: abbreviation: ArachnoServer category: Organism-specific databases homepage: http://www.arachnoserver.org name: ArachnoServer prefix: DB-0145 publications: - doi: 10.1093/bioinformatics/btx661 pubmed: '29069336' araport: description: Website with general information about Arabidopsis and functionalities such as a genomic viewer homepage: https://www.araport.org/ mappings: miriam: tair.name ncbi: Araport uniprot: DB-0221 miriam: deprecated: false description: The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. The name of a Locus is unique and used by TAIR, TIGR, and MIPS. homepage: https://www.arabidopsis.org/index.jsp id: 00000976 name: TAIR gene name namespaceEmbeddedInLui: false pattern: ^AT.G[0-9]{5}$ prefix: tair.name sampleId: AT5G05330 uri_format: https://www.arabidopsis.org/servlets/TairObject?type=locus&name=$1 name: Arabidopsis Information Portal ncbi: example: AT1G01010 homepage: https://www.araport.org/ name: Arabidopsis Information Portal prefix: Araport publications: - doi: 10.1093/nar/gku1200 pmc: PMC4383980 pubmed: '25414324' title: 'Araport: the Arabidopsis information portal.' year: 2014 uniprot: abbreviation: Araport category: Organism-specific databases homepage: https://bar.utoronto.ca/thalemine/begin.do name: Arabidopsis Information Portal prefix: DB-0221 publications: - doi: 10.1093/nar/gku1200 pubmed: '25414324' uri_format: https://bar.utoronto.ca/thalemine/portal.do?externalids=$1 uri_format: https://www.arabidopsis.org/servlets/TairObject?type=locus&name=$1 archdb: fairsharing: abbreviation: ArchDB contact: email: narcis.fernandez@gmail.com name: Narcis Fernandez-Fuentes orcid: 0000-0002-6421-1080 description: ArchDB is a compilation of structural classifications of loops extracted from known protein structures. The structural classification is based on the geometry and conformation of the loop. The geometry is defined by four internal variables and the type of regular flanking secondary structures, resulting in 10 different loop types. Loops in ArchDB have been classified using an improved version (Espadaler et al.) of the original ArchType program published in 1997 by Oliva et al. homepage: http://sbi.imim.es/archdb name: ArchDB prefix: FAIRsharing.tp9z4q publications: - doi: 10.1093/nar/gkh002 pubmed_id: 14681390 title: 'ArchDB: automated protein loop classification as a tool for structural genomics.' - doi: 10.1093/nar/gkt1189 pubmed_id: 24265221 title: 'ArchDB 2014: structural classification of loops in proteins.' subjects: - Life Science mappings: fairsharing: FAIRsharing.tp9z4q prefixcommons: archdb prefixcommons: description: ArchDB is a compilation of structural classifications of loops extracted from known protein structures. Loops in ArchDB have been classified using an improved version (Espadaler et al.) of the original ArchType program published in 1997 by Oliva et al.. example: '39421' homepage: http://sbi.imim.es/archdb keywords: - classification - protein name: ArchDB pattern: ^\d+$ prefix: archdb pubmed_ids: - '24265221' uri_format: http://sbi.imim.es/cgi-bin/archdb//loops.pl?loop=$1 publications: - doi: 10.1093/nar/gkt1189 pmc: PMC3964960 pubmed: '24265221' title: 'ArchDB 2014: structural classification of loops in proteins.' year: 2013 - doi: 10.1093/nar/gkh002 pmc: PMC308737 pubmed: '14681390' title: 'ArchDB: automated protein loop classification as a tool for structural genomics.' year: 2004 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 ardb: biocontext: 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&field=ni&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&field=ni&term=$1 ark: banana: ark biocontext: is_identifiers: true is_obo: false prefix: ARK uri_format: http://identifiers.org/ark/$1 contact: email: jakkbl@gmail.com github: jkunze name: John Kunze orcid: 0000-0001-7604-8041 contributor_extras: - email: jakkbl@gmail.com github: jkunze name: John Kunze orcid: 0000-0001-7604-8041 - email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 example: /53355/cl010066723 fairsharing: abbreviation: ARK Identifier description: "Archival Resource Keys (ARKs) serve as persistent identifiers, or\ \ stable, trusted references for information objects. Among other things, they\ \ aim to be web addresses (URLs) that don\u2019t return 404 Page Not Found errors.\ \ The ARK Alliance is an open global community supporting the ARK infrastructure\ \ on behalf of research and scholarship. End users, especially researchers,\ \ rely on ARKs for long term access to the global scientific and cultural record.\ \ Since 2001 some 8.2 billion ARKs have been created by over 1000 organizations\ \ \u2014 libraries, data centers, archives, museums, publishers, government\ \ agencies, and vendors. They identify anything digital, physical, or abstract.\ \ ARKs are open, mainstream, non-paywalled, decentralized persistent identifiers\ \ that can be created by an organization as soon as it is registered with a\ \ NAAN (Name Assigning Authority Number). Once registered, an ARK organization\ \ can create unlimited numbers of ARKs and publicize them via the n2t.net global\ \ resolver or via their own local resolver." homepage: https://arks.org/ name: Archival Resource Key Identifier prefix: FAIRsharing.f928f1 publications: [] subjects: - Data Management - Subject Agnostic twitter: ARKsInTheOpen homepage: https://arks.org mappings: biocontext: ARK fairsharing: FAIRsharing.f928f1 miriam: ark n2t: ark miriam: deprecated: false description: "Archival Resource Keys (ARKs) serve as persistent identifiers, or\ \ stable, trusted references for information objects. Among other things, they\ \ aim to be web addresses (URLs) that don\u2019t return 404 Page Not Found errors.\ \ The ARK Alliance is an open global community supporting the ARK infrastructure\ \ on behalf of research and scholarship. End users, especially researchers,\ \ rely on ARKs for long term access to the global scientific and cultural record.\ \ Since 2001 some 8.2 billion ARKs have been created by over 1000 organizations\ \ \u2014 libraries, data centers, archives, museums, publishers, government\ \ agencies, and vendors. They identify anything digital, physical, or abstract.\ \ ARKs are open, mainstream, non-paywalled, decentralized persistent identifiers\ \ that can be created by an organization as soon as it is registered with a\ \ NAAN (Name Assigning Authority Number). Once registered, an ARK organization\ \ can create unlimited numbers of ARKs and publicize them via the n2t.net global\ \ resolver or via their own local resolver." homepage: https://arks.org id: 00000592 name: Archival Resource Key (ARK) namespaceEmbeddedInLui: true pattern: ^(ark\:)/*[0-9A-Za-z]+(?:/[\w/.=*+@\$-]*)?(?:\?.*)?$ prefix: ark sampleId: /53355/cl010066723 uri_format: 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:$1 name: Archival Resource Key pattern: ^/*[0-9A-Za-z]+(?:/[\w/.=*+@\$-]*)?(?:\?.*)?$ references: - https://n2t.net/e/about.html twitter: ARKsInTheOpen 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_$1 bioportal: contact: email: mcarthua@mcmaster.ca name: Andrew G. McArthur description: The Antibiotic Resistance Ontology describes antibiotic resistance genes and mutations, their products, mechanisms, and associated phenotypes, as well as antibiotics and their molecular targets. It is integrated with the Comprehensive Antibiotic Resistance Database, a curated resource containing high quality reference data on the molecular basis of antimicrobial resistance. homepage: https://github.com/arpcard/aro name: Antibiotic Resistance Ontology prefix: ARO download_obo: http://purl.obolibrary.org/obo/aro.obo example: '1000001' mappings: aberowl: ARO biocontext: ARO bioportal: ARO obofoundry: aro ols: aro ontobee: ARO obofoundry: appears_in: - scdo contact: mcarthua@mcmaster.ca contact.github: agmcarthur contact.label: Andrew G. McArthur contact.orcid: 0000-0002-1142-3063 deprecated: false description: Antibiotic resistance genes and mutations domain: microbiology download.owl: http://purl.obolibrary.org/obo/aro.owl homepage: https://github.com/arpcard/aro license: CC BY 4.0 license.url: https://creativecommons.org/licenses/by/4.0/ name: Antibiotic Resistance Ontology preferredPrefix: ARO prefix: aro publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/31665441 title: 'CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database.' repository: https://github.com/arpcard/aro ols: description: Antibiotic resistance genes and mutations download: http://purl.obolibrary.org/obo/aro.owl homepage: https://github.com/arpcard/aro name: Antibiotic Resistance Ontology prefix: aro ontobee: library: Library name: Antibiotic Resistance Ontology prefix: ARO pattern: ^\d{7}$ 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/$1 fairsharing: abbreviation: ArrayExpress description: ArrayExpress is a database of functional genomics experiments that can be queried and the data downloaded. It includes gene expression data from microarray and high throughput sequencing studies. Data is collected to MIAME and MINSEQE standards. Experiments are submitted directly to ArrayExpress or are imported from the NCBI GEO database. homepage: https://www.ebi.ac.uk/arrayexpress/ name: ArrayExpress prefix: FAIRsharing.6k0kwd publications: - doi: 10.1093/nar/gkg091 pubmed_id: 12519949 title: ArrayExpress--a public repository for microarray gene expression data at the EBI. - doi: 10.1093/nar/gku1057 pubmed_id: 25361974 title: ArrayExpress update-simplifying data submissions. - doi: 10.1093/nar/gky964 pubmed_id: 30357387 title: "ArrayExpress update \u2013 from bulk to single-cell expression data" subjects: - Functional Genomics twitter: ArrayExpressEBI mappings: biocontext: ARRAYEXPRESS cellosaurus: ArrayExpress fairsharing: FAIRsharing.6k0kwd miriam: arrayexpress n2t: arrayexpress prefixcommons: arrayexpress re3data: r3d100010222 miriam: deprecated: false description: ArrayExpress is a public repository for microarray data, which is aimed at storing MIAME-compliant data in accordance with Microarray Gene Expression Data (MGED) recommendations. homepage: https://www.ebi.ac.uk/arrayexpress/ id: '00000036' name: ArrayExpress namespaceEmbeddedInLui: false pattern: ^[AEP]-\w{4}-\d+$ 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/gky964 pmc: PMC6323929 pubmed: '30357387' title: ArrayExpress update - from bulk to single-cell expression data. year: 2019 - doi: 10.1093/nar/gku1057 pmc: PMC4383899 pubmed: '25361974' title: ArrayExpress update--simplifying data submissions. year: 2014 - doi: 10.1093/nar/gkg091 pmc: PMC165538 pubmed: '12519949' title: ArrayExpress--a public repository for microarray gene expression data at the EBI. year: 2003 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 contact: email: mbaudis@me.com name: Michael Baudis orcid: 0000-0002-9903-4248 description: Part of the Progenetix project, the arrayMap database facilitates the study of the genetics of human cancer. The Progenetix project provides the data customisation and visualization tools to mine the available data. The arrayMap database is developed by the group "Theoretical Cytogenetics and Oncogenomics" at the Department of Molecular Life Sciences of the University of Zurich. homepage: http://arraymap.org license: https://creativecommons.org/licenses/by-nc-nd/2.5/ch name: arrayMap - Genomic Array Data for Cancer CNV Profiles prefix: FAIRsharing.1fbc5y publications: - doi: 10.1371/journal.pone.0036944 pubmed_id: 22629346 title: 'arrayMap: a reference resource for genomic copy number imbalances in human malignancies.' - doi: 10.1093/nar/gku1123 pubmed_id: 25428357 title: 'arrayMap 2014: an updated cancer genome resource.' - doi: 10.1186/1471-2164-15-82 pubmed_id: 24476156 title: Chromothripsis-like patterns are recurring but heterogeneously distributed features in a survey of 22,347 cancer genome screens. - doi: 10.1093/nar/gkv1310 pubmed_id: 26615188 title: 'The SIB Swiss Institute of Bioinformatics'' resources: focus on curated databases.' subjects: - Genomics - Bioinformatics - Life Science - Biomedical Science twitter: progenetix mappings: biocontext: ARRAYMAP fairsharing: FAIRsharing.1fbc5y miriam: arraymap n2t: arraymap re3data: r3d100012630 miriam: deprecated: false description: arrayMap is a collection of pre-processed oncogenomic array data sets and CNA (somatic copy number aberrations) profiles. CNA are a type of mutation commonly found in cancer genomes. arrayMap data is assembled from public repositories and supplemented with additional sources, using custom curation pipelines. This information has been mapped to multiple editions of the reference human genome. homepage: https://www.arraymap.org id: '00000621' name: ArrayMap namespaceEmbeddedInLui: false pattern: ^[\w\-:,]{3,64}$ prefix: arraymap sampleId: icdom:8500_3 uri_format: https://www.arraymap.org/pgx:$1 n2t: description: arrayMap is a collection of pre-processed oncogenomic array data sets and CNA (somatic copy number aberrations) profiles. CNA are a type of mutation commonly found in cancer genomes. arrayMap data is assembled from public repositories and supplemented with additional sources, using custom curation pipelines. This information has been mapped to multiple editions of the reference human genome. example: icdom:8500_3 homepage: https://www.arraymap.org name: ArrayMap namespaceEmbeddedInLui: false pattern: ^[\w\-:,]{3,64}$ prefix: arraymap uri_format: https://www.arraymap.org/pgx:$1 publications: - doi: 10.1093/nar/gkv1310 pmc: PMC4702916 pubmed: '26615188' title: 'The SIB Swiss Institute of Bioinformatics'' resources: focus on curated databases.' year: 2015 - doi: 10.1093/nar/gku1123 pmc: PMC4383937 pubmed: '25428357' title: 'arrayMap 2014: an updated cancer genome resource.' year: 2014 - doi: 10.1186/1471-2164-15-82 pmc: PMC3909908 pubmed: '24476156' title: Chromothripsis-like patterns are recurring but heterogeneously distributed features in a survey of 22,347 cancer genome screens. year: 2014 - doi: 10.1371/journal.pone.0036944 pmc: PMC3356349 pubmed: '22629346' title: 'arrayMap: a reference resource for genomic copy number imbalances in human malignancies.' year: 2012 re3data: description: arrayMap is a repository of cancer genome profiling data. Original) from primary repositories (e.g. NCBI GEO, EBI ArrayExpress, TCGA) is re-processed and annotated for metadata. Unique visualization of the processed data allows critical evaluation of data quality and genome information. Structured metadata provides easy access to summary statistics, with a focus on copy number aberrations in cancer entities. 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/$1 mappings: biocontext: ARXIV miriam: arxiv n2t: arxiv prefixcommons: arxiv wikidata: P818 miriam: deprecated: false description: arXiv is an e-print service in the fields of physics, mathematics, non-linear science, computer science, and quantitative biology. homepage: https://arxiv.org/ id: '00000035' name: arXiv namespaceEmbeddedInLui: false pattern: ^(\w+(\-\w+)?(\.\w+)?)?\d{4,7}(\.\d+(v\d+)?)?$ 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/$1 wikidata: database: Q18920853 description: identifier of a document in arXiv pre-print archive example: - '0806.2878' - '1109.1746' homepage: http://arxiv.org/abs/ name: arXiv ID pattern: ^(\d{4}.\d{4,5}|[a-z\-]+(\.[A-Z]{2})?\/\d{7})(v\d+)?$ prefix: P818 uri_format: http://arxiv.org/abs/$1 asap: biocontext: 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. homepage: https://asap.ahabs.wisc.edu/asap/home.php name: A Systematic Annotation Package prefix: FAIRsharing.anpa6 publications: - doi: 10.1093/nar/gkg125 pubmed_id: 12519969 title: ASAP, a systematic annotation package for community analysis of genomes. subjects: - Developmental Biology - Life Science - Comparative Genomics go: homepage: https://asap.genetics.wisc.edu/asap/ASAP1.htm name: A Systematic Annotation Package for Community Analysis of Genomes prefix: ASAP uri_format: https://asap.genetics.wisc.edu/asap/feature_info.php?FeatureID=$1 mappings: biocontext: ASAP fairsharing: FAIRsharing.anpa6 go: ASAP miriam: asap n2t: asap ncbi: ASAP prefixcommons: asap re3data: r3d100010666 miriam: deprecated: false description: ASAP (a systematic annotation package for community analysis of genomes) stores bacterial genome sequence and functional characterization data. It includes multiple genome sequences at various stages of analysis, corresponding experimental data and access to collections of related genome resources. homepage: http://asap.ahabs.wisc.edu/asap/home.php id: 00000283 name: ASAP namespaceEmbeddedInLui: false pattern: ^[A-Za-z0-9-]+$ 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/gkj164 pmc: PMC1347526 pubmed: '16381899' title: 'ASAP: a resource for annotating, curating, comparing, and disseminating genomic data.' year: 2006 - doi: 10.1093/nar/gkg125 pmc: PMC165572 pubmed: '12519969' title: ASAP, a systematic annotation package for community analysis of genomes. year: 2003 re3data: description: 'ASAP (a systematic annotation package for community analysis of genomes) is a relational database and web interface developed to store, update and distribute genome sequence data and gene expression data collected by or in collaboration with researchers at the University of Wisconsin - Madison. ASAP was designed to facilitate ongoing community annotation of genomes and to grow with genome projects as they move from the preliminary data stage through post-sequencing functional analysis. The ASAP database includes multiple genome sequences at various stages of analysis, and gene expression data from preliminary experiments.' homepage: https://asap.ahabs.wisc.edu/asap/home.php name: ASAP prefix: r3d100010666 synonyms: - A systematic annotation package for community analysis of genomes xrefs: fairsharing: FAIRsharing.anpa6 nif: 0000-02571 scr: 001849 ascl: biocontext: is_identifiers: true is_obo: false prefix: ASCL uri_format: http://identifiers.org/ascl/$1 fairsharing: abbreviation: ASCL description: The Astrophysics Source Code Library (ASCL) is a free online registry for source code of interest to astronomers and astrophysicists. It provides code that has been used in research that has appeared in, or been submitted to, peer-reviewed publications.Peer-reviewed papers that describe methods or experiments involving the development or use of source code are added by the ASCL team. homepage: http://ascl.net/ name: Astrophysics Source Code Library prefix: FAIRsharing.wb0txg publications: - doi: 10.5334/jors.bv pubmed_id: null title: 'Looking before Leaping: Creating a Software Registry' subjects: - Astrophysics and Astronomy twitter: asclnet mappings: biocontext: ASCL fairsharing: FAIRsharing.wb0txg miriam: ascl n2t: ascl re3data: r3d100011865 miriam: deprecated: false description: The Astrophysics Source Code Library (ASCL) is a free online registry for software that have been used in research that has appeared in, or been submitted to, peer-reviewed publications. The ASCL is indexed by the SAO/NASA Astrophysics Data System (ADS) and Web of Science's Data Citation Index (WoS DCI), and is citable by using the unique ascl ID assigned to each code. The ascl ID can be used to link to the code entry by prefacing the number with ascl.net (i.e., ascl.net/1201.001). homepage: http://ascl.net/ id: '00000641' name: Astrophysics Source Code Library namespaceEmbeddedInLui: false pattern: ^[0-9\.]+$ 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 publications: - doi: 10.5334/jors.bv pmc: null pubmed: null title: 'Looking before Leaping: Creating a Software Registry' year: 2015 re3data: description: The Astrophysics Source Code Library (ASCL) is a free online registry for source codes of interest to astronomers and astrophysicists and lists codes that have been used in research that has appeared in, or been submitted to, peer-reviewed publications. The ASCL is citable by using the unique ascl ID assigned to each code. The ascl ID can be used to link to the code entry by prefacing the number with ascl.net (i.e., ascl.net/1201.001). homepage: http://ascl.net/ name: Astrophysics Source Code Library prefix: r3d100011865 synonyms: - ASCL - ASCL.net Astrophysics Source Code Library xrefs: fairsharing: FAIRsharing.wb0txg issn: 2381-2028 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=$1 publications: - doi: 10.1093/nar/gkm997 pmc: PMC2238918 pubmed: '17999994' title: 'Update of ASRP: the Arabidopsis Small RNA Project database.' year: 2007 - doi: 10.1093/nar/gki127 pmc: PMC540081 pubmed: '15608278' title: 'ASRP: the Arabidopsis Small RNA Project Database.' year: 2005 astd: comment: This resource doesn't exist on the web anymore deprecated: true edam: description: Identifier of an object from the ASTD database. name: ASTD obsolete: false prefix: '2367' mappings: edam: '2367' prefixcommons: astd prefixcommons: description: The Alternative Splicing and Transcript Diversity (ASTD) database project is creating a database of alternative splice events and transcripts of genes from human, mouse and rat. Full length transcripts are generated with the aim of understanding the mechanism of alternative splicing on a genome-wide scale. example: ENSG00000136147 homepage: http://www.ebi.ac.uk/astd/ keywords: - gene - transcript - alternative splicing name: Alternative Splicing and Transcript Diversity pattern: ^ENSG\d+$ prefix: astd pubmed_ids: - '19059335' uri_format: http://www.ebi.ac.uk/astd/geneview.html?acc=$1 provides: ensembl publications: - doi: 10.1016/j.ygeno.2008.11.003 pmc: null pubmed: '19059335' title: 'ASTD: The Alternative Splicing and Transcript Diversity database.' year: 2008 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 atc: aberowl: description: The Anatomical Therapeutic Chemical (ATC) Classification System is used for the classification of active ingredients of drugs according to the organ or system on which they act and their therapeutic, pharmacological and chemical properties. It is controlled by the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC), and was first published in 1976. name: Anatomical Therapeutic Chemical Classification prefix: ATC version: 2016AB bartoc: abbreviation: ATC description: In the Anatomical Therapeutic Chemical (ATC) classification system, the active substances are divided into different groups according to the organ or system on which they act and their therapeutic, pharmacological and chemical properties. Drugs are classified in groups at five different levels. The drugs are divided into fourteen main groups (1st level), with pharmacological/therapeutic subgroups (2nd level). The 3rd and 4th levels are chemical/pharmacological/therapeutic subgroups and the 5th level is the chemical substance. The 2nd, 3rd and 4th levels are often used to identify pharmacological subgroups when that is considered more appropriate than therapeutic or chemical subgroups. name: Anatomical Therapeutic Chemical Classification System prefix: '449' wikidata_database: Q192093 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: 2022AB 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. homepage: http://www.whocc.no/atc/structure_and_principles/ 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 hl7: description: WHO ATC, Anatomical Therapeutic Chemical classification. The classification system divides drugs into different groups according to the organ or system on which they act and/or their therapeutic and chemical characteristics. It contains several subsets. homepage: http://www.who-umc.org/ name: WHO Anatomical Therapeutic Chemical classification organization: World Health Organization preferred_prefix: whoATC prefix: 2.16.840.1.113883.6.73 status: Complete mappings: aberowl: ATC bartoc: '449' biocontext: ATC bioportal: ATC edam: '3103' fairsharing: FAIRsharing.1a27h8 hl7: 2.16.840.1.113883.6.73 miriam: atc n2t: atc prefixcommons: atc 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=$1 publications: - doi: null pmc: null pubmed: '7368387' title: '[New classification of drugs. The Medical list and the Drug catalogue are introduced in Anatomical--Therapeutic--Chemical classification code (ACT-code) in 1981].' year: 1980 - doi: 10.1007/s002280000200 pmc: null pubmed: '11214783' title: Different versions of the anatomical therapeutic chemical classification system and the defined daily dose--are drug utilisation data comparable? year: 2000 - doi: 10.1007/s002280000200 pmc: null pubmed: '11214783' title: Different versions of the anatomical therapeutic chemical classification system and the defined daily dose--are drug utilisation data comparable? year: null - doi: null pmc: null pubmed: '7368387' title: '[New classification of drugs. The Medical list and the Drug catalogue are introduced in Anatomical--Therapeutic--Chemical classification code (ACT-code) in 1981].' year: null synonyms: - ATC_code - ATTC wikidata: database: Q192093 description: therapeutic chemical identification code per ATC example: - A02BC04 - D08AX08 homepage: https://www.whocc.no/ name: ATC code pattern: ^[A-V]([0-9][0-9]([A-Z]([A-Z]([0-9][0-9])?)?)?)[0-9]$ prefix: P267 uri_format: https://www.whocc.no/atc_ddd_index/?code=$1 atcc: biocontext: 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/$1 fairsharing: abbreviation: ATCC description: ATCC authenticates microorganisms and cell lines and manages logistics of long-term preservation and distribution of cultures for the scientific community. ATCC supports the cultures it acquires and authenticates with expert technical support, intellectual property management and characterization data. homepage: http://www.atcc.org/ name: American Type Culture Collection database prefix: FAIRsharing.j0ezpm publications: [] subjects: - Virology - Life Science - Epidemiology hl7: description: American Type Culture Collection name: ATC preferred_prefix: ATC prefix: 2.16.840.1.113883.6.77 status: Pending homepage: https://www.lgcstandards-atcc.org mappings: biocontext: ATCC cellosaurus: ATCC fairsharing: FAIRsharing.j0ezpm hl7: 2.16.840.1.113883.6.77 miriam: atcc n2t: atcc ncbi: ATCC miriam: deprecated: false description: The American Type Culture Collection (ATCC) is a private, nonprofit biological resource center whose mission focuses on the acquisition, authentication, production, preservation, development and distribution of standard reference microorganisms, cell lines and other materials for research in the life sciences. homepage: http://www.atcc.org/ id: 00000284 name: ATCC namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: atcc sampleId: '11303' uri_format: https://www.atcc.org/products/$1 n2t: description: The American Type Culture Collection (ATCC) is a private, nonprofit biological resource center whose mission focuses on the acquisition, authentication, production, preservation, development and distribution of standard reference microorganisms, cell lines and other materials for research in the life sciences. example: '11303' homepage: http://www.atcc.org/ name: ATCC in Virginia namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: atcc uri_format: http://www.lgcstandards-atcc.org/Products/All/$1.aspx name: American Type Culture Collection ncbi: example: '123456' homepage: http://www.atcc.org/ name: American Type Culture Collection database prefix: ATCC pattern: ^([A-Z]+-)?\d+$ 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_$1 bioportal: contact: email: sbhdbe@mst.edu name: AmphiAnat list description: A taxonomy of Amphibia homepage: http://www.amphibanat.org name: Amphibian Taxonomy Ontology prefix: ATO version: See Remote Site example: '0000000' fairsharing: abbreviation: ATO description: Amphibian Taxonomy Ontology is an ontology of Amphibian species and genres. It is being integrated into UBERON resource homepage: http://purl.bioontology.org/ontology/ATO name: Amphibian Taxonomy Ontology prefix: FAIRsharing.ayjdsm publications: [] subjects: [] mappings: aberowl: ATO biocontext: ATO bioportal: ATO fairsharing: FAIRsharing.ayjdsm obofoundry: ato obofoundry: contact: david.c.blackburn@gmail.com contact.label: David Blackburn deprecated: true domain: organisms homepage: http://www.amphibanat.org name: Amphibian taxonomy prefix: ato pattern: ^\d{7}$ 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: matthieu.reichstadt@inrae.fr name: Matthieu Reichstadt 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.' homepage: http://www.atol-ontology.com/en/atol-2/ license: CC-BY-4.0 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/$1 bacdive: fairsharing: abbreviation: BacDive contact: email: contact@bacdive.de name: Lorenz Reimer orcid: 0000-0002-7805-0660 description: "BacDive\u2014the Bacterial Diversity Metadatabase merges detailed\ \ strain-linked information on the different aspects of bacterial and archaeal\ \ biodiversity. BacDive contains entries for over 63,000 strains and provides\ \ information on their taxonomy, morphology, physiology, sampling and concomitant\ \ environmental conditions as well as molecular biology." homepage: https://bacdive.dsmz.de/ license: CC BY-NC 4.0 name: Bacterial Diversity Metadatabase prefix: FAIRsharing.aSszvY publications: - doi: 10.1093/nar/gkv983 pubmed_id: 26424852 title: BacDive--The Bacterial Diversity Metadatabase in 2016. - doi: 10.1016/j.jbiotec.2017.05.004 pubmed_id: 28487186 title: Mobilization and integration of bacterial phenotypic data-Enabling next generation biodiversity analysis through the BacDive metadatabase. - doi: 10.1093/nar/gkt1058 pubmed_id: 24214959 title: BacDive--the Bacterial Diversity Metadatabase. - doi: 10.1093/nar/gky879 pubmed_id: 30256983 title: 'BacDive in 2019: bacterial phenotypic data for High-throughput biodiversity analysis.' subjects: - Biodiversity - Life Science - Microbiology mappings: fairsharing: FAIRsharing.aSszvY miriam: bacdive n2t: bacdive re3data: r3d100013060 wikidata: P2946 miriam: deprecated: false description: "BacDive\u2014the Bacterial Diversity Metadatabase merges detailed\ \ strain-linked information on the different aspects of bacterial and archaeal\ \ biodiversity." homepage: https://bacdive.dsmz.de/ id: '00000676' name: Bacterial Diversity Metadatabase namespaceEmbeddedInLui: false pattern: ^[0-9]+$ prefix: bacdive sampleId: '131392' uri_format: https://bacdive.dsmz.de/strain/$1 n2t: description: BacDive—the Bacterial Diversity Metadatabase merges detailed strain-linked information on the different aspects of bacterial and archaeal biodiversity. example: '131392' homepage: https://bacdive.dsmz.de/ name: Bacterial Diversity Metadatabase namespaceEmbeddedInLui: false pattern: ^[0-9]+$ prefix: bacdive uri_format: https://bacdive.dsmz.de/strain/$1 publications: - doi: 10.1093/nar/gky879 pmc: PMC6323973 pubmed: '30256983' title: 'BacDive in 2019: bacterial phenotypic data for High-throughput biodiversity analysis.' year: 2019 - doi: 10.1016/j.jbiotec.2017.05.004 pmc: null pubmed: '28487186' title: Mobilization and integration of bacterial phenotypic data-Enabling next generation biodiversity analysis through the BacDive metadatabase. year: 2017 - doi: 10.1093/nar/gkv983 pmc: PMC4702946 pubmed: '26424852' title: BacDive--The Bacterial Diversity Metadatabase in 2016. year: 2015 - doi: 10.1093/nar/gkt1058 pmc: PMC3965005 pubmed: '24214959' title: BacDive--the Bacterial Diversity Metadatabase. year: 2013 - doi: 10.1093/nar/gkv983 pmc: null pubmed: '26424852' title: BacDive--The Bacterial Diversity Metadatabase in 2016. year: null - doi: 10.1016/j.jbiotec.2017.05.004 pmc: null pubmed: '28487186' title: Mobilization and integration of bacterial phenotypic data-Enabling next generation biodiversity analysis through the BacDive metadatabase. year: null - doi: 10.1093/nar/gkt1058 pmc: null pubmed: '24214959' title: BacDive--the Bacterial Diversity Metadatabase. year: null - doi: 10.1093/nar/gky879 pmc: null pubmed: '30256983' title: 'BacDive in 2019: bacterial phenotypic data for High-throughput biodiversity analysis.' year: null 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' wikidata: database: Q25349390 description: identifier for a microorganism, in the BacDive database example: - '8607' name: BacDive ID pattern: ^\d{1,6}$ prefix: P2946 uri_format: https://bacdive.dsmz.de/strain/$1 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. homepage: http://bactibase.hammamilab.org/main.php license: http://opendatacommons.org/licenses/pddl/1.0 name: 'Bactibase: database dedicated to bacteriocins' prefix: FAIRsharing.5f5mfm publications: - doi: 10.1186/1471-2180-10-22 pubmed_id: 20105292 title: 'BACTIBASE second release: a database and tool platform for bacteriocin characterization.' - doi: 10.1186/1471-2180-7-89 pubmed_id: 17941971 title: 'BACTIBASE: a new web-accessible database for bacteriocin characterization.' subjects: - Life Science homepage: http://bactibase.hammamilab.org mappings: fairsharing: FAIRsharing.5f5mfm prefixcommons: bactibase re3data: r3d100012755 name: Bactibase prefixcommons: description: BACTIBASE contains calculated or predicted physicochemical properties of 177 bacteriocins produced by both Gram-positive and Gram-negative bacteria. The information in this database is very easy to extract and allows rapid prediction of relationships structure/function and target organisms of these peptides and therefore better exploitation of their biological activity in both the medical and food sectors. example: BAC152 homepage: http://bactibase.pfba-lab-tun.org/main.php keywords: - protein name: 'Bactibase: database dedicated to bacteriocins' pattern: ^BA\d+$ prefix: bactibase uri_format: http://bactibase.pfba-lab-tun.org/$1 publications: - doi: 10.1186/1471-2180-10-22 pmc: PMC2824694 pubmed: '20105292' title: 'BACTIBASE second release: a database and tool platform for bacteriocin characterization.' year: 2010 - doi: 10.1186/1471-2180-7-89 pmc: PMC2211298 pubmed: '17941971' title: 'BACTIBASE: a new web-accessible database for bacteriocin characterization.' year: 2007 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: contact: email: sschurer@med.miami.edu name: Stephan Schurer 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. homepage: http://www.bioassayontology.org/ name: BioAssay Ontology prefix: BAO publication: http://www.bioassayontology.org/ version: 2.7.3 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. homepage: http://bioassayontology.org license: CC-BY-4.0 name: BioAssay Ontology prefix: FAIRsharing.mye76w publications: - doi: 10.1186/2041-1480-5-S1-S5 pubmed_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.' repository: https://github.com/BioAssayOntology/BAO/wiki 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: 10.1186/2041-1480-5-s1-s5 pmc: PMC4108877 pubmed: '25093074' title: 'Evolving BioAssay Ontology (BAO): modularization, integration and applications.' year: 2014 - doi: 10.1371/journal.pone.0049198 pmc: PMC3498356 pubmed: '23155465' title: Formalization, annotation and analysis of diverse drug and probe screening assay datasets using the BioAssay Ontology (BAO). year: 2012 - doi: 10.1186/1471-2105-12-257 pmc: PMC3149580 pubmed: '21702939' title: 'BioAssay Ontology (BAO): a semantic description of bioassays and high-throughput screening results.' year: 2011 - doi: 10:1371/journal.pone.0049198 pmc: null pubmed: '10' title: Digitoxin metabolism by rat liver microsomes. year: 1975 synonyms: - BAO bartoc: contact: email: andreas.ledl1@fhnw.ch github: null name: Andreas Ledl orcid: 0000-0002-0629-0446 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: "The Basic Register of Thesauri, Ontologies & Classifications (BARTOC)\ \ is a database of Knowledge Organization Systems and KOS related registries.\n\ The main goal of BARTOC is to list as many Knowledge Organization Systems as possible\ \ at one place in order to achieve greater visibility, highlight their features,\ \ make them searchable and comparable, and foster knowledge sharing. BARTOC includes\ \ any kind of KOS from any subject area, in any language, any publication format,\ \ and any form of accessibility. BARTOC\u2019s search interface is available in\ \ 20 European languages and provides two search options: Basic Search by keywords,\ \ and Advanced Search by taxonomy terms. A circle of editors has gathered around\ \ BARTOC from all across Europe and BARTOC has been approved by the International\ \ Society for Knowledge Organization (ISKO)." example: '241' fairsharing: abbreviation: BARTOC description: "The Basel Register of Thesauri, Ontologies & Classifications (BARTOC)\ \ is a database of Knowledge Organization Systems (KOS) and KOS -related registries.\ \ Its main goal is to list as many KOS as possible in one place in order to\ \ achieve greater visibility, make them searchable and comparable, and foster\ \ knowledge sharing. BARTOC includes any kind of KOS from any subject area,\ \ in any language, any publication format, and any form of accessibility. BARTOC\u2019\ s search interface is available in 20 European languages." homepage: https://bartoc.org/ license: http://opendatacommons.org/licenses/pddl/1.0 name: Basel Register of Thesauri, Ontologies and Classifications prefix: FAIRsharing.f1777e publications: [] repository: https://github.com/gbv/bartoc.org subjects: - Knowledge and Information Systems - Ontology and Terminology homepage: https://bartoc.org license: PDDL 1.0 mappings: fairsharing: FAIRsharing.f1777e wikidata: P2689 name: Basic Register of Thesauri, Ontologies & Classifications pattern: ^[1-9][0-9]*$ repository: https://github.com/gbv/bartoc.org uri_format: https://bartoc.org/en/node/$1 wikidata: prefix: P2689 bbkg: mappings: miriam: bbkg miriam: deprecated: false description: Blue Brain Project's published data as knowledge graphs and Web Studios. homepage: https://portal.bluebrain.epfl.ch id: 00000903 name: Blue Brain Project Knowledge Graph namespaceEmbeddedInLui: false pattern: ^[-\w]+(?:\/[-\w]+)(?:\/\b[0-9a-f]{8}\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\b[0-9a-f]{12}\b)$ 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/$1 download_owl: https://github.com/obi-bcgo/bcgo/raw/master/ontology/bcgo.owl example: '0000015' mappings: aberowl: BCGO biocontext: BCGO bioportal: BCGO cellosaurus: BCGO obofoundry: bcgo ontobee: BCGO obofoundry: contact: jiezheng@pennmedicine.upenn.edu contact.github: zhengj2007 contact.label: Jie Zheng contact.orcid: 0000-0002-2999-0103 deprecated: true description: An application ontology built for beta cell genomics studies. domain: anatomy and development download.owl: http://purl.obolibrary.org/obo/bcgo.owl homepage: https://github.com/obi-bcgo/bcgo license: CC BY 3.0 license.url: http://creativecommons.org/licenses/by/3.0/ name: Beta Cell Genomics Ontology prefix: bcgo repository: https://github.com/obi-bcgo/bcgo ontobee: library: Library name: Beta Cell Genomics Ontology prefix: BCGO pattern: ^\d{7}$ 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. homepage: https://github.com/BiodiversityOntologies/bco license: CC0-1.0 name: Biological Collections Ontology prefix: FAIRsharing.8ktkqy publications: - doi: 10.1371/journal.pone.0089606 pubmed_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. domain: organisms download.owl: http://purl.obolibrary.org/obo/bco.owl homepage: https://github.com/BiodiversityOntologies/bco license: CC0 1.0 license.url: https://creativecommons.org/publicdomain/zero/1.0/ name: Biological Collections Ontology preferredPrefix: BCO prefix: bco publications: - id: https://doi.org/10.1371/journal.pone.0089606 title: 'Semantics in Support of Biodiversity Knowledge Discovery: An Introduction to the Biological Collections Ontology and Related Ontologies' repository: https://github.com/BiodiversityOntologies/bco ols: description: An ontology to support the interoperability of biodiversity data, including data on museum collections, environmental/metagenomic samples, and ecological surveys. download: 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=$1 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 example: '60316' homepage: https://catalog.bcrc.firdi.org.tw keywords: - cell lines mappings: cellosaurus: BCRC name: BCRC Strain Collection Catalog pattern: ^\d+$ 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/$1 fairsharing: abbreviation: BeetleBase description: BeetleBase is a community resource for Tribolium genetics, genomics and developmental biology. The database is built on the Chado generic data model, and is able to store various types of data, ranging from genome sequences to mutant phenotypes. homepage: http://www.beetlebase.org/ name: BeetleBase prefix: FAIRsharing.h5f091 publications: - doi: 10.1093/nar/gkp807 pubmed_id: 19820115 title: 'BeetleBase in 2010: revisions to provide comprehensive genomic information for Tribolium castaneum.' subjects: - Computational Biology - Life Science mappings: biocontext: BEETLEBASE fairsharing: FAIRsharing.h5f091 miriam: beetlebase n2t: beetlebase ncbi: BEETLEBASE prefixcommons: beetlebase re3data: r3d100010921 miriam: deprecated: false description: BeetleBase is a comprehensive sequence database and community resource for Tribolium genetics, genomics and developmental biology. It incorporates information about genes, mutants, genetic markers, expressed sequence tags and publications. homepage: http://beetlebase.org/ id: '00000157' name: BeetleBase namespaceEmbeddedInLui: false pattern: ^TC\d+$ 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/$1 fairsharing: abbreviation: BEGDB description: The Benchmark Energy & Geometry Database (BEGDB) collects results of highly accurate QM calculations of molecular structures, energies and properties. These data can serve as benchmarks for testing and parameterization of other computational methods. homepage: http://www.begdb.org/ name: The Benchmark Energy & Geometry Database prefix: FAIRsharing.nbe4fq publications: - doi: 10.1135/cccc20081261 pubmed_id: null title: 'Quantum Chemical Benchmark Energy and Geometry Database for Molecular Clusters and Complex Molecular Systems (www.begdb.com): A Users Manual and Examples' subjects: - Life Science mappings: biocontext: BEGDB fairsharing: FAIRsharing.nbe4fq miriam: begdb n2t: begdb re3data: r3d100011166 miriam: deprecated: false description: The Benchmark Energy & Geometry Database (BEGDB) collects results of highly accurate quantum mechanics (QM) calculations of molecular structures, energies and properties. These data can serve as benchmarks for testing and parameterization of other computational methods. homepage: http://www.begdb.com id: '00000622' name: Benchmark Energy & Geometry Database namespaceEmbeddedInLui: false pattern: ^[0-9]+$ prefix: begdb sampleId: '4214' uri_format: http://www.begdb.com/index.php?action=oneMolecule&state=show&id=$1 n2t: description: The Benchmark Energy & Geometry Database (BEGDB) collects results of highly accurate quantum mechanics (QM) calculations of molecular structures, energies and properties. These data can serve as benchmarks for testing and parameterization of other computational methods. example: '4214' homepage: http://www.begdb.com name: Benchmark Energy & Geometry Database namespaceEmbeddedInLui: false pattern: ^[0-9]+$ prefix: begdb uri_format: http://www.begdb.com/index.php?action=oneMolecule&state=show&id=$1 publications: - doi: 10.1135/cccc20081261 pmc: null pubmed: null title: 'Quantum Chemical Benchmark Energy and Geometry Database for Molecular Clusters and Complex Molecular Systems (www.begdb.com): A Users Manual and Examples' year: 2008 re3data: description: The Benchmark Energy & Geometry Database (BEGDB) collects results of highly accurate QM calculations of molecular structures, energies and properties. These data can serve as benchmarks for testing and parameterization of other computational methods. homepage: http://www.begdb.org/ name: Benchmark Energy & Geometry Database prefix: r3d100011166 synonyms: - BEGDB xrefs: fairsharing: FAIRsharing.nbe4fq 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 keywords: - cell lines 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 contact: email: support@bel.bio name: William Hayes orcid: 0000-0003-0728-781X description: BEL is a language for representing scientific findings in the life sciences in a reusable, shareable, and computable form. BEL is designed to represent scientific findings by capturing causal and correlative relationships in context, where context can include information about the biological and experimental system in which the relationships were observed, the supporting publications cited and the process of curation. BEL is intended as a knowledge capture and interchange medium, supporting the operation of systems that integrate knowledge derived from independent efforts. The language is designed to be use-neutral, facilitating the storage and use of structured knowledge for inference by applications through a knowledge assembly process that can create computable biological networks. While BEL does not prescribe any particular assembly process or any particular knowledge format for the output of an assembly process, a suite of software components called the BEL Framework provides everything necessary to create, compile, assemble, and deliver computable knowledge models to BEL-aware applications. The current version of BEL provides the means to describe biological interactions qualitatively but not to quantify the magnitude or rate of these interactions. This limitation is by design because this quantitative information has significant variability and is not consistently reported in the literature. It is our hope that future versions of BEL can accommodate these additional data. homepage: https://bel.bio license: CC-BY-4.0 name: Biological Expression Language prefix: FAIRsharing.dp0jvd publications: [] subjects: - Biology homepage: https://biological-expression-language.github.io/ 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." homepage: https://www.iso.org/standard/74572.html license: CC-BY-4.0 name: "ISO/IEC 21838-2:2021 Information technology \u2014 Top-level ontologies\ \ (TLO) \u2014 Part 2: Basic Formal Ontology (BFO)" prefix: FAIRsharing.wcpd6f publications: [] repository: https://github.com/bfo-ontology/BFO subjects: - Subject Agnostic go: description: An upper ontology used by Open Bio Ontologies (OBO) Foundry. BFO contains upper-level classes as well as core relations such as part_of (BFO_0000050) name: Basic Formal Ontology prefix: BFO mappings: aberowl: BFO agroportal: BFO biocontext: BFO bioportal: BFO fairsharing: FAIRsharing.wcpd6f go: BFO obofoundry: bfo ols: bfo ontobee: BFO 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. domain: upper download.obo: http://purl.obolibrary.org/obo/bfo.obo download.owl: http://purl.obolibrary.org/obo/bfo.owl homepage: http://ifomis.org/bfo/ license: CC BY 4.0 license.url: http://creativecommons.org/licenses/by/4.0/ 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/$1 mappings: biocontext: BGEE.GENE miriam: bgee.gene n2t: bgee.gene prefixcommons: bgee miriam: deprecated: false description: Bgee is a database to retrieve and compare gene expression patterns in multiple species, produced from multiple data types (RNA-Seq, Affymetrix, in situ hybridization, and EST data). This collection references genes in Bgee. homepage: https://bgee.org/ id: 00000418 name: Bgee gene namespaceEmbeddedInLui: false pattern: ^[A-Za-z]+\d+$ 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=$1 prefixcommons: description: Bgee is a database to retrieve and compare gene expression patterns between animal species. Bgee first maps heterogeneous expression data (currently EST, Affymetrix, and in situ hybridization data) on anatomical and developmental ontologies. Then, in order to perform automated cross species comparisons, homology relationships across anatomical ontologies, and comparison criteria between developmental ontologies, are designed. example: FBgn0041195 homepage: http://bgee.unil.ch keywords: - gene expression name: Bgee DataBase for Gene Expression Evolution pattern: ^[A-Z]+\d+$ prefix: bgee uri_format: http://bgee.unil.ch/bgee/bgee?page=gene&action=expression&gene_id=$1 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/ keywords: - bibliometrics 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 contact: email: silvio.peroni@unibo.it name: Silvio Peroni orcid: 0000-0003-0530-4305 description: The Bibliometric Data Ontology (BiDO) is a modular ontology that allows the description of numerical and categorical bibliometric data (e.g., journal impact factor, author h-index, categories describing research careers) in RDF. homepage: http://www.sparontologies.net/ontologies/bido license: CC-BY-4.0 name: 'Bibliometric Data Ontology ' prefix: FAIRsharing.d7f0a9 publications: [] repository: https://github.com/sparontologies/bido subjects: - Subject Agnostic twitter: sparontologies 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_$1 deprecated: true example: '0000000' fairsharing: abbreviation: BILA description: This is a record of the Bilateria anatomy terminology and ontology. We have been unable to find any further information about this resource. homepage: http://purl.bioontology.org/ontology/BILA name: Bilateria anatomy prefix: FAIRsharing.eqgjeq publications: [] subjects: - Anatomy mappings: biocontext: BILA fairsharing: FAIRsharing.eqgjeq obofoundry: bila prefixcommons: 4dxpress obofoundry: contact: henrich@embl.de contact.label: Thorsten Heinrich deprecated: true domain: anatomy and development download.owl: http://purl.obolibrary.org/obo/bila.owl homepage: http://4dx.embl.de/4DXpress name: Bilateria anatomy prefix: bila pattern: ^\d{7}$ prefixcommons: description: This database provides a platform to query and compare gene expression data during the development of the major model animals (zebrafish, drosophila, medaka, mouse). The high resolution expression data was acquired through whole mount in situ hybridsation-, antibody- or transgenic experiments. example: '98967' homepage: http://4dx.embl.de/4DXpress keywords: - gene expression name: 4DXpress gene expression in major animals pattern: ^\d+$ prefix: 4dxpress pubmed_ids: - '17916571' uri_format: http://4dx.embl.de/4DXpress/reg/all/cview/gene.do?geneID=$1 publications: - doi: 10.1093/nar/gkm797 pmc: PMC2238840 pubmed: '17916571' title: '4DXpress: a database for cross-species expression pattern comparisons.' year: 2007 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: 10.1093/nar/gkg056 pmc: PMC165503 pubmed: '12519993' title: 'BIND: the Biomolecular Interaction Network Database.' year: 2003 - doi: 10.1093/bioinformatics/16.5.465 pmc: null pubmed: '10871269' title: BIND--a data specification for storing and describing biomolecular interactions, molecular complexes and pathways. year: 2000 uri_format: http://www.bind.ca/Action?identifier=bindid&idsearch=$1 bindingdb: biocontext: is_identifiers: true is_obo: false prefix: BINDINGDB uri_format: http://identifiers.org/bindingDB/$1 fairsharing: abbreviation: BindingDB contact: email: mgilson@health.ucsd.edu name: Michael K. Gilson orcid: 0000-0002-3375-1738 description: BindingDB enables research by making a growing collection of high-quality, quantitative, protein-ligand binding data findable and usable. Funded by NIGMS/NIH. homepage: http://www.bindingdb.org license: https://creativecommons.org/licenses/by-nc-nd/2.5 name: BindingDB database of measured binding affinities prefix: FAIRsharing.3b36hk publications: - doi: 10.1093/nar/gkl999 pubmed_id: 17145705 title: 'BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities.' subjects: - Drug Discovery - Chemistry - Life Science - Computational Chemistry - Medicinal Chemistry mappings: biocontext: BINDINGDB fairsharing: FAIRsharing.3b36hk miriam: bindingdb n2t: bindingdb prefixcommons: bindingdb re3data: r3d100012074 uniprot: DB-0127 miriam: deprecated: false description: BindingDB is the first public database of protein-small molecule affinity data. homepage: https://www.bindingdb.org id: '00000264' name: BindingDB namespaceEmbeddedInLui: false pattern: ^\w\d+$ 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/gkv1072 pmc: PMC4702793 pubmed: '26481362' title: 'BindingDB in 2015: A public database for medicinal chemistry, computational chemistry and systems pharmacology.' year: 2015 - doi: 10.1093/nar/gkl999 pmc: PMC1751547 pubmed: '17145705' title: 'BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities.' year: 2006 re3data: description: 'BindingDB is a public, web-accessible knowledgebase of measured binding affinities, focusing chiefly on the interactions of proteins considered to be candidate drug-targets with ligands that are small, drug-like molecules. BindingDB supports medicinal chemistry and drug discovery via literature awareness and development of structure-activity relations (SAR and QSAR); validation of computational chemistry and molecular modeling approaches such as docking, scoring and free energy methods; chemical biology and chemical genomics; and basic studies of the physical chemistry of molecular recognition. BindingDB also includes a small collection of host-guest binding data of interest to chemists studying supramolecular systems. The data collection derives from a variety of measurement techniques, including enzyme inhibition and kinetics, isothermal titration calorimetry, NMR, and radioligand and competition assays. BindingDB includes data extracted from the literature and from US Patents by the BindingDB project, selected PubChem confirmatory BioAssays, and ChEMBL entries for which a well defined protein target ("TARGET_TYPE=''PROTEIN''") is provided.' 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: abbreviation: BindingDB category: Chemistry databases homepage: https://www.bindingdb.org/ name: BindingDB database of measured binding affinities prefix: DB-0127 publications: - doi: 10.1093/nar/gkv1072 pubmed: '26481362' 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/$1 mappings: biocontext: BIOCATALOGUE.SERVICE miriam: biocatalogue.service n2t: biocatalogue.service prefixcommons: biocatalogue miriam: deprecated: false description: The BioCatalogue provides a common interface for registering, browsing and annotating Web Services to the Life Science community. Registered services are monitored, allowing the identification of service problems and changes and the filtering-out of unavailable or unreliable resources. BioCatalogue is free to use, for all. homepage: https://www.biocatalogue.org/ id: '00000140' name: BioCatalogue namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: biocatalogue.service sampleId: '614' uri_format: https://www.biocatalogue.org/services/$1 n2t: description: The BioCatalogue provides a common interface for registering, browsing and annotating Web Services to the Life Science community. Registered services are monitored, allowing the identification of service problems and changes and the filtering-out of unavailable or unreliable resources. BioCatalogue is free to use, for all. example: '614' homepage: https://www.biocatalogue.org/ name: BioCatalogue at EMBL-EBI namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: biocatalogue.service uri_format: https://www.biocatalogue.org/services/$1 name: BioCatalogue Service prefixcommons: description: The BioCatalogue provides a common interface for registering, browsing and annotating Web Services to the Life Science community. Registered services are monitored, allowing the identification of service problems and changes and the filtering-out of unavailable or unreliable resources. BioCatalogue is free to use, for all. example: '614' homepage: http://www.biocatalogue.org/ keywords: - registry name: Curated catalogue of Life Science Web Services pattern: ^\d+$ prefix: biocatalogue pubmed_ids: - '20484378' uri_format: http://www.biocatalogue.org/services/$1 publications: - doi: 10.1093/nar/gkq394 pmc: PMC2896129 pubmed: '20484378' title: 'BioCatalogue: a universal catalogue of web services for the life sciences.' year: 2010 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=$1 mappings: biocontext: BIOCYC edam: '2104' go: BioCyc miriam: biocyc n2t: biocyc prefixcommons: biocyc uniprot: DB-0005 miriam: deprecated: false description: BioCyc is a collection of Pathway/Genome Databases (PGDBs) which provides an electronic reference source on the genomes and metabolic pathways of sequenced organisms. homepage: http://biocyc.org id: 00000194 name: BioCyc namespaceEmbeddedInLui: false pattern: ^[A-Z-0-9]+(\:)?[A-Za-z0-9+_.%-:]+$ prefix: biocyc sampleId: ECOLI:CYT-D-UBIOX-CPLX uri_format: http://biocyc.org/getid?id=$1 n2t: description: BioCyc is a collection of Pathway/Genome Databases (PGDBs) which provides an electronic reference source on the genomes and metabolic pathways of sequenced organisms. example: ECOLI:CYT-D-UBIOX-CPLX homepage: http://biocyc.org name: BioCyc at SRI International namespaceEmbeddedInLui: false pattern: ^[A-Z-0-9]+(\:)?[A-Za-z0-9+_.%-:]+$ prefix: biocyc uri_format: http://biocyc.org/getid?id=$1 prefixcommons: description: The BioCyc collection of Pathway/Genome Databases (PGDBs) provides electronic reference sources on the pathways and genomes of different organisms. example: ECOLI:CYT-D-UBIOX-CPLX homepage: http://www.biocyc.org/ keywords: - genome - pathway - sequence name: BioCyc Database Collection pattern: ^\w+\:[A-Za-z0-9-]+$ prefix: biocyc pubmed_ids: - '16246909' uri_format: http://biocyc.org/ECOLI/NEW-IMAGE?object=$1 publications: - doi: 10.1093/nar/gkv1164 pmc: PMC4702838 pubmed: '26527732' title: The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. year: 2015 - doi: 10.1093/nar/gki892 pmc: PMC1266070 pubmed: '16246909' title: Expansion of the BioCyc collection of pathway/genome databases to 160 genomes. year: 2005 uniprot: abbreviation: BioCyc category: Enzyme and pathway databases homepage: https://www.biocyc.org/ name: BioCyc Collection of Pathway/Genome Databases prefix: DB-0005 publications: - doi: 10.1093/nar/gkv1164 pubmed: '26527732' uri_format: https://biocyc.org/getid?id=$1 biofactoid: contact: email: jeffvin.wong@utoronto.ca github: jvwong name: Jeffrey Wong orcid: 0000-0002-8912-5699 contributor: email: benjamin_gyori@hms.harvard.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 description: Biofactoid is a web-based system that empowers authors to capture and share machine-readable summaries of molecular-level interactions described in their publications. example: fdb8a927-45c3-48b7-9743-cbb5e16837fa github_request_issue: 700 homepage: https://biofactoid.org/ keywords: - biocuration - database - relationships license: CC0-1.0 name: Biofactoid pattern: ^[0-9a-fA-F]{8}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{12}$ publications: - doi: 10.7554/elife.68292 pmc: PMC8683078 pubmed: '34860157' title: Author-sourced capture of pathway knowledge in computable form using Biofactoid. year: 2021 repository: https://github.com/PathwayCommons/factoid reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: https://biofactoid.org/document/$1 biogrid: biocontext: 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." homepage: http://www.thebiogrid.org name: Biological General Repository for Interaction Datasets prefix: FAIRsharing.9d5f5r publications: - doi: 10.1093/nar/gkj109 pubmed_id: 16381927 title: 'BioGRID: a general repository for interaction datasets.' - doi: 10.1186/gb-2003-4-3-r23 pubmed_id: 12620108 title: 'The GRID: the General Repository for Interaction Datasets.' - doi: 10.1002/pro.3978 pubmed_id: 33070389 title: 'The BioGRID database: A comprehensive biomedical resource of curated protein, genetic, and chemical interactions.' - doi: 10.1093/nar/gky1079 pubmed_id: 30476227 title: 'The BioGRID interaction database: 2019 update' repository: https://github.com/BioGRID subjects: - Cheminformatics - Biochemistry - Bioinformatics - Chemical Biology - Proteomics - Life Science - Systems Biology twitter: biogrid mappings: biocontext: BIOGRID fairsharing: FAIRsharing.9d5f5r miriam: biogrid n2t: biogrid prefixcommons: biogrid re3data: r3d100010350 uniprot: DB-0184 miriam: deprecated: false description: BioGRID is a database of physical and genetic interactions in Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, and Schizosaccharomyces pombe. homepage: http://thebiogrid.org/ id: 00000058 name: BioGRID namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: biogrid sampleId: '31623' uri_format: http://thebiogrid.org/$1 n2t: description: BioGRID is a database of physical and genetic interactions in Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, and Schizosaccharomyces pombe. example: '31623' homepage: http://thebiogrid.org/ name: BioGRID database of physical and genetic interactions namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: biogrid uri_format: http://thebiogrid.org/$1 prefixcommons: description: BioGRID is a database of physical and genetic interactions in Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, and Schizosaccharomyces pombe. example: '31623' homepage: http://www.thebiogrid.org keywords: - protein - gene - interaction name: Biological General Repository for Interaction Datasets pattern: ^\d+$ prefix: biogrid pubmed_ids: - '16381927' synonyms: - grid uri_format: http://thebiogrid.org/$1 publications: - doi: 10.1002/pro.3978 pmc: PMC7737760 pubmed: '33070389' title: 'The BioGRID database: A comprehensive biomedical resource of curated protein, genetic, and chemical interactions.' year: 2020 - doi: 10.1093/nar/gky1079 pmc: PMC6324058 pubmed: '30476227' title: 'The BioGRID interaction database: 2019 update.' year: 2019 - doi: 10.1093/nar/gkq1116 pmc: PMC3013707 pubmed: '21071413' title: 'The BioGRID Interaction Database: 2011 update.' year: 2010 - doi: 10.1093/nar/gkj109 pmc: PMC1347471 pubmed: '16381927' title: 'BioGRID: a general repository for interaction datasets.' year: 2006 - doi: 10.1186/gb-2003-4-3-r23 pmc: PMC153463 pubmed: '12620108' title: 'The GRID: the General Repository for Interaction Datasets.' year: 2003 re3data: description: The Biological General Repository for Interaction Datasets (BioGRID) is a public database that archives and disseminates genetic and protein interaction data from model organisms and humans. BioGRID is an online interaction repository with data compiled through comprehensive curation efforts. All interaction data are freely provided through our search index and available via download in a wide variety of standardized formats. 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: abbreviation: BioGRID category: Protein-protein interaction databases homepage: https://thebiogrid.org/ name: The Biological General Repository for Interaction Datasets (BioGRID) prefix: DB-0184 publications: - doi: 10.1093/nar/gkq1116 pubmed: '21071413' 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/$1 biolegend: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: BioLegend is a life sciences supply vendor. example: '3403' homepage: https://www.biolegend.com keywords: - antibodies - assays - life sciences - reagents - vendor name: BioLegend pattern: ^\d+$ 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/52/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 contact: email: cjmungall@lbl.gov github: cmungall name: Chris Mungall orcid: 0000-0002-6601-2165 fairsharing: abbreviation: biolink contact: email: smoxon@lbl.gov name: Sierra Moxon orcid: 0000-0002-8719-7760 description: 'A high level datamodel of biological entities (genes, diseases, phenotypes, pathways, individuals, substances, etc) and their associations. Biolink Model is designed as a way of standardizing types and relational structures in knowledge graphs (KGs), where the KG may be either a property graph or RDF triple store. The schema is expressed as a YAML, which may be translated into a number of different representations including OWL, Python dataclasses, GraphQL and more. The schema assumes a property graph, where nodes represent individual entities, and edges represent relationship between entities. Biolink Model provides a schema for representing both nodes and edges. The model itself can be divided into a few parts: Entities (subjects and objects), Predicates (relationships between core concepts), Associations (statements including evidence and provenance), Entity Slots (node properties), and Edge Slots (edge properties).' homepage: https://biolink.github.io/biolink-model/ license: Apache 2.0 License name: Biolink Model prefix: FAIRsharing.ad9d85 publications: [] repository: https://github.com/biolink/biolink-model subjects: - Functional Genomics - Medical Biotechnology - Biomedical Science - Translational Medicine - Medical Informatics homepage: https://biolink.github.io/biolink-model/ mappings: aberowl: BIOLINK biolink: biolink bioportal: BIOLINK fairsharing: FAIRsharing.ad9d85 miriam: biolink 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/$1 biomagresbank: mappings: prefixcommons: biomagresbank prefixcommons: description: A repository for Data from NMR Spectroscopy on Proteins, Peptides, and Nucleic Acids. example: '10046' homepage: http://www.bmrb.wisc.edu/ keywords: - protein name: BioMagResBank pattern: ^\d+$ prefix: biomagresbank uri_format: http://www.bmrb.wisc.edu/data_library/generate_summary.php?bmrbId=$1 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 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_$1 bioportal: contact: email: sed-ml-editors@googlegroups.com name: SED-ML Editors description: The Kinetic Simulation Algorithm Ontology (KiSAO) is an ontology of algorithms for simulating and analyzing biological models, as well as the characteristics of these algorithms, their input parameters, and their outputs. In addition, KiSAO captures relationships among algorithms, their parameters, and their outputs. homepage: http://biomodels.net/kisao/ name: Kinetic Simulation Algorithm Ontology prefix: KISAO publication: https://doi.org/10.1038/msb.2011.77 version: '2.30' example: '0000057' fairsharing: abbreviation: KiSAO contact: email: lenov@ebi.ac.uk name: "Nicolas Le Nov\xE8re" orcid: 0000-0002-6309-7327 description: The Kinetic Simulation Algorithm Ontology aims at providing support in unambiguously referring to simulation algorithms when describing a simulation experiment. It describes and classifies existing algorithms and their inter-relationships through the algorithm characteristics and parameters. homepage: http://co.mbine.org/standards/kisao name: Kinetic Simulation Algorithm Ontology prefix: FAIRsharing.jcg19w publications: - doi: 10.1038/msb.2011.77 pubmed_id: 22027554 title: Controlled vocabularies and semantics in systems biology. subjects: - Bioinformatics - Computer Science mappings: aberowl: KISAO biocontext: KISAO bioportal: KISAO fairsharing: FAIRsharing.jcg19w miriam: biomodels.kisao n2t: biomodels.kisao obofoundry: kisao ols: kisao ontobee: KISAO prefixcommons: kisao miriam: deprecated: false description: The Kinetic Simulation Algorithm Ontology (KiSAO) is an ontology that describes simulation algorithms and methods used for biological kinetic models, and the relationships between them. This provides a means to unambiguously refer to simulation algorithms when describing a simulation experiment. homepage: http://bioportal.bioontology.org/ontologies/KISAO id: 00000108 name: KiSAO namespaceEmbeddedInLui: false pattern: ^KISAO_\d+$ 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:$1 namespace_in_lui: true obofoundry: contact: jonrkarr@gmail.com contact.github: jonrkarr contact.label: Jonathan Karr contact.orcid: 0000-0002-2605-5080 deprecated: false description: A classification of algorithms for simulating biology, their parameters, and their outputs domain: simulation download.owl: http://purl.obolibrary.org/obo/kisao.owl homepage: https://github.com/SED-ML/KiSAO license: Artistic License 2.0 license.url: http://opensource.org/licenses/Artistic-2.0 name: Kinetic Simulation Algorithm Ontology preferredPrefix: KISAO prefix: kisao publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/22027554 title: Controlled vocabularies and semantics in systems biology repository: https://github.com/SED-ML/KiSAO ols: description: A classification of algorithms for simulating biology, their parameters, and their outputs download: http://purl.obolibrary.org/obo/kisao.owl homepage: https://github.com/SED-ML/KiSAO name: Kinetic Simulation Algorithm Ontology prefix: kisao version: '2.30' ontobee: library: Library name: Kinetic Simulation Algorithm Ontology prefix: KISAO pattern: ^\d+$ 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: - biomodels.kisao - 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/$1 bioportal: contact: email: biomodels-net-support@lists.sf.net name: BioModels.net team description: The TErminology for the Description of DYnamics (TEDDY) project aims to provide an ontology for dynamical behaviours, observable dynamical phenomena, and control elements of bio-models and biological systems in Systems Biology and Synthetic Biology. homepage: http://teddyontology.sourceforge.net/ name: Terminology for the Description of Dynamics prefix: TEDDY publication: http://www.nature.com/msb/journal/v7/n1/full/msb201177.html version: rel-2014-04-24 (inferred) download_owl: http://svn.code.sf.net/p/teddyontology/code/teddy/tags/current/teddy-inferred.owl example: '0000066' fairsharing: abbreviation: TEDDY description: The TErminology for the Description of DYnamics (TEDDY) project aims to provide an ontology for dynamical behaviours, observable dynamical phenomena, and control elements of bio-models and biological systems in Systems Biology and Synthetic Biology. homepage: http://co.mbine.org/standards/teddy name: TErminology for the Description of DYnamics prefix: FAIRsharing.w9jvbt publications: - doi: 10.1038/msb.2011.77 pubmed_id: 22027554 title: Controlled vocabularies and semantics in systems biology. subjects: - Neurophysiology - Synthetic Biology - Systems Biology mappings: aberowl: TEDDY biocontext: BIOMODELS.TEDDY bioportal: TEDDY fairsharing: FAIRsharing.w9jvbt miriam: biomodels.teddy n2t: biomodels.teddy ols: teddy prefixcommons: teddy miriam: deprecated: false description: The Terminology for Description of Dynamics (TEDDY) is an ontology for dynamical behaviours, observable dynamical phenomena, and control elements of bio-models and biological systems in Systems Biology and Synthetic Biology. homepage: http://teddyontology.sourceforge.net/ id: '00000107' name: TEDDY namespaceEmbeddedInLui: false pattern: ^TEDDY_\d{7}$ 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=$1&ver=1 biopixie: comment: This resource doesn't exist on the web anymore deprecated: true mappings: prefixcommons: biopixie prefixcommons: description: bioPIXIE is a novel system for biological data integration and visualization. It allows you to discover interaction networks and pathways in which your gene(s) (e.g. BNI1, YFL039C) of interest participate. example: '12' homepage: http://pixie.princeton.edu/pixie/ keywords: - gene - interaction name: biological Process Inference from eXperimental Interaction Evidence/Microarray Experiment Functional Integration Technology pattern: ^\d+$ prefix: biopixie synonyms: - biopixie_mefit uri_format: http://avis.princeton.edu/pixie/viewgraph.php?graphID=$1 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 bioportal: biocontext: is_identifiers: true is_obo: false prefix: BIOPORTAL uri_format: http://identifiers.org/bioportal/$1 example_extras: - SEPIO - pseudo - FBBi fairsharing: abbreviation: BioPortal contact: email: support@bioontology.org name: John Graybeal orcid: 0000-0001-6875-5360 description: "BioPortal is a library of biomedical ontologies and terminologies\ \ developed in Web Ontology Language (OWL), Resource Description Framework (RDF)(S),\ \ Open Biological and Biomedical Ontologies (OBO) format, and Prot\xE9g\xE9\ \ frames and Rich Release Format. BioPortal groups ontologies by domain to aid\ \ discoverability and allows users to browse, search and visualize the content\ \ of ontologies. BioPortal also provides ontology recommendation, text annotation,\ \ ontology mapping, and a reference index to resources like PubMed." homepage: http://bioportal.bioontology.org/ name: BioPortal prefix: FAIRsharing.4m97ah publications: - doi: 10.1093/nar/gkr469 pubmed_id: 21672956 title: 'BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications.' repository: http://github.com/ncbo subjects: - Life Science - Ontology and Terminology twitter: bioontology mappings: biocontext: BIOPORTAL fairsharing: FAIRsharing.4m97ah miriam: bioportal n2t: bioportal prefixcommons: bioportal re3data: r3d100012344 miriam: deprecated: false description: "BioPortal is an open repository of biomedical ontologies that provides\ \ access via Web services and Web browsers to ontologies developed in OWL, RDF,\ \ OBO format and Prot\xE9g\xE9 frames. BioPortal functionality includes the\ \ ability to browse, search and visualize ontologies." homepage: http://bioportal.bioontology.org/ id: 00000187 name: BioPortal namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: bioportal sampleId: '1046' uri_format: http://bioportal.bioontology.org/ontologies/$1 n2t: description: BioPortal is an open repository of biomedical ontologies that provides access via Web services and Web browsers to ontologies developed in OWL, RDF, OBO format and Protégé frames. BioPortal functionality includes the ability to browse, search and visualize ontologies. example: '1046' homepage: http://bioportal.bioontology.org/ name: BioPortal at National Center for Biomedical Ontology namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: bioportal uri_format: http://bioportal.bioontology.org/ontologies/$1 pattern: ^(\d+)|(\w+)$ prefixcommons: description: BioPortal is an open repository of biomedical ontologies that provides access via Web services and Web browsers to ontologies developed in OWL, RDF, OBO format and Protege frames. BioPortal functionality includes the ability to browse, search and visualize ontologies. example: '1046' homepage: http://bioportal.bioontology.org/ keywords: - ontology name: BioPortal pattern: ^\d+$ prefix: bioportal pubmed_ids: - '19483092' uri_format: http://bioportal.bioontology.org/ontologies/$1 publications: - doi: 10.1093/nar/gkr469 pmc: PMC3125807 pubmed: '21672956' title: 'BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications.' year: 2011 - doi: 10.1093/nar/gkp440 pmc: PMC2703982 pubmed: '19483092' title: 'BioPortal: ontologies and integrated data resources at the click of a mouse.' year: 2009 re3data: description: 'BioPortal is an open repository of biomedical ontologies, a service that provides access to those ontologies, and a set of tools for working with them. BioPortal provides a wide range of such tools, either directly via the BioPortal web site, or using the BioPortal web service REST API. BioPortal also includes community features for adding notes, reviews, and even mappings to specific ontologies. BioPortal has four major product components: the web application; the API services; widgets, or applets, that can be installed on your own site; and a Virtual Appliance version that is available for download or through Amazon Web Services machine instance (AMI). There is also a beta release SPARQL endpoint.' 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/$1 fairsharing: abbreviation: BioProject description: A BioProject is a collection of biological data related to a single initiative, originating from a single organization or from a consortium. A BioProject record provides users a single place to find links to the diverse data types generated for that project. The BioProject database is a searchable collection of complete and incomplete (in-progress) large-scale sequencing, assembly, annotation, and mapping projects for cellular organisms. homepage: https://www.ncbi.nlm.nih.gov/bioproject/ name: NCBI BioProject prefix: FAIRsharing.aqhv1y publications: - doi: 10.1093/nar/gkr1163 pubmed_id: 22139929 title: 'BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata.' subjects: - Life Science has_canonical: ena.embl mappings: biocontext: BIOPROJECT fairsharing: FAIRsharing.aqhv1y miriam: bioproject n2t: bioproject re3data: r3d100013330 miriam: deprecated: false description: "BioProject provides an organizational framework to access metadata\ \ about research projects and the data from the projects that are deposited\ \ into different databases. It provides information about a project\u2019s scope,\ \ material, objectives, funding source and general relevance categories." homepage: http://trace.ddbj.nig.ac.jp/bioproject/ id: 00000349 name: BioProject namespaceEmbeddedInLui: false pattern: ^PRJ[DEN][A-Z]\d+$ 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=$1 n2t: description: BioProject provides an organizational framework to access metadata about research projects and the data from the projects that are deposited into different databases. It provides information about a project’s scope, material, objectives, funding source and general relevance categories. example: PRJDB3 homepage: https://www.ncbi.nlm.nih.gov/bioproject name: BioProject at NCBI namespaceEmbeddedInLui: false pattern: ^PRJ[DEN][A-Z]\d+$ prefix: bioproject uri_format: https://www.ncbi.nlm.nih.gov/bioproject?term=$1 publications: - doi: 10.1093/nar/gkr1163 pmc: PMC3245069 pubmed: '22139929' title: 'BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata.' year: 2011 re3data: description: The BioProject database is a searcheable collection of complete and incomplete (in-progress) large-scale molecular projects including genome sequencing and assembly, transcriptome, metagenomic, annotation, expression and mapping projects. BioProject provides a central point to link to all data associated with a project in the NCBI molecular and literature databases. 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 fairsharing: abbreviation: bioregistry contact: email: cthoyt@gmail.com name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The Bioregistry is an open source, community curated registry, meta-registry, and compact identifier resolver. homepage: https://bioregistry.io license: CC0-1.0 name: Bioregistry prefix: FAIRsharing.250a8c publications: - doi: 10.1101/2022.07.08.499378 pubmed_id: null title: Unifying the Identification of Biomedical Entities with the Bioregistry repository: https://github.com/biopragmatics/bioregistry subjects: - Cheminformatics - Bioinformatics - Computational Biology - Life Science - Ontology and Terminology - Computational Chemistry twitter: bioregistry homepage: https://bioregistry.io mappings: fairsharing: FAIRsharing.250a8c 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: 2022 repository: https://github.com/biopragmatics/bioregistry uri_format: https://bioregistry.io/registry/$1 bioregistry.collection: contact: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Manually curated collections of resources stored in the bioregistry example: '0000001' homepage: https://bioregistry.io/collection keywords: - registry name: Bioregistry Collections pattern: ^\d{7}$ 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/ keywords: - data integration - data science - metaregistry - registry name: Bioregistry Metaregistry uri_format: https://bioregistry.io/metaregistry/$1 bioregistry.schema: contact: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Schema for the export of the Bioregistry as RDF example: '0000001' homepage: https://bioregistry.io/schema keywords: - registry name: Bioregistry Schema pattern: ^\d{7}$ 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/$1 homepage: https://biorxiv.org keywords: - preprints - publishing mappings: go: bioRxiv wikidata: P3951 name: bioRxiv pattern: ^(\d{4}\.\d{2}\.\d{2}\.)?\d{6,8}(v\d{1,3})?$ 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/$1 wikidata: database: Q19835482 description: identifier of a document in BioRxiv, a preprint repository for the biological sciences launched in November 2013 example: - 028522 - 2021.09.10.459803 homepage: http://biorxiv.org/search/limit_from:2010-01-01%20limit_to:2017-02-16%20numresults:10%20sort:relevance-rank%20format_result:standard name: BioRxiv ID pattern: ^(\d{4}\.\d{2}\.\d{2}\.)?\d{6}$ prefix: P3951 uri_format: https://doi.org/10.1101/$1 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/$1 fairsharing: abbreviation: BioSample description: "The NCBI BioSample database stores submitter-supplied descriptive\ \ information, or metadata, about the biological materials from which data stored\ \ in NCBI\u2019s primary data archives are derived. NCBI\u2019s archives host\ \ data from diverse types of samples from any species, so the BioSample database\ \ is similarly diverse; typical examples of a BioSample include a cell line,\ \ a primary tissue biopsy, an individual organism or an environmental isolate.\ \ The BioSample database promotes the use of structured and consistent attribute\ \ names and values that describe what the samples are as well as information\ \ about their provenance, where appropriate." homepage: https://www.ncbi.nlm.nih.gov/biosample name: NCBI BioSample prefix: FAIRsharing.qr6pqk publications: - doi: 10.1093/nar/gkr1163 pubmed_id: 22139929 title: 'BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata.' subjects: - Biology mappings: biocontext: BIOSAMPLE cellosaurus: BioSamples fairsharing: FAIRsharing.qr6pqk miriam: biosample n2t: biosample re3data: r3d100012828 miriam: deprecated: false description: The BioSample Database stores information about biological samples used in molecular experiments, such as sequencing, gene expression or proteomics. It includes reference samples, such as cell lines, which are repeatedly used in experiments. Accession numbers for the reference samples will be exchanged with a similar database at NCBI, and DDBJ (Japan). Record access may be affected due to different release cycles and inter-institutional synchronisation. homepage: https://www.ebi.ac.uk/biosamples/ id: '00000350' name: BioSample namespaceEmbeddedInLui: false pattern: ^SAM[NED](\w)?\d+$ prefix: biosample providers: - code: ncbi description: BioSample at NCBI homepage: http://www.ncbi.nlm.nih.gov/biosample name: BioSample at NCBI uri_format: http://www.ncbi.nlm.nih.gov/biosample?term=$1 - code: ddbj description: BioSample at DNA Data Bank of Japan homepage: 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/$1 publications: - doi: 10.1093/nar/gkr1163 pmc: PMC3245069 pubmed: '22139929' title: 'BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata.' year: 2011 re3data: description: The BioSample database contains descriptions of biological source materials used in experimental assays. homepage: https://www.ncbi.nlm.nih.gov/biosample/ name: BioSample prefix: r3d100012828 synonyms: - BioSample at the NCBI xrefs: fairsharing: FAIRsharing.qr6pqk nlx: '143929' omics: '01024' scr: 004854 synonyms: - biosamples biosimulations: mappings: miriam: biosimulations re3data: r3d100013361 miriam: deprecated: false description: BioSimulations is an open repository of simulation projects, including simulation experiments, their results, and data visualizations of their results. BioSimulations supports a broad range of model languages, modeling frameworks, simulation algorithms, and simulation software tools. homepage: https://icahn.mssm.edu/ id: 00000880 name: biosimulations namespaceEmbeddedInLui: false pattern: ^[a-zA-Z0-9_-]{3,}$ 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 contact: email: karr@mssm.edu name: Jonathan Karr orcid: 0000-0002-2605-5080 description: BioSimulators is a registry of containerized biosimulation tools that provide consistent command-line interfaces. The BioSimulations web application helps investigators browse this registry to find simulation tools that have the capabilities (supported modeling frameworks, simulation algorithms, and modeling formats) needed for specific modeling projects. homepage: https://biosimulators.org name: BioSimulators prefix: FAIRsharing.pwEima publications: [] repository: https://github.com/biosimulators/Biosimulators/issues/new/choose subjects: - Computational Biology - Systems Biology mappings: fairsharing: FAIRsharing.pwEima miriam: biosimulators re3data: r3d100013432 miriam: deprecated: false description: BioSimulators is a registry of containerized simulation tools that support a common interface. The containers in BioSimulators support a range of modeling frameworks (e.g., logical, constraint-based, continuous kinetic, discrete kinetic), simulation algorithms (e.g., CVODE, FBA, SSA), and modeling formats (e.g., BGNL, SBML, SED-ML). homepage: https://biosimulators.org/ id: '00000767' name: BioSimulators namespaceEmbeddedInLui: false pattern: '[a-zA-Z0-9-_]+' prefix: biosimulators sampleId: vcell uri_format: https://biosimulators.org/simulators/$1 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. homepage: https://www.ebi.ac.uk/biostudies/ name: BioStudies prefix: FAIRsharing.mtjvme publications: - doi: 10.1093/nar/gkx965 pubmed_id: 29069414 title: The BioStudies database-one stop shop for all data supporting a life sciences study. - doi: 10.15252/msb.20156658 pubmed_id: 26700850 title: The BioStudies database. subjects: - Life Science - Biomedical Science 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 publications: - doi: 10.1093/nar/gkx965 pmc: PMC5753238 pubmed: '29069414' title: The BioStudies database-one stop shop for all data supporting a life sciences study. year: 2018 - doi: 10.15252/msb.20156658 pmc: PMC4704487 pubmed: '26700850' title: The BioStudies database. year: 2015 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/$1 fairsharing: abbreviation: BioSystems description: The NCBI BioSystems database centralizes and cross-links existing biological systems databases, increasing their utility and target audience by integrating their pathways and systems into NCBI resources. The resource provides categorical information on genes, proteins and small molecules of biosystems. homepage: https://www.ncbi.nlm.nih.gov/biosystems/ license: http://opendatacommons.org/licenses/pddl/1.0 name: NCBI BioSystems Database prefix: FAIRsharing.w2eeqr publications: - doi: 10.1093/nar/gkp858 pubmed_id: 19854944 title: The NCBI BioSystems database. subjects: - Biology - Systems Biology mappings: biocontext: BIOSYSTEMS fairsharing: FAIRsharing.w2eeqr miriam: biosystems n2t: biosystems prefixcommons: biosystems re3data: r3d100011033 miriam: deprecated: false description: The NCBI BioSystems database centralizes and cross-links existing biological systems databases, increasing their utility and target audience by integrating their pathways and systems into NCBI resources. homepage: https://www.ncbi.nlm.nih.gov/biosystems/ id: 00000097 name: BioSystems namespaceEmbeddedInLui: false pattern: ^\d+$ 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 re3data: description: "<<>>!!!>>>\nThis retirement includes the representation of BioSystems\ \ records in the NCBI Entrez system and viewers of BioSystems content. \nNCBI\ \ now provides metabolic pathway and other biosystems data through the regularly\ \ updated PubChem Pathways resource (https://pubchemdocs.ncbi.nlm.nih.gov/pathways)\ \ that offers a fresh, extended, and more modern interface." homepage: https://www.ncbi.nlm.nih.gov/biosystems/ name: NCBI BioSystems Database prefix: r3d100011033 synonyms: - NCBI BioSystems xrefs: fairsharing: FAIRsharing.w2eeqr miriam: 00000097 nlx: '69646' scr: 004690 biotools: biocontext: is_identifiers: true is_obo: false prefix: BIOTOOLS uri_format: http://identifiers.org/biotools/$1 description: BioTools is a registry of databases and software with tools, services, and workflows for biological and biomedical research. example: bioregistry fairsharing: abbreviation: bio.tools description: bio.tools is a registry of information about bioinformatics software and data services. It was created to help researchers in biological and biomedical science to find and use such resources. homepage: https://bio.tools/ license: CC-BY-4.0 name: bio.tools prefix: FAIRsharing.63520c publications: - doi: 10.1093/nar/gkv1116 pubmed_id: 26538599 title: 'Tools and data services registry: a community effort to document bioinformatics resources.' repository: http://github.com/bio-tools/biotoolsregistry/ subjects: - Bioinformatics - Biomedical Science - Biology mappings: biocontext: BIOTOOLS fairsharing: FAIRsharing.63520c miriam: biotools n2t: biotools re3data: r3d100013668 miriam: deprecated: false description: Tool and data services registry. homepage: https://bio.tools/ id: '00000616' name: BioTools namespaceEmbeddedInLui: false pattern: ^[-A-Za-z0-9\_]*$ prefix: biotools sampleId: uniprotkb uri_format: https://bio.tools/$1 n2t: description: Tool and data services registry. example: uniprotkb homepage: https://bio.tools/ name: BioTools namespaceEmbeddedInLui: false pattern: ^[A-Za-z0-9\_]*$ prefix: biotools uri_format: https://bio.tools/$1 pattern: ^[-A-Za-z0-9\_]*$ publications: - doi: 10.1093/nar/gkv1116 pmc: PMC4702812 pubmed: '26538599' title: 'Tools and data services registry: a community effort to document bioinformatics resources.' year: 2015 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 keywords: - biologics - life sciences - vendor name: BIOZIL uri_format: https://www.biozol.de/en/product/$1 birnlex: aberowl: description: The BIRN Project lexicon will provide entities for data and database annotation for the BIRN project, covering anatomy, disease, data collection, project management and experimental design. download_owl: http://aber-owl.net/media/ontologies/BIRNLEX/1/birnlex.owl homepage: http://xwiki.nbirn.net:8080/xwiki/bin/view/%20BIRN-OTF-Public/Home name: Biomedical Informatics Research Network Project Lexicon prefix: BIRNLEX version: 1.3.1 bioportal: contact: email: wbug@ncmir.ucsd.edu name: William Bug description: The BIRN Project lexicon will provide entities for data and database annotation for the BIRN project, covering anatomy, disease, data collection, project management and experimental design. homepage: http://xwiki.nbirn.net:8080/xwiki/bin/view/%20BIRN-OTF-Public/Home name: Biomedical Informatics Research Network Project Lexicon prefix: BIRNLEX version: 1.3.1 comment: Part of the NeuroLex namespace now contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The BIRN Project lexicon will provide entities for data and database annotation for the BIRN project, covering anatomy, disease, data collection, project management and experimental design. example: '2023' fairsharing: abbreviation: BIRNLEX description: The BIRN Project lexicon will provide entities for data and database annotation for the BIRN project, covering anatomy, disease, data collection, project management and experimental design. homepage: http://xwiki.nbirn.net:8080/xwiki/bin/view/%20BIRN-OTF-Public/Home name: Biomedical Informatics Research Network Project Lexicon prefix: FAIRsharing.jedbbt publications: [] subjects: [] homepage: https://bioportal.bioontology.org/ontologies/BIRNLEX mappings: aberowl: BIRNLEX bioportal: BIRNLEX fairsharing: FAIRsharing.jedbbt name: Biomedical Informatics Research Network Lexicon pattern: ^\d+$ 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 contact: email: silvio.peroni@unibo.it name: Silvio Peroni orcid: 0000-0003-0530-4305 description: 'the Bibliographic Reference Ontology (BiRO) is an ontology meant to define bibliographic records, bibliographic references, and their compilation into bibliographic collections and bibliographic lists, respectively. ' homepage: http://www.sparontologies.net/ontologies/biro license: CC-BY-4.0 name: 'Bibliographic Reference Ontology ' prefix: FAIRsharing.99da5f publications: [] repository: https://github.com/sparontologies/biro subjects: - Subject Agnostic twitter: sparontologies 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/$1 bitbucket: fairsharing: abbreviation: Bitbucket description: Bitbucket is a Git-based source code repository hosting service owned by Atlassian. It provides a number of different access levels, from free through to premium paid services. Users can create public or private repositories, the latter of which is restricted to 5 users under the free plan. homepage: https://bitbucket.org/ name: Bitbucket prefix: FAIRsharing.fc3431 publications: [] subjects: - Knowledge and Information Systems - Subject Agnostic - Software Engineering mappings: fairsharing: FAIRsharing.fc3431 miriam: bitbucket re3data: r3d100013478 miriam: deprecated: false description: Bitbucket is a Git-based source code repository hosting service owned by Atlassian. homepage: https://www.atlassian.com/ id: 00000899 name: Bitbucket namespaceEmbeddedInLui: false pattern: ^[0-9A-Za-z-_\.]+/[0-9A-Za-z-_\.]+$ prefix: bitbucket sampleId: andreadega/systems-biology-compiler uri_format: https://bitbucket.org/$1 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:$1 bmrb: fairsharing: abbreviation: BMRB description: BMRB collects, annotates, archives, and disseminates (worldwide in the public domain) the important spectral and quantitative data derived from NMR spectroscopic investigations of biological macromolecules and metabolites. Its goal is to empower scientists in their analysis of the structure, dynamics, and chemistry of biological systems and to support further development of the field of biomolecular NMR spectroscopy. homepage: https://bmrb.io/ license: CC0-1.0 name: Biological Magnetic Resonance Data Bank prefix: FAIRsharing.p06nme publications: - doi: 10.1007/s10858-008-9221-y pubmed_id: 18288446 title: 'BioMagResBank (BMRB) as a partner in the Worldwide Protein Data Bank (wwPDB): new policies affecting biomolecular NMR depositions.' - doi: 10.1093/nar/gkm957 pubmed_id: 17984079 title: BioMagResBank. subjects: - Structural Biology mappings: fairsharing: FAIRsharing.p06nme miriam: bmrb re3data: r3d100010191 uniprot: DB-0256 miriam: deprecated: false description: BMRB collects, annotates, archives, and disseminates (worldwide in the public domain) the important spectral and quantitative data derived from NMR spectroscopic investigations of biological macromolecules and metabolites. The goal is to empower scientists in their analysis of the structure, dynamics, and chemistry of biological systems and to support further development of the field of biomolecular NMR spectroscopy. homepage: http://www.bmrb.wisc.edu/ id: '00000716' name: Biological Magnetic Resonance Data Bank namespaceEmbeddedInLui: false pattern: ^(bmr|bmse|bmst)?[0-9]{1,6}$ prefix: bmrb sampleId: '15000' uri_format: http://rest.bmrb.wisc.edu/bmrb/$1/html publications: - doi: 10.1007/s10858-008-9221-y pmc: PMC2268728 pubmed: '18288446' title: 'BioMagResBank (BMRB) as a partner in the Worldwide Protein Data Bank (wwPDB): new policies affecting biomolecular NMR depositions.' year: 2008 - doi: 10.1093/nar/gkm957 pmc: PMC2238925 pubmed: '17984079' title: BioMagResBank. year: 2007 re3data: description: BioMagResBank (BMRB) is the publicly-accessible depository for NMR results from peptides, proteins, and nucleic acids recognized by the International Society of Magnetic Resonance and by the IUPAC-IUBMB-IUPAB Inter-Union Task Group on the Standardization of Data Bases of Protein and Nucleic Acid Structures Determined by NMR Spectroscopy. In addition, BMRB provides reference information and maintains a collection of NMR pulse sequences and computer software for biomolecular NMR homepage: http://www.bmrb.wisc.edu/ name: Biological Magnetic Resonance Data Bank prefix: r3d100010191 synonyms: - BMRB - BioMagResBank - Biological Magnetic Resonance Databank xrefs: fairsharing: FAIRsharing.p06nme nif: 0000-21058 omics: 02858 scr: 002296 uniprot: abbreviation: BMRB category: 3D structure databases homepage: https://bmrb.io/ name: Biological Magnetic Resonance Data Bank prefix: DB-0256 publications: - doi: 10.1093/nar/gkm957 pubmed: '17984079' uri_format: https://bmrb.io/data_library/summary/protein.php?uniprot=$1 bmrb.restraint: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The NMR Restraints Grid contains the original NMR data as collected for over 2500 protein and nucleic acid structures with corresponding PDB entries. In addition to the original restraints, most of the distance, dihedral angle and RDC restraint data (>85%) were parsed, and those in over 500 entries were converted and filtered. The converted and filtered data sets constitute the DOCR and FRED databases respectively. example: '28789' homepage: https://restraintsgrid.bmrb.io/NRG/MRGridServlet keywords: - chemistry - nmr - spectrometry name: NMR Restraints Grid pattern: ^\d+$ 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/$1 mappings: biocontext: BOLD.TAXONOMY miriam: bold.taxonomy n2t: bold.taxonomy ncbi: BOLD prefixcommons: bold wikidata: P3606 miriam: deprecated: false description: The Barcode of Life Data System (BOLD) is an informatics workbench aiding the acquisition, storage, analysis and publication of DNA barcode records. The associated taxonomy browser shows the progress of DNA barcoding and provides sample collection site distribution, and taxon occurence information. homepage: http://www.boldsystems.org/ id: 00000158 name: BOLD Taxonomy namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: bold.taxonomy sampleId: '27267' uri_format: http://www.boldsystems.org/index.php/Taxbrowser_Taxonpage?taxid=$1 n2t: description: The Barcode of Life Data System (BOLD) is an informatics workbench aiding the acquisition, storage, analysis and publication of DNA barcode records. The associated taxonomy browser shows the progress of DNA barcoding and provides sample collection site distribution, and taxon occurence information. example: '27267' homepage: http://www.boldsystems.org/ name: BOLD taxonomy browser namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: bold.taxonomy uri_format: http://www.boldsystems.org/index.php/Taxbrowser_Taxonpage?taxid=$1 ncbi: example: EPAF263 homepage: http://www.barcodinglife.com name: Barcode of Life database prefix: BOLD prefixcommons: description: The Barcode of Life Data Systems (BOLD) is an online workbench that aids collection, management, analysis, and use of DNA barcodes. It consists of 3 components (MAS, IDS, and ECS) that each address the needs of various groups in the barcoding community. example: '27267' homepage: http://www.barcodinglife.com keywords: - DNA name: The Barcode of Life Data Systems pattern: ^\d+$ 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 wikidata: database: Q16934719 description: identifier for a taxon in boldsystems.org example: - '286001' - '38074' name: BOLD Systems taxon ID prefix: P3606 uri_format: http://www.boldsystems.org/index.php/TaxBrowser_TaxonPage?taxid=$1 bootstrep: biocontext: is_identifiers: false is_obo: true prefix: BOOTSTREP uri_format: http://purl.obolibrary.org/obo/BOOTSTREP_$1 mappings: biocontext: BOOTSTREP obofoundry: bootstrep obofoundry: contact: vlee@ebi.ac.uk contact.label: Vivian Lee deprecated: true domain: chemistry and biochemistry homepage: http://www.ebi.ac.uk/Rebholz-srv/GRO/GRO.html name: Gene Regulation Ontology prefix: bootstrep bpdb: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: 'Database of biopesticides maintained by the University of Hertfordshire ' example: '2404' homepage: https://sitem.herts.ac.uk/aeru/bpdb/index.htm keywords: - biology - biopesticides - pesticides name: Bio-Pesticides DataBase pattern: ^\d+$ 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. homepage: https://www.brenda-enzymes.org/ license: CC-BY-4.0 name: BRENDA Enzyme Database prefix: FAIRsharing.etp533 publications: - doi: 10.1016/S0968-0004(01)02027-8 pubmed_id: 11796225 title: 'BRENDA: a resource for enzyme data and metabolic information.' - doi: 10.1093/nar/30.1.47 pubmed_id: 11752250 title: BRENDA, enzyme data and metabolic information. - doi: 10.1093/nar/gkh081 pubmed_id: 14681450 title: 'BRENDA, the enzyme database: updates and major new developments.' - doi: 10.1016/S1096-7176(03)00008-9 pubmed_id: 12850129 title: Review of the BRENDA Database. - doi: 10.1093/nar/gku1068 pubmed_id: 25378310 title: 'BRENDA in 2015: exciting developments in its 25th year of existence.' - doi: 10.1093/nar/gkl972 pubmed_id: 17202167 title: 'BRENDA, AMENDA and FRENDA: the enzyme information system in 2007.' - doi: 10.1093/nar/gkn820 pubmed_id: 18984617 title: 'BRENDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009.' - doi: 10.1093/nar/gks1049 pubmed_id: 23203881 title: 'BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA.' - doi: 10.1093/nar/gkq1089 pubmed_id: 21062828 title: BRENDA, the enzyme information system in 2011. - doi: S0168-1656(17)30183-9 pubmed_id: 28438579 title: The BRENDA enzyme information system-From a database to an expert system. subjects: - Life Science go: homepage: http://www.brenda-enzymes.info name: BRENDA, The Comprehensive Enzyme Information System prefix: BRENDA uri_format: https://www.brenda-enzymes.info/enzyme.php?ecno=$1 mappings: biocontext: BRENDA fairsharing: FAIRsharing.etp533 go: BRENDA miriam: brenda n2t: brenda prefixcommons: brenda re3data: r3d100010616 miriam: deprecated: false description: BRENDA is a collection of enzyme functional data available to the scientific community. Data on enzyme function are extracted directly from the primary literature The database covers information on classification and nomenclature, reaction and specificity, functional parameters, occurrence, enzyme structure and stability, mutants and enzyme engineering, preparation and isolation, the application of enzymes, and ligand-related data. homepage: https://www.brenda-enzymes.org/ id: '00000071' name: BRENDA namespaceEmbeddedInLui: false pattern: ^((\d+\.-\.-\.-)|(\d+\.\d+\.-\.-)|(\d+\.\d+\.\d+\.-)|(\d+\.\d+\.\d+\.\d+))$ prefix: brenda sampleId: 1.1.1.1 uri_format: https://www.brenda-enzymes.org/php/result_flat.php4?ecno=$1 n2t: description: BRENDA is a collection of enzyme functional data available to the scientific community. Data on enzyme function are extracted directly from the primary literature The database covers information on classification and nomenclature, reaction and specificity, functional parameters, occurrence, enzyme structure and stability, mutants and enzyme engineering, preparation and isolation, the application of enzymes, and ligand-related data. example: 1.1.1.1 homepage: https://www.brenda-enzymes.org/ name: Brenda enzyme database namespaceEmbeddedInLui: false pattern: ^((\d+\.-\.-\.-)|(\d+\.\d+\.-\.-)|(\d+\.\d+\.\d+\.-)|(\d+\.\d+\.\d+\.\d+))$ prefix: brenda uri_format: https://www.brenda-enzymes.org/php/result_flat.php4?ecno=$1 name: BRENDA Enzyme prefixcommons: description: BRENDA is the main collection of enzyme functional data available to the scientific community. example: 1.1.1.1 homepage: http://www.brenda-enzymes.org keywords: - enzyme name: The Comprehensive Enzyme Information System pattern: ^((\d+\.-\.-\.-)|(\d+\.\d+\.-\.-)|(\d+\.\d+\.\d+\.-)|(\d+\.\d+\.\d+\.\d+))$ prefix: brenda pubmed_ids: - '18984617' uri_format: http://www.brenda-enzymes.org/php/result_flat.php4?ecno=$1 provides: eccode publications: - doi: 10.1016/j.jbiotec.2017.04.020 pmc: null pubmed: '28438579' title: The BRENDA enzyme information system-From a database to an expert system. year: 2017 - doi: 10.1093/nar/gku1068 pmc: PMC4383907 pubmed: '25378310' title: 'BRENDA in 2015: exciting developments in its 25th year of existence.' year: 2014 - doi: 10.1093/nar/gks1049 pmc: PMC3531171 pubmed: '23203881' title: 'BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA.' year: 2012 - doi: 10.1093/nar/gkq1089 pmc: PMC3013686 pubmed: '21062828' title: BRENDA, the enzyme information system in 2011. year: 2010 - doi: 10.1093/nar/gkn820 pmc: PMC2686525 pubmed: '18984617' title: 'BRENDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009.' year: 2008 - doi: 10.1093/nar/gkl972 pmc: PMC1899097 pubmed: '17202167' title: 'BRENDA, AMENDA and FRENDA: the enzyme information system in 2007.' year: 2007 - doi: 10.1093/nar/gkh081 pmc: PMC308815 pubmed: '14681450' title: 'BRENDA, the enzyme database: updates and major new developments.' year: 2004 - doi: 10.1016/s1096-7176(03)00008-9 pmc: null pubmed: '12850129' title: Review of the BRENDA Database. year: 2003 - doi: 10.1016/s0968-0004(01)02027-8 pmc: null pubmed: '11796225' title: 'BRENDA: a resource for enzyme data and metabolic information.' year: 2002 - doi: 10.1093/nar/30.1.47 pmc: PMC99121 pubmed: '11752250' title: BRENDA, enzyme data and metabolic information. year: 2002 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 brenda.ligand: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Information for ligands in the BRENDA database. example: '278' homepage: https://www.brenda-enzymes.de/ligand.php keywords: - chemistry - structrual bioinformatics name: BRENDA Ligand pattern: ^\d+$ uri_format: https://www.brenda-enzymes.de/ligand.php?brenda_ligand_id=$1 brenda.ligandgroup: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Information for ligand groups (chemical classes). example: '18030' homepage: https://www.brenda-enzymes.de/ligand.php keywords: - chemistry - grouping - structrual bioinformatics name: BRENDA Ligand Group pattern: ^\d+$ 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/30/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: '2022-11-16' download_json: http://purl.obolibrary.org/obo/bspo.json download_obo: https://raw.githubusercontent.com/obophenotype/biological-spatial-ontology/master/bspo.obo example: 0000029 fairsharing: abbreviation: BSPO contact: email: cjmungall@lbl.gov name: Chris Mungall orcid: 0000-0002-6601-2165 description: 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. homepage: http://bioportal.bioontology.org/ontologies/BSPO license: CC-BY-3.0 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 domain: anatomy and development download.obo: http://purl.obolibrary.org/obo/bspo.obo download.owl: http://purl.obolibrary.org/obo/bspo.owl homepage: https://github.com/obophenotype/biological-spatial-ontology license: CC BY 3.0 license.url: http://creativecommons.org/licenses/by/3.0/ name: Biological Spatial Ontology preferredPrefix: BSPO prefix: bspo publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/25140222 title: 'Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology.' repository: https://github.com/obophenotype/biological-spatial-ontology ols: description: An ontology for respresenting spatial concepts, anatomical axes, gradients, regions, planes, sides and surfaces. These concepts can be used at multiple biological scales and in a diversity of taxa, including plants, animals and fungi. The BSPO is used to provide a source of anatomical location descriptors for logically defining anatomical entity classes in anatomy ontologies. download: 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_$1 example: 0000590 fairsharing: abbreviation: BTO description: A structured controlled vocabulary for the source of an enzyme. It comprises terms for tissues, cell lines, cell types and cell cultures from uni- and multicellular organisms. homepage: http://www.brenda-enzymes.info name: BRENDA tissue / enzyme source prefix: FAIRsharing.1414v8 publications: - doi: 10.1093/nar/gkq968 pubmed_id: 21030441 title: 'The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources.' - doi: 10.1093/nar/gky1048 pubmed_id: 30395242 title: 'BRENDA in 2019: a European ELIXIR core data resource.' - doi: 10.1093/nar/gkh081 pubmed_id: 14681450 title: 'BRENDA, the enzyme database: updates and major new developments.' - doi: 10.1093/nar/gku1068 pubmed_id: 25378310 title: 'BRENDA in 2015: exciting developments in its 25th year of existence.' - doi: 10.1093/nar/gks1049 pubmed_id: 23203881 title: 'BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA.' subjects: - Enzymology - Life Science go: description: A structured controlled vocabulary for the source of an enzyme comprising tissues, cell lines, cell types and cell cultures. name: BRENDA tissue / enzyme ontology prefix: BTO mappings: aberowl: BTO biocontext: BTO bioportal: BTO cellosaurus: BTO fairsharing: FAIRsharing.1414v8 go: BTO miriam: bto n2t: bto obofoundry: bto ols: bto ontobee: BTO prefixcommons: bto wikidata: P5501 miriam: deprecated: false description: The Brenda tissue ontology is a structured controlled vocabulary eastablished to identify the source of an enzyme cited in the Brenda enzyme database. It comprises terms of tissues, cell lines, cell types and cell cultures from uni- and multicellular organisms. homepage: https://www.ebi.ac.uk/ols/ontologies/bto id: '00000111' name: Brenda Tissue Ontology namespaceEmbeddedInLui: true pattern: ^BTO:\d{7}$ 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:$1 name: BRENDA Tissue Ontology obofoundry: contact: c.dudek@tu-braunschweig.de contact.github: chdudek contact.label: Christian-Alexander Dudek contact.orcid: 0000-0001-9117-7909 deprecated: false description: A structured controlled vocabulary for the source of an enzyme comprising tissues, cell lines, cell types and cell cultures. domain: anatomy and development download.json: http://purl.obolibrary.org/obo/bto.json download.obo: http://purl.obolibrary.org/obo/bto.obo download.owl: http://purl.obolibrary.org/obo/bto.owl homepage: http://www.brenda-enzymes.org license: CC BY 4.0 license.url: https://creativecommons.org/licenses/by/4.0/ name: BRENDA tissue / enzyme source preferredPrefix: BTO prefix: bto publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/21030441 title: 'The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources' repository: https://github.com/BRENDA-Enzymes/BTO ols: description: A structured controlled vocabulary for the source of an enzyme comprising tissues, cell lines, cell types and cell cultures. download: http://purl.obolibrary.org/obo/bto.owl name: The BRENDA Tissue Ontology (BTO) prefix: bto version: '2021-10-26' version.iri: http://purl.obolibrary.org/obo/bto/releases/2021-10-26/bto.owl ontobee: library: Library name: BRENDA tissue / enzyme source prefix: BTO pattern: ^\d{7}$ 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/gky1048 pmc: PMC6323942 pubmed: '30395242' title: 'BRENDA in 2019: a European ELIXIR core data resource.' year: 2019 - doi: 10.1093/nar/gku1068 pmc: PMC4383907 pubmed: '25378310' title: 'BRENDA in 2015: exciting developments in its 25th year of existence.' year: 2014 - doi: 10.1093/nar/gks1049 pmc: PMC3531171 pubmed: '23203881' title: 'BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA.' year: 2012 - doi: 10.1093/nar/gkq968 pmc: PMC3013802 pubmed: '21030441' title: 'The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources.' year: 2010 - doi: 10.1093/nar/gkh081 pmc: PMC308815 pubmed: '14681450' title: 'BRENDA, the enzyme database: updates and major new developments.' year: 2004 synonyms: - BTO wikidata: database: Q4836352 description: identifier in the Brenda Tissue Ontology example: - BTO:0000562 - BTO:0001172 homepage: https://www.brenda-enzymes.org/ontology.php?ontology_id=3 name: Brenda Tissue Ontology ID pattern: ^BTO:\d+$ prefix: P5501 uri_format: https://www.brenda-enzymes.org/ontology.php?ontology_id=3&id_go=$1 bugbase.expt: biocontext: 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 uri_format: http://bugs.sgul.ac.uk/bugsbase/tabs/experiment.php?action=view&expt_id=$1 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=$1&action=view n2t: description: BugBase is a MIAME-compliant microbial gene expression and comparative genomic database. It stores experimental annotation and multiple raw and analysed data formats, as well as protocols for bacterial microarray designs. This collection references design protocols. example: '67' homepage: http://bugs.sgul.ac.uk/E-BUGS name: BugBase Protocol at University of London namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: bugbase.protocol uri_format: http://bugs.sgul.ac.uk/bugsbase/tabs/protocol.php?protocol_id=$1&action=view uri_format: http://bugs.sgul.ac.uk/bugsbase/tabs/protocol.php?action=view&protocol_id=$1 bykdb: biocontext: is_identifiers: true is_obo: false prefix: BYKDB uri_format: http://identifiers.org/bykdb/$1 fairsharing: abbreviation: BYKdb description: The Bacterial protein tYrosine Kinase database (BYKdb) contains computer-annotated BY-kinase sequences. The database web interface allows static and dynamic queries and provides integrated analysis tools including sequence annotation. homepage: http://bykdb.ibcp.fr name: Bacterial protein tYrosine Kinase database prefix: FAIRsharing.jr30xc publications: - doi: 10.1016/s0378-1119(97)00554-4 pubmed_id: 9434192 title: Characterization of a bacterial gene encoding an autophosphorylating protein tyrosine kinase. - doi: 10.1093/bioinformatics/btn462 pubmed_id: 18772155 title: Identification of the idiosyncratic bacterial protein tyrosine kinase (BY-kinase) family signature. - doi: 10.1007/s00726-009-0237-8 pubmed_id: 19189200 title: 'Tyrosine-kinases in bacteria: from a matter of controversy to the status of key regulatory enzymes.' - doi: 10.1093/nar/gkr915 pubmed_id: 22080550 title: 'BYKdb: the Bacterial protein tYrosine Kinase database.' subjects: - Life Science mappings: biocontext: BYKDB fairsharing: FAIRsharing.jr30xc miriam: bykdb n2t: bykdb prefixcommons: bykdb miriam: deprecated: false description: The bacterial tyrosine kinase database (BYKdb) that collects sequences of putative and authentic bacterial tyrosine kinases, providing structural and functional information. homepage: https://bykdb.ibcp.fr/BYKdb/ id: '00000253' name: BYKdb namespaceEmbeddedInLui: false pattern: ^[A-Z0-9]+$ 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: 10.1016/s0378-1119(97)00554-4 pmc: null pubmed: '9434192' title: Characterization of a bacterial gene encoding an autophosphorylating protein tyrosine kinase. year: 1997 - doi: 10.1093/nar/gkr915 pmc: PMC3245071 pubmed: '22080550' title: 'BYKdb: the Bacterial protein tYrosine Kinase database.' year: 2011 - doi: 10.1007/s00726-009-0237-8 pmc: null pubmed: '19189200' title: 'Tyrosine-kinases in bacteria: from a matter of controversy to the status of key regulatory enzymes.' year: 2009 - doi: 10.1093/bioinformatics/btn462 pmc: null pubmed: '18772155' title: Identification of the idiosyncratic bacterial protein tyrosine kinase (BY-kinase) family signature. year: 2008 c4o: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: An ontology that permits the number of in-text citations of a cited source to be recorded, together with their textual citation contexts, along with the number of citations a cited entity has received globally on a particular date. example: InTextReferencePointer fairsharing: abbreviation: C4O contact: email: silvio.peroni@unibo.it name: Silvio Peroni orcid: 0000-0003-0530-4305 description: The Citation Counting and Context Characterisation Ontology (C4O) is an ontology that permits the number of in-text citations of a cited source to be recorded, together with their textual citation contexts, along with the number of citations a cited entity has received globally on a particular date; homepage: http://www.sparontologies.net/ontologies/c4o license: CC-BY-4.0 name: 'Citation Counting and Context Characterization Ontology ' prefix: FAIRsharing.beb855 publications: [] repository: https://github.com/sparontologies/c4o subjects: - Subject Agnostic twitter: sparontologies 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/$1 edam: description: A unique identifier of an item from the CABRI database. name: CABRI obsolete: false prefix: '2380' fairsharing: abbreviation: CABRI contact: email: paolo.romano@hsanmartino.it name: Paolo Romano orcid: 0000-0003-4694-3883 description: CABRI provides an integrated resource including catalogues of strains of different organism types, genetic materials and other biologicals resources of European culture collections so that the user world-wide can access these relevant data during one searching session through a common entry point and get in touch with collections for ordering products to be delivered to their place of work. homepage: http://www.cabri.org name: Common Access to Biological Resources and Information prefix: FAIRsharing.qx2rvz publications: - doi: 10.1002/cfg.376 pubmed_id: 18629057 title: Interoperability of CABRI Services and Biochemical Pathways Databases. - doi: null pubmed_id: 16231959 title: The role of informatics in the coordinated management of biological resources collections. subjects: - Molecular biology - Medical Microbiology - Applied Microbiology - Virology - Molecular Microbiology - Microbiology mappings: biocontext: CABRI edam: '2380' fairsharing: FAIRsharing.qx2rvz miriam: cabri n2t: cabri ncbi: CABRI miriam: deprecated: false description: CABRI (Common Access to Biotechnological Resources and Information) is an online service where users can search a number of European Biological Resource Centre catalogues. It lists the availability of a particular organism or genetic resource and defines the set of technical specifications and procedures which should be used to handle it. homepage: http://www.cabri.org/ id: '00000261' name: CABRI namespaceEmbeddedInLui: false pattern: ^([A-Za-z]+)?(\_)?([A-Za-z-]+)\:([A-Za-z0-9 ]+)$ prefix: cabri providers: - code: 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+[$1] ncbi: example: ACC 424 name: Common Access to Biological Resources and Information Project prefix: CABRI publications: - doi: 10.1002/cfg.376 pmc: PMC2447341 pubmed: '18629057' title: Interoperability of CABRI Services and Biochemical Pathways Databases. year: 2004 - doi: 10.2165/00822942-200594030-00002 pmc: null pubmed: '16231959' title: The role of informatics in the coordinated management of biological resources collections. year: 2005 cadsr: mappings: miriam: cadsr n2t: cadsr miriam: deprecated: false description: The US National Cancer Institute (NCI) maintains and administers data elements, forms, models, and components of these items in a metadata registry referred to as the Cancer Data Standards Registry and Repository, or caDSR. homepage: https://wiki.nci.nih.gov/display/caDSR/caDSR+Wiki id: 00000695 name: Cancer Data Standards Registry and Repository namespaceEmbeddedInLui: false pattern: ^[0-9]*$ 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/$1 fairsharing: abbreviation: CAMEO contact: email: torsten.schwede@unibas.ch name: Torsten Schwede orcid: 0000-0003-2715-335X description: Continuous automated benchmarking of computational protein structure prediction methods (and model quality estimation techniques). CAMEO assessment is based on blind predictions for weekly pre-released targets from PDB. Benchmarking results are made available as reference data for methods development. homepage: http://cameo3d.org/ license: http://cameo3d.org/cameong_terms name: Continuously Automated Model Evaluation prefix: FAIRsharing.dq34p2 publications: - doi: 10.1093/database/bat031 pubmed_id: 23624946 title: The Protein Model Portal--a comprehensive resource for protein structure and model information. subjects: - Life Science mappings: biocontext: CAMEO fairsharing: FAIRsharing.dq34p2 miriam: cameo n2t: cameo miriam: deprecated: false description: The goal of the CAMEO (Continuous Automated Model EvaluatiOn) community project is to continuously evaluate the accuracy and reliability of protein structure prediction servers, offering scores on tertiary and quaternary structure prediction, model quality estimation, accessible surface area prediction, ligand binding site residue prediction and contact prediction services in a fully automated manner. These predictions are regularly compared against reference structures from PDB. homepage: https://cameo3d.org id: '00000623' name: CAMEO namespaceEmbeddedInLui: false pattern: ^[0-9\-_]+$ prefix: cameo sampleId: 2019-08-03_00000089_1 uri_format: https://www.cameo3d.org/sp/targets/target/$1 n2t: description: The goal of the CAMEO (Continuous Automated Model EvaluatiOn) community project is to continuously evaluate the accuracy and reliability of protein structure prediction servers, offering scores on tertiary and quaternary structure prediction, model quality estimation, accessible surface area prediction, ligand binding site residue prediction and contact prediction services in a fully automated manner. These predictions are regularly compared against reference structures from PDB. example: 2018-03-24_00000030_1 homepage: https://cameo3d.org name: CAMEO namespaceEmbeddedInLui: false pattern: ^[0-9\-_]+$ prefix: cameo uri_format: https://www.cameo3d.org/sp/targets/target/$1 name: Continuous Automated Model Evaluation publications: - doi: 10.1093/database/bat031 pmc: PMC3889916 pubmed: '23624946' title: The Protein Model Portal--a comprehensive resource for protein structure and model information. year: 2013 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 contact: email: haendel@ohsu.edu name: Melissa Haendel orcid: 0000-0001-9114-8737 description: The Common Anatomy Reference Ontology (CARO) is being developed to facilitate interoperability between existing anatomy ontologies for different species, and will provide a template for building new anatomy ontologies. homepage: http://bioportal.bioontology.org/ontologies/CARO?p=summary name: Common Anatomy Reference Ontology prefix: FAIRsharing.3kcgmr publications: - doi: 10.1007/978-1-84628-885-2_16 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 domain: anatomy and development download.owl: http://purl.obolibrary.org/obo/caro.owl homepage: https://github.com/obophenotype/caro/ license: CC BY 4.0 license.url: https://creativecommons.org/licenses/by/4.0/ name: Common Anatomy Reference Ontology preferredPrefix: CARO prefix: caro repository: https://github.com/obophenotype/caro ols: description: 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}$ providers: - code: obo.1 description: This incorrect encoding was found inside IDO-COVID-19 homepage: http://purl.obolibrary.org name: Nonstandard OBO PURL uri_format: http://purl.obolibrary.org/obo/ido.owl/CARO_$1 publications: - doi: 10.1007/978-1-84628-885-2_16 pmc: null pubmed: null title: "CARO \u2013 The Common Anatomy Reference Ontology" year: 2008 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. homepage: https://www.cas.org/support/documentation/chemical-substances/faqs#2 name: CAS Registry Number prefix: FAIRsharing.r7Kwy7 publications: - doi: 10.1021/acs.jcim.2c00268 pubmed_id: null title: 'CAS Common Chemistry in 2021: Expanding Access to Trusted Chemical Information for the Scientific Community' 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 publications: - doi: 10.1021/acs.jcim.2c00268 pmc: PMC9199008 pubmed: '35559614' title: 'CAS Common Chemistry in 2021: Expanding Access to Trusted Chemical Information for the Scientific Community.' year: 2022 synonyms: - CASID - CAS_RN - SECONDARY_CAS_RN - cas_id uri_format: https://commonchemistry.cas.org/detail?cas_rn=$1 wikidata: database: Q102507 description: identifier for a chemical substance or compound per Chemical Abstract Service's Registry database example: - 1474034-05-3 - 15307-86-5 homepage: https://scifinder.cas.org name: CAS Registry Number pattern: ^[1-9]\d{1,6}-\d{2}-\d$ prefix: P231 uri_format: https://commonchemistry.cas.org/detail?cas_rn=$1 casspc: comment: Jim Balhoff said that Catalog of Fishes does not publish their data in a machine readable format, but a long time ago they sent a CSV dump to help in the development of TTO and VTO. These ontologies are effectively retired and CASSPC terms are only also used in Phenoscape. 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). homepage: http://www.cathdb.info/ name: CATH prefix: FAIRsharing.xgcyyn publications: - doi: 10.1093/nar/gkw1098 pubmed_id: 27899584 title: 'CATH: an expanded resource to predict protein function through structure and sequence.' - doi: 10.1016/s0969-2126(97)00260-8 pubmed_id: 9309224 title: CATH--a hierarchic classification of protein domain structures. - doi: 10.1016/j.biochi.2015.08.004 pubmed_id: 26253692 title: The history of the CATH structural classification of protein domains. - doi: 10.1093/bioinformatics/btw473 pubmed_id: 27477482 title: 'Functional classification of CATH superfamilies: a domain-based approach for protein function annotation.' - doi: 10.1093/nar/gkx1069 pubmed_id: 29112716 title: 'Gene3D: Extensive prediction of globular domains in proteins.' - doi: 10.1093/nar/gky1097 pubmed_id: 30398663 title: 'CATH: expanding the horizons of structure-based functional annotations for genome sequences.' - doi: 10.1093/nar/gkaa1079 pubmed_id: 33237325 title: 'CATH: increased structural coverage of functional space.' - doi: 10.1093/nar/gku947 pubmed_id: 25348408 title: 'CATH: comprehensive structural and functional annotations for genome sequences.' - doi: null pubmed_id: 11788987 title: 'The CATH protein family database: a resource for structural and functional annotation of genomes.' subjects: - Evolutionary Biology - Biology twitter: CATHDatabase 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 - doi: 10.1093/nar/gkaa1079 pmc: PMC7778904 pubmed: '33237325' title: 'CATH: increased structural coverage of functional space.' year: 2021 - doi: 10.1093/nar/gky1097 pmc: PMC6323983 pubmed: '30398663' title: 'CATH: expanding the horizons of structure-based functional annotations for genome sequences.' year: 2019 - doi: 10.1093/nar/gkx1069 pmc: PMC5753370 pubmed: '29112716' title: 'Gene3D: Extensive prediction of globular domains in proteins.' year: 2018 - doi: 10.1093/nar/gkw1098 pmc: PMC5210570 pubmed: '27899584' title: 'CATH: an expanded resource to predict protein function through structure and sequence.' year: 2016 - doi: 10.1093/bioinformatics/btw473 pmc: PMC5018379 pubmed: '27477482' title: 'Functional classification of CATH superfamilies: a domain-based approach for protein function annotation.' year: 2016 - doi: 10.1016/j.biochi.2015.08.004 pmc: PMC4678953 pubmed: '26253692' title: The history of the CATH structural classification of protein domains. year: 2015 - doi: 10.1093/nar/gku947 pmc: PMC4384018 pubmed: '25348408' title: 'CATH: comprehensive structural and functional annotations for genome sequences.' year: 2014 - doi: null pmc: null pubmed: '11788987' title: 'The CATH protein family database: a resource for structural and functional annotation of genomes.' year: 2002 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. homepage: http://www.cazy.org/ name: The Carbohydrate-Active enZYmes Database prefix: FAIRsharing.ntyq70 publications: - doi: 10.1093/nar/gkn663 pubmed_id: 18838391 title: 'The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics.' - doi: 10.1093/nar/gkt1178 pubmed_id: 24270786 title: The carbohydrate-active enzymes database (CAZy) in 2013. subjects: - Life Science - Glycomics go: description: The CAZy database describes the families of structurally-related catalytic and carbohydrate-binding modules (or functional domains) of enzymes that degrade, modify, or create glycosidic bonds. homepage: http://www.cazy.org/ name: Carbohydrate Active EnZYmes prefix: CAZY uri_format: http://www.cazy.org/$1.html mappings: biocontext: CAZY fairsharing: FAIRsharing.ntyq70 go: CAZY miriam: cazy n2t: cazy prefixcommons: cazy re3data: r3d100012321 uniprot: DB-0136 miriam: deprecated: false description: The Carbohydrate-Active Enzyme (CAZy) database is a resource specialized in enzymes that build and breakdown complex carbohydrates and glycoconjugates. These enzymes are classified into families based on structural features. homepage: http://www.cazy.org/ id: 00000195 name: CAZy namespaceEmbeddedInLui: false pattern: ^(GT|GH|PL|CE|CBM)\d+(\_\d+)?$ prefix: cazy sampleId: GT10 uri_format: http://www.cazy.org/$1.html n2t: description: The Carbohydrate-Active Enzyme (CAZy) database is a resource specialized in enzymes that build and breakdown complex carbohydrates and glycoconjugates. These enzymes are classified into families based on structural features. example: GT10 homepage: http://www.cazy.org/ name: CAZy at CNRS namespaceEmbeddedInLui: false pattern: ^(GT|GH|PL|CE|CBM)\d+(\_\d+)?$ prefix: cazy uri_format: http://www.cazy.org/$1.html prefixcommons: description: The CAZy database describes the families of structurally-related catalytic and carbohydrate-binding modules (or functional domains) of enzymes that degrade, modify, or create glycosidic bonds. example: GT10 homepage: http://www.cazy.org/ keywords: - classification - polysaccharide name: The Carbohydrate-Active enZYmes Database pattern: ^GT\d+$ prefix: cazy pubmed_ids: - '18838391' uri_format: http://www.cazy.org/$1.html publications: - doi: 10.1093/nar/gkt1178 pmc: PMC3965031 pubmed: '24270786' title: The carbohydrate-active enzymes database (CAZy) in 2013. year: 2013 - doi: 10.1093/nar/gkn663 pmc: PMC2686590 pubmed: '18838391' title: 'The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics.' year: 2008 re3data: description: CAZy is a specialist database dedicated to the display and analysis of genomic, structural and biochemical information on Carbohydrate-Active Enzymes (CAZymes). CAZy data are accessible either by browsing sequence-based families or by browsing the content of genomes in carbohydrate-active enzymes. New genomes are added regularly shortly after they appear in the daily releases of GenBank. New families are created based on published evidence for the activity of at least one member of the family and all families are regularly updated, both in content and in description. homepage: http://www.cazy.org/ name: Carbohydrate-Active enZYmes Database prefix: r3d100012321 synonyms: - CAZy xrefs: fairsharing: FAIRsharing.ntyq70 nif: 0000-02642 omics: '01677' scr: 012909 uniprot: abbreviation: CAZy category: Protein family/group databases homepage: http://www.cazy.org/ name: Carbohydrate-Active enZymes prefix: DB-0136 publications: - doi: 10.1093/nar/gkt1178 pubmed: '24270786' uri_format: http://www.cazy.org/fam/$1.html cba: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: 'CBA: http://www.cba.ac.cn/ and the Shanghai Institutes for Biological Sciences (SIBS at http://www.sibs.ac.cn/) provide EBI with citation data not available in MEDLINE.' example: '375364' homepage: http://www.cba.ac.cn keywords: - bibliography name: Chinese Biological Abstracts pattern: ^\d+$ uri_format: https://europepmc.org/article/CBA/$1 cbioportal: fairsharing: abbreviation: cBioPortal description: The cBioPortal for Cancer Genomics provides visualization, analysis and download of large-scale cancer genomics data sets. homepage: http://www.cbioportal.org name: cBioPortal for Cancer Genomics prefix: FAIRsharing.6L6MjA publications: - doi: 10.1126/scisignal.2004088 pubmed_id: 23550210 title: Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal. - doi: 10.1158/2159-8290.CD-12-0095 pubmed_id: 22588877 title: 'The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data.' repository: https://github.com/cBioPortal/cbioportal subjects: - Genomics - Proteomics - Biomedical Science - Preclinical Studies twitter: cbioportal mappings: fairsharing: FAIRsharing.6L6MjA miriam: cbioportal n2t: cbioportal miriam: deprecated: false description: The cBioPortal for Cancer Genomics provides visualization, analysis and download of large-scale cancer genomics data sets. homepage: http://www.cbioportal.org id: 00000679 name: The cBioPortal for Cancer Genomics namespaceEmbeddedInLui: false pattern: ^[a-z0-9\_]+$ prefix: cbioportal sampleId: laml_tcga_pub uri_format: http://www.cbioportal.org/study?id=$1#summary n2t: description: The cBioPortal for Cancer Genomics provides visualization, analysis and download of large-scale cancer genomics data sets. example: laml_tcga_pub homepage: http://www.cbioportal.org name: The cBioPortal for Cancer Genomics namespaceEmbeddedInLui: false pattern: ^[a-z0-9\_]+$ prefix: cbioportal uri_format: http://www.cbioportal.org/study?id=$1#summary publications: - doi: 10.1126/scisignal.2004088 pmc: PMC4160307 pubmed: '23550210' title: Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal. year: 2013 - doi: 10.1158/2159-8290.cd-12-0095 pmc: PMC3956037 pubmed: '22588877' title: 'The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data.' year: 2012 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=$1 fairsharing: abbreviation: CCDS description: The Consensus CDS (CCDS) project is a collaborative effort to identify a core set of human and mouse protein coding regions that are consistently annotated and of high quality. The long term goal is to support convergence towards a standard set of gene annotations. homepage: http://www.ncbi.nlm.nih.gov/CCDS/ license: http://opendatacommons.org/licenses/pddl/1.0 name: The Consensus CDS prefix: FAIRsharing.46s4nt publications: - doi: 10.1101/gr.080531.108 pubmed_id: 19498102 title: 'The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes.' subjects: - Life Science mappings: biocontext: CCDS fairsharing: FAIRsharing.46s4nt miriam: ccds n2t: ccds prefixcommons: ccds uniprot: DB-0187 miriam: deprecated: false description: The Consensus CDS (CCDS) project is a collaborative effort to identify a core set of human and mouse protein coding regions that are consistently annotated and of high quality. The CCDS set is calculated following coordinated whole genome annotation updates carried out by the NCBI, WTSI, and Ensembl. The long term goal is to support convergence towards a standard set of gene annotations. homepage: http://www.ncbi.nlm.nih.gov/CCDS/ id: '00000375' name: Consensus CDS namespaceEmbeddedInLui: false pattern: ^CCDS\d+\.\d+$ prefix: ccds sampleId: CCDS13573.1 uri_format: http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&DATA=$1 n2t: description: The Consensus CDS (CCDS) project is a collaborative effort to identify a core set of human and mouse protein coding regions that are consistently annotated and of high quality. The CCDS set is calculated following coordinated whole genome annotation updates carried out by the NCBI, WTSI, and Ensembl. The long term goal is to support convergence towards a standard set of gene annotations. example: CCDS13573.1 homepage: http://www.ncbi.nlm.nih.gov/CCDS/ name: Consensus CDS at NCBI namespaceEmbeddedInLui: false pattern: ^CCDS\d+\.\d+$ prefix: ccds uri_format: http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&DATA=$1 prefixcommons: description: The Consensus CDS (CCDS) project is a collaborative effort to identify a core set of human and mouse protein coding regions that are consistently annotated and of high quality. The long term goal is to support convergence towards a standard set of gene annotations. example: '4824' homepage: http://www.ncbi.nlm.nih.gov/CCDS/ keywords: - protein - gene name: The Consensus CDS pattern: ^\d+$ 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: abbreviation: CCDS category: Sequence databases homepage: https://www.ncbi.nlm.nih.gov/CCDS name: The Consensus CDS (CCDS) project prefix: DB-0187 publications: - doi: 10.1101/gr.080531.108 pubmed: '19498102' 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/$1 bioportal: contact: email: mironov@bio.ntnu.no name: Vladimir Mironov description: An application ontology integrating knowledge about the eukaryotic cell cycle. homepage: http://www.semantic-systems-biology.org/cco/ name: Cell Cycle Ontology prefix: CCO publication: http://genomebiology.com/2009/10/5/R58 version: '2.10' contact: email: kuiper@bio.ntnu.no github: makuintnu name: Martin Kuiper orcid: 0000-0002-1171-9876 download_obo: https://www.bio.ntnu.no/ontology/CCO/cco.obo download_owl: https://www.bio.ntnu.no/ontology/CCO/cco.owl fairsharing: abbreviation: CCO contact: email: kuiper@bio.ntnu.no name: Martin Kuiper orcid: 0000-0002-1171-9876 description: CCO contains genes, proteins, interactions (comprising genes or proteins that participate in them), processes from the cell cycle subtree of GO, molecular functions (GO), taxa, and ontological constructs (like an upper level ontology and relationships) to stick everything together. homepage: https://www.biogateway.eu/tools/#CCO name: Cell Cycle Ontology prefix: FAIRsharing.xhwrnr publications: - doi: 10.1186/gb-2009-10-5-r58 pubmed_id: 19480664 title: 'The Cell Cycle Ontology: an application ontology for the representation and integrated analysis of the cell cycle process.' subjects: - Functional Genomics - Genomics - Proteomics - Life Science mappings: aberowl: CCO biocontext: CCO bioportal: CCO fairsharing: FAIRsharing.xhwrnr miriam: cco n2t: cco ols: cco prefixcommons: cco miriam: deprecated: false description: The Cell Cycle Ontology is an application ontology that captures and integrates detailed knowledge on the cell cycle process. homepage: https://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=CCO id: '00000234' name: Cell Cycle Ontology namespaceEmbeddedInLui: true pattern: ^CCO:\w+$ 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/10/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: CC-BY-4.0 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 contact: email: balhoff@gmail.com name: Jim Balhoff orcid: 0000-0002-8688-6599 description: Comparative Data Analysis Ontology (CDAO) is a formalization of concepts and relations relevant to evolutionary comparative analysis, such as phylogenetic trees, OTUs (operational taxonomic units) and compared characters (including molecular characters as well as other types). homepage: https://github.com/evoinfo/cdao license: CC0-1.0 name: Comparative Data Analysis Ontology prefix: FAIRsharing.kay31r publications: - doi: 10.4137/ebo.s2320 pubmed_id: 19812726 title: Initial implementation of a comparative data analysis ontology. repository: https://github.com/evoinfo/cdao/issues 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 domain: organisms download.owl: http://purl.obolibrary.org/obo/cdao.owl homepage: https://github.com/evoinfo/cdao license: CC0 1.0 license.url: https://creativecommons.org/publicdomain/zero/1.0/ name: Comparative Data Analysis Ontology preferredPrefix: CDAO prefix: cdao publications: - id: https://doi.org/10.4137/EBO.S2320 title: Initial Implementation of a Comparative Data Analysis Ontology repository: https://github.com/evoinfo/cdao ols: description: 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. homepage: https://www.publicsafety.gc.ca/cnt/rsrcs/cndn-dsstr-dtbs/index-en.aspx name: Canadian Disaster Database prefix: FAIRsharing.ea287c publications: [] subjects: - Geology - Earth Science go: homepage: https://www.ncbi.nlm.nih.gov/cdd name: Conserved Domain Database at NCBI prefix: CDD uri_format: http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=$1 mappings: biocontext: CDD edam: '2666' fairsharing: FAIRsharing.ea287c go: CDD miriam: cdd n2t: cdd ncbi: CDD prefixcommons: cdd re3data: r3d100012041 uniprot: DB-0214 miriam: deprecated: false description: The Conserved Domain Database (CDD) is a collection of multiple sequence alignments and derived database search models, which represent protein domains conserved in molecular evolution. homepage: https://www.ncbi.nlm.nih.gov/sites/entrez?db=cdd id: 00000119 name: Conserved Domain Database namespaceEmbeddedInLui: false pattern: ^(cd)?\d{5}$ prefix: cdd sampleId: cd00400 uri_format: https://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=$1 n2t: description: The Conserved Domain Database (CDD) is a collection of multiple sequence alignments and derived database search models, which represent protein domains conserved in molecular evolution. example: cd00400 homepage: https://www.ncbi.nlm.nih.gov/sites/entrez?db=cdd name: Conserved Domain Database at NCBI namespaceEmbeddedInLui: false pattern: ^(cd)?\d{5}$ prefix: cdd uri_format: https://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=$1 ncbi: example: 02194 homepage: https://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml name: Conserved Domain Database prefix: CDD prefixcommons: description: The Conserved Domain Database (CDD) brings together several collections of multiple sequence alignments representing conserved domains, including NCBI-curated domains, which use 3D-structure information to explicitly to define domain boundaries and provide insights into sequence/structure/function relationships, as well as domain models imported from a number of external source databases (Pfam, SMART, COG, PRK, TIGRFAM). example: cd00400 homepage: http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml keywords: - protein - structure name: Conserved Domain Database pattern: ^cd\d{5}$ prefix: cdd pubmed_ids: - '18984618' uri_format: http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=$1 publications: - doi: 10.1093/nar/gku1221 pmc: PMC4383992 pubmed: '25414356' title: 'CDD: NCBI''s conserved domain database.' year: 2014 - doi: 10.1093/nar/gkn845 pmc: PMC2686570 pubmed: '18984618' title: 'CDD: specific functional annotation with the Conserved Domain Database.' year: 2008 re3data: description: 'The Canadian Disaster Database (CDD) contains detailed disaster information on more than 1000 natural, technological and conflict events (excluding war) that have happened since 1900 at home or abroad and that have directly affected Canadians. Message since 2022-01: The Canadian Disaster Database geospatial view is temporarily out of service. We apologize for the inconvenience. The standard view of the database is still available.' homepage: https://www.publicsafety.gc.ca/cnt/rsrcs/cndn-dsstr-dtbs/index-en.aspx name: Canadian Disaster Database prefix: r3d100012041 synonyms: - BDC - "Base de donn\xE9es canadienne sur les catastrophes" - CDD xrefs: fairsharing: FAIRsharing.ea287c uniprot: abbreviation: CDD category: Family and domain databases homepage: https://www.ncbi.nlm.nih.gov/cdd name: Conserved Domains Database prefix: DB-0214 publications: - doi: doi pubmed: '25414356' 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/9/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. domain: diet, metabolomics, and nutrition download.obo: http://purl.obolibrary.org/obo/cdno.obo download.owl: http://purl.obolibrary.org/obo/cdno.owl homepage: https://cdno.info/ license: CC BY 3.0 license.url: https://creativecommons.org/licenses/by/3.0/ name: Compositional Dietary Nutrition Ontology preferredPrefix: CDNO prefix: cdno publications: - id: https://doi.org/10.1002/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}$ publications: - doi: 10.1002/csc2.20092 pmc: null pubmed: null title: Knowledge representation and data sharing to unlock crop variation for nutritional food security year: 2020 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=$1 cdt: appears_in: - ohd bartoc: abbreviation: CDT description: The Code on Dental Procedures and Nomenclature is used to provide for the efficient processing of dental claims, and to populate an Electronic Health Record. homepage: http://www.ada.org/en/publications/cdt license: http://rightsstatements.org/vocab/InC/1.0 name: Code on Dental Procedures and Nomenclature prefix: '20299' contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The Code on Dental Procedures and Nomenclature (the CDT Code) assures consistency in documenting dental treatment. download_owl: https://github.com/oral-health-and-disease-ontologies/ohd-ontology/blob/master/src/ontology/older/CDTCodes%20as%20Classes_pruned.owl example: '1000001' hl7: description: Version of Current Dental Terminology (CDT) version 4, included in the Healthcare Common Procedure Coding System (HCPCS).Request rejected. This is a duplicate of OID 2.16.840.1.113883.6.13 name: Current Dental Terminology preferred_prefix: CDT prefix: 2.16.840.1.113883.6.116 status: Rejected homepage: https://www.ada.org/publications/CDT mappings: bartoc: '20299' hl7: 2.16.840.1.113883.6.116 name: Current Dental Terminology pattern: ^\d{7}$ 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/$1 fairsharing: abbreviation: null description: This library is a public and easily accessible resource database of images, videos, and animations of cells, capturing a wide diversity of organisms, cell types, and cellular processes. The purpose of this database is to advance research on cellular activity, with the ultimate goal of improving human health. It is a repository for images, movies, and animations of cells from a variety of organisms that demonstrate cellular architecture and functions. This comprehensive library is designed as a public resource first and foremost for research, and secondarily as a tool for education. The long-term goal is the construction of a library of images that will serve as primary data for research. homepage: http://www.cellimagelibrary.org name: Cell Image Library prefix: FAIRsharing.8t18te publications: - doi: 10.1093/nar/gks1257 pubmed_id: 23203874 title: 'The cell: an image library-CCDB: a curated repository of microscopy data.' subjects: - Life Science - Cell Biology twitter: CellImageLibrar mappings: biocontext: CELLIMAGE fairsharing: FAIRsharing.8t18te miriam: cellimage n2t: cellimage prefixcommons: cellimage re3data: r3d100000023 miriam: deprecated: false description: "The Cell: An Image Library\u2122 is a freely accessible, public\ \ repository of reviewed and annotated images, videos, and animations of cells\ \ from a variety of organisms, showcasing cell architecture, intracellular functionalities,\ \ and both normal and abnormal processes." homepage: http://cellimagelibrary.org/ id: '00000257' name: Cell Image Library namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: cellimage sampleId: '24801' uri_format: http://cellimagelibrary.org/images/$1 n2t: description: 'The Cell: An Image Library™ is a freely accessible, public repository of reviewed and annotated images, videos, and animations of cells from a variety of organisms, showcasing cell architecture, intracellular functionalities, and both normal and abnormal processes.' example: '24801' homepage: http://cellimagelibrary.org/ name: Cell Image Library at American Society for Cell Biology namespaceEmbeddedInLui: false pattern: ^\d+$ 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 publications: - doi: 10.1093/nar/gks1257 pmc: PMC3531121 pubmed: '23203874' title: 'The cell: an image library-CCDB: a curated repository of microscopy data.' year: 2012 re3data: description: This library is a public and easily accessible resource database of images, videos, and animations of cells, capturing a wide diversity of organisms, cell types, and cellular processes. The Cell Image Library has been merged with "Cell Centered Database" in 2017. The purpose of the database is to advance research on cellular activity, with the ultimate goal of improving human health. homepage: http://www.cellimagelibrary.org/home name: The Cell Image Library prefix: r3d100000023 synonyms: - CIL - The Cell xrefs: fairsharing: FAIRsharing.8t18te nif: 0000-37639 omics: '05631' scr: '003510' 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 contact: email: Amos.Bairoch@sib.swiss name: Amos Bairoch orcid: 0000-0003-2826-6444 description: 'The Cellosaurus is a knowledge resource on cell lines. It attempts to describe all cell lines used in biomedical research. Its scope includes: Immortalized cell lines; naturally immortal cell lines (example: stem cell lines); finite life cell lines when those are distributed and used widely; vertebrate cell line with an emphasis on human, mouse and rat cell lines; and invertebrate (insects and ticks) cell lines. Its scope does not include primary cell lines (with the exception of the finite life cell lines described above) and plant cell lines.' homepage: https://www.cellosaurus.org license: CC-BY-4.0 name: Cellosaurus prefix: FAIRsharing.hkk309 publications: - doi: 10.1002/ijc.32639 pubmed_id: 31444973 title: 'CLASTR: The Cellosaurus STR similarity search tool - A precious help for cell line authentication.' - doi: 10.7171/jbt.18-2902-002 pubmed_id: 29805321 title: The Cellosaurus, a Cell-Line Knowledge Resource. subjects: - Life Science homepage: https://cellosaurus.org 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://www.cellosaurus.org/ id: 00000598 name: Cellosaurus namespaceEmbeddedInLui: false pattern: ^CVCL_[A-Z0-9]{4}(\.txt)?$ prefix: cellosaurus sampleId: CVCL_0030 uri_format: https://www.cellosaurus.org/$1 n2t: description: 'The Cellosaurus is a knowledge resource on cell lines. It attempts to describe all cell lines used in biomedical research. Its scope includes: Immortalized cell lines; naturally immortal cell lines (example: stem cell lines); finite life cell lines when those are distributed and used widely; vertebrate cell line with an emphasis on human, mouse and rat cell lines; and invertebrate (insects and ticks) cell lines. Its scope does not include primary cell lines (with the exception of the finite life cell lines described above) and plant cell lines.' example: CVCL_0030 homepage: https://web.expasy.org/cellosaurus/ name: Cellosaurus through SIB namespaceEmbeddedInLui: false pattern: CVCL_[A-Z0-9]{4} prefix: cellosaurus uri_format: https://web.expasy.org/cellosaurus/$1 name: Cellosaurus pattern: ^[A-Z0-9]{4}$ 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 publications: - doi: 10.1002/ijc.32639 pmc: null pubmed: '31444973' title: 'CLASTR: The Cellosaurus STR similarity search tool - A precious help for cell line authentication.' year: 2019 - doi: 10.7171/jbt.18-2902-002 pmc: PMC5945021 pubmed: '29805321' title: The Cellosaurus, a Cell-Line Knowledge Resource. year: 2018 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_$1 wikidata: database: Q21014462 description: Cellosaurus cell line identifier example: - CVCL_0030 - CVCL_0440 name: Cellosaurus ID pattern: ^CVCL_[A-Z\d][A-Z\d][A-Z\d][A-Z\d]$ prefix: P3289 uri_format: https://www.cellosaurus.org/$1 cellosaurus.resource: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The set of prefixes used in the Cellosaurus resource example: 4DN homepage: https://web.expasy.org/cellosaurus/ keywords: - cell lines - cells - registry name: Cellosaurus Registry 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/$1 cemo: contact: email: n.queralt_rosinach@lumc.nl github: NuriaQueralt name: "N\xFAria Queralt Rosinach" orcid: 0000-0003-0169-8159 contributor: email: benjamin_gyori@hms.harvard.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 description: The covid-19 epidemiology and monitoring ontology (cemo) provides a common ontological model to make epidemiological quantitative data for monitoring the covid-19 outbreak machine-readable and interoperable to facilitate its exchange, integration and analysis, to eventually support evidence-based rapid response. download_json: https://raw.githubusercontent.com/cthoyt/covid19-epidemiology-ontology/add-artifacts/owl/cemo.json download_owl: https://raw.githubusercontent.com/NuriaQueralt/covid19-epidemiology-ontology/main/owl/cemo.owl example: secondary_attack_rate github_request_issue: 593 homepage: https://github.com/NuriaQueralt/covid19-epidemiology-ontology license: CC0-1.0 name: The COVID-19 epidemiology and monitoring ontology pattern: ^[0-9a-z_-]+$ providers: - code: obo description: This represents misconfigured base IRIs, even though this ontology isn't an OBO Foundry ontology homepage: http://purl.obolibrary.org/obo/ name: Legacy OBO PURL uri_format: http://purl.obolibrary.org/obo/cemo.owl#$1 repository: https://github.com/NuriaQueralt/covid19-epidemiology-ontology reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 uri_format: https://biopragmatics.github.io/providers/cemo/$1 ceph: aberowl: description: An anatomical and developmental ontology for cephalopods download_owl: http://aber-owl.net/media/ontologies/CEPH/2/ceph.owl homepage: https://github.com/obophenotype/cephalopod-ontology name: Cephalopod Ontology prefix: CEPH biocontext: is_identifiers: false is_obo: true prefix: CEPH uri_format: http://purl.obolibrary.org/obo/CEPH_$1 bioportal: contact: email: cjmungall@lbl.gov name: Chris Mungall description: An anatomical and developmental ontology for cephalopods homepage: https://github.com/obophenotype/cephalopod-ontology name: Cephalopod Ontology prefix: CEPH download_obo: https://raw.githubusercontent.com/obophenotype/cephalopod-ontology/master/ceph.obo example: 0000109 fairsharing: abbreviation: CEPH description: An anatomical and developmental ontology for cephalopods homepage: https://github.com/obophenotype/cephalopod-ontology name: Cephalopod Ontology prefix: FAIRsharing.p58bm4 publications: [] subjects: [] mappings: aberowl: CEPH biocontext: CEPH bioportal: CEPH fairsharing: FAIRsharing.p58bm4 obofoundry: ceph ols: ceph ontobee: CEPH obofoundry: contact: cjmungall@lbl.gov contact.github: cmungall contact.label: Chris Mungall contact.orcid: 0000-0002-6601-2165 deprecated: true description: An anatomical and developmental ontology for cephalopods domain: anatomy and development download.obo: http://purl.obolibrary.org/obo/ceph.obo download.owl: http://purl.obolibrary.org/obo/ceph.owl homepage: https://github.com/obophenotype/cephalopod-ontology license: CC BY 3.0 license.url: http://creativecommons.org/licenses/by/3.0/ name: Cephalopod Ontology prefix: ceph repository: https://github.com/obophenotype/cephalopod-ontology ols: description: An anatomical and developmental ontology for cephalopods download: http://purl.obolibrary.org/obo/ceph.owl homepage: https://github.com/obophenotype/cephalopod-ontology name: Cephalopod Ontology prefix: ceph version: '2016-01-12' version.iri: http://purl.obolibrary.org/obo/ceph/releases/2016-01-12/ceph.owl ontobee: library: Library name: Cephalopod Ontology prefix: CEPH pattern: ^\d{7}$ 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. homepage: http://www.candidagenome.org/ name: Candida Genome Database prefix: FAIRsharing.j7j53 publications: - doi: 10.1093/nar/gki003 pubmed_id: 15608216 title: The Candida Genome Database (CGD), a community resource for Candida albicans gene and protein information. - doi: 10.1093/nar/gkr945 pubmed_id: 22064862 title: 'The Candida genome database incorporates multiple Candida species: multispecies search and analysis tools with curated gene and protein information for Candida albicans and Candida glabrata.' subjects: - Life Science go: homepage: http://www.candidagenome.org/ name: Candida Genome Database prefix: CGD synonyms: - CGDID uri_format: http://www.candidagenome.org/cgi-bin/locus.pl?dbid=$1 mappings: biocontext: CGD fairsharing: FAIRsharing.j7j53 go: CGD miriam: cgd n2t: cgd ncbi: CGD prefixcommons: cgd re3data: r3d100010617 uniprot: DB-0126 miriam: deprecated: false description: The Candida Genome Database (CGD) provides access to genomic sequence data and manually curated functional information about genes and proteins of the human pathogen Candida albicans. It collects gene names and aliases, and assigns gene ontology terms to describe the molecular function, biological process, and subcellular localization of gene products. homepage: http://www.candidagenome.org/ id: '00000145' name: Candida Genome Database namespaceEmbeddedInLui: false pattern: ^CAL\d{7}$ prefix: cgd sampleId: CAL0003079 uri_format: http://www.candidagenome.org/cgi-bin/locus.pl?dbid=$1 n2t: description: The Candida Genome Database (CGD) provides access to genomic sequence data and manually curated functional information about genes and proteins of the human pathogen Candida albicans. It collects gene names and aliases, and assigns gene ontology terms to describe the molecular function, biological process, and subcellular localization of gene products. example: CAL0003079 homepage: http://www.candidagenome.org/ name: Candida Genome Database at Stanford University namespaceEmbeddedInLui: false pattern: ^CAL\d{7}$ prefix: cgd uri_format: http://www.candidagenome.org/cgi-bin/locus.pl?dbid=$1 ncbi: example: CAL0005934 homepage: http://www.candidagenome.org/ name: Candida Genome Database prefix: CGD prefixcommons: description: The Candida Genome Database (CGD) provides access to genomic sequence data and manually curated functional information about genes and proteins of the human pathogen Candida albicans. It collects gene names and aliases, and assigns gene ontology terms to describe the molecular function, biological process, and subcellular localization of gene products. example: CAL0003079 homepage: http://www.candidagenome.org/ keywords: - eukaryotic - genome - nucleotide name: Candida Genome Database pattern: ^CAL\d{7}$ prefix: cgd pubmed_ids: - '15608216' uri_format: http://www.candidagenome.org/cgi-bin/locus.pl?dbid=$1 publications: - doi: 10.1093/nar/gkw924 pmc: PMC5210628 pubmed: '27738138' title: 'The Candida Genome Database (CGD): incorporation of Assembly 22, systematic identifiers and visualization of high throughput sequencing data.' year: 2016 - doi: 10.1093/nar/gkr945 pmc: PMC3245171 pubmed: '22064862' title: 'The Candida genome database incorporates multiple Candida species: multispecies search and analysis tools with curated gene and protein information for Candida albicans and Candida glabrata.' year: 2011 - doi: 10.1093/nar/gki003 pmc: PMC539957 pubmed: '15608216' title: The Candida Genome Database (CGD), a community resource for Candida albicans gene and protein information. year: 2005 re3data: description: Candida Genome Database, a resource for genomic sequence data and gene and protein information for Candida albicans and related species. CGD is based on the Saccharomyces Genome Database. The Candida Genome Database (CGD) provides online access to genomic sequence data and manually curated functional information about genes and proteins of the human pathogen Candida albicans and related species. C. albicans is the best studied of the human fungal pathogens. It is a common commensal organism of healthy individuals, but can cause debilitating mucosal infections and life-threatening systemic infections, especially in immunocompromised patients. C. albicans also serves as a model organism for the study of other fungal pathogens. homepage: http://www.candidagenome.org/ name: Candida Genome Database prefix: r3d100010617 synonyms: - CGD xrefs: fairsharing: FAIRsharing.j7j53 nif: 0000-02634 omics: 03098 scr: '002036' uniprot: abbreviation: CGD category: Organism-specific databases homepage: http://www.candidagenome.org/ name: Candida Genome Database prefix: DB-0126 publications: - doi: 10.1093/nar/gkw924 pubmed: '27738138' uri_format: http://www.candidagenome.org/cgi-bin/locus.pl?dbid=$1 cghdb: cellosaurus: category: Cell line databases/resources homepage: 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/$1 fairsharing: abbreviation: CGSC description: The CGSC Database of E. coli genetic information includes genotypes and reference information for the strains in the CGSC collection, the names, synonyms, properties, and map position for genes, gene product information, and information on specific mutations and references to primary literature. homepage: https://cgsc.biology.yale.edu/ name: Coli Genetic Stock Center prefix: FAIRsharing.1tbrdz publications: - doi: 10.1016/S0076-6879(06)21001-2 pubmed_id: 17352909 title: Strain collections and genetic nomenclature. subjects: - Life Science go: homepage: http://cgsc.biology.yale.edu/ name: CGSC prefix: CGSC mappings: biocontext: CGSC fairsharing: FAIRsharing.1tbrdz go: CGSC miriam: cgsc n2t: cgsc prefixcommons: cgsc re3data: r3d100010585 miriam: deprecated: false description: The CGSC Database of E. coli genetic information includes genotypes and reference information for the strains in the CGSC collection, the names, synonyms, properties, and map position for genes, gene product information, and information on specific mutations and references to primary literature. homepage: http://cgsc.biology.yale.edu/index.php id: 00000295 name: CGSC Strain namespaceEmbeddedInLui: false pattern: ^\d+$ 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 publications: - doi: 10.1016/s0076-6879(06)21001-2 pmc: null pubmed: '17352909' title: Strain collections and genetic nomenclature. year: 2007 re3data: description: The CGSC Database of E. coli genetic information includes genotypes and reference information for the strains in the CGSC collection, the names, synonyms, properties, and map position for genes, gene product information, and information on specific mutations and references to primary literature. The public version of the database includes this information and can be queried directly via this CGSC DB WebServer homepage: https://cgsc2.biology.yale.edu/ name: E. coli Genetic Resources at Yale prefix: r3d100010585 synonyms: - CGSC - The Coli Genetic Stock Center xrefs: fairsharing: FAIRsharing.1tbrdz miriam: '00100377' nif: 0000-21083 scr: '002303' 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/178/chebi.owl homepage: http://www.ebi.ac.uk/chebi name: Chemical Entities of Biological Interest prefix: CHEBI bartoc: abbreviation: ChEBI description: "Chemical Entities of Biological Interest (ChEBI) is a freely available\ \ dictionary of molecular entities focused on \u2018small\u2019 chemical compounds.\ \ The term \u2018molecular entity\u2019 refers to any constitutionally or isotopically\ \ distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer,\ \ etc., identifiable as a separately distinguishable entity. The molecular entities\ \ in question are either products of nature or synthetic products used to intervene\ \ in the processes of living organisms. ChEBI incorporates an ontological classification,\ \ whereby the relationships between molecular entities or classes of entities\ \ and their parents and/or children are specified." homepage: http://www.ebi.ac.uk/chebi/ name: Chemical Entities of Biological Interest prefix: '558' wikidata_database: Q902623 biocontext: 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: '217' 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 contact: email: venkat@ebi.ac.uk name: Venkat orcid: 0000-0002-6850-9888 description: "Chemical Entities of Biological Interest (ChEBI) is a free dictionary\ \ that describes 'small\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." homepage: http://www.ebi.ac.uk/chebi/ license: CC-BY-4.0 name: Chemical Entities of Biological Interest prefix: FAIRsharing.62qk8w publications: - doi: 10.1002/0471250953.bi1409s26 pubmed_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 twitter: chebit go: homepage: http://www.ebi.ac.uk/chebi/ name: Chemical Entities of Biological Interest prefix: CHEBI synonyms: - ChEBI uri_format: http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:$1 mappings: aberowl: CHEBI bartoc: '558' biocontext: CHEBI bioportal: CHEBI cellosaurus: ChEBI cheminf: '000407' edam: '1174' fairsharing: FAIRsharing.62qk8w go: CHEBI miriam: chebi n2t: chebi obofoundry: chebi ols: chebi ontobee: CHEBI prefixcommons: chebi re3data: r3d100012626 wikidata: P683 miriam: deprecated: false description: Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on 'small' chemical compounds. homepage: https://www.ebi.ac.uk/chebi/ id: '00000002' name: ChEBI namespaceEmbeddedInLui: true pattern: ^CHEBI:\d+$ 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:$1 name: Chemical Entities of Biological Interest obofoundry: appears_in: - cdno - chiro - cl - ecocore - ecto - envo - fobi - foodon - genepio - maxo - mco - ons - pcl - proco - uberon - xpo - scdo contact: amalik@ebi.ac.uk contact.github: amalik01 contact.label: Adnan Malik contact.orcid: 0000-0001-8123-5351 deprecated: false description: A structured classification of molecular entities of biological interest focusing on 'small' chemical compounds. domain: chemistry and biochemistry download.obo: http://purl.obolibrary.org/obo/chebi.obo download.owl: http://purl.obolibrary.org/obo/chebi.owl homepage: http://www.ebi.ac.uk/chebi license: CC BY 4.0 license.url: https://creativecommons.org/licenses/by/4.0/ name: Chemical Entities of Biological Interest preferredPrefix: CHEBI prefix: chebi publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/26467479 title: 'ChEBI in 2016: Improved services and an expanding collection of metabolites.' repository: https://github.com/ebi-chebi/ChEBI twitter: chebit ols: description: A structured classification of molecular entities of biological interest focusing on 'small' chemical compounds. download: http://purl.obolibrary.org/obo/chebi.owl homepage: http://www.ebi.ac.uk/chebi name: Chemical Entities of Biological Interest prefix: chebi version: '211' version.iri: http://purl.obolibrary.org/obo/chebi/211/chebi.owl ontobee: library: Foundry name: Chemical Entities of Biological Interest prefix: CHEBI pattern: ^\d+$ 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/gkv1031 pmc: PMC4702775 pubmed: '26467479' title: 'ChEBI in 2016: Improved services and an expanding collection of metabolites.' year: 2015 - doi: 10.1093/nar/gks1146 pmc: PMC3531142 pubmed: '23180789' title: 'The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013.' year: 2012 - doi: 10.1093/nar/gkp886 pmc: PMC2808869 pubmed: '19854951' title: 'Chemical Entities of Biological Interest: an update.' year: 2009 - doi: 10.1002/0471250953.bi1409s26 pmc: null pubmed: '19496059' title: 'ChEBI: an open bioinformatics and cheminformatics resource.' year: 2009 - doi: 10.1093/nar/gkm791 pmc: PMC2238832 pubmed: '17932057' title: 'ChEBI: a database and ontology for chemical entities of biological interest.' year: 2007 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:$1 wikidata: database: Q902623 description: "identifier from\_database and ontology of molecular entities focused\ \ on 'small' chemical compounds" example: - '18153' - '27518' - '28969' homepage: https://www.ebi.ac.uk/chebi miriam: chebi name: ChEBI ID pattern: ^\d+$ prefix: P683 uri_format: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:$1 uri_format_rdf: - http://purl.obolibrary.org/obo/CHEBI_$1 chembank: biocontext: is_identifiers: true is_obo: false prefix: CHEMBANK uri_format: http://identifiers.org/chembank/$1 biolink: is_identifiers: false is_obo: false prefix: ChemBank uri_format: http://chembank.broadinstitute.org/chemistry/viewMolecule.htm?cbid=$1 comment: This resource doesn't exist on the web anymore deprecated: true mappings: biocontext: CHEMBANK biolink: ChemBank prefixcommons: chembank prefixcommons: description: ChemBank is a public, web-based informatics environment created by the Broad Institute's Chemical Biology Program and funded in large part by the National Cancer Institute's Initiative for Chemical Genetics (ICG). example: '1000000' homepage: http://chembank.broad.harvard.edu keywords: - chemical - metabolite name: ChemBank pattern: ^\d+$ prefix: chembank pubmed_ids: - '17947324' uri_format: http://chembank.broadinstitute.org/chemistry/viewMolecule.htm?cbid=$1 publications: - doi: 10.1093/nar/gkm843 pmc: PMC2238881 pubmed: '17947324' title: 'ChemBank: a small-molecule screening and cheminformatics resource database.' year: 2007 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 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 integrating data records extracted from medicinal chemistry literature, from deposited data sets, as well as other public data sources. It brings together chemical, bioactivity and genomic data to aid the translation of genomic information into effective new drugs. Information regarding the compounds tested (including their chemical structures), the biological or physicochemical assays performed on these and the targets of these assays are recorded in a structured form, standardized, and annotated with controlled vocabularies to allow users to address a broad range of drug discovery questions. homepage: https://www.ebi.ac.uk/chembl license: CC BY-SA 3.0 name: ChEMBL prefix: FAIRsharing.m3jtpg publications: - doi: 10.1093/nar/gkr777 pubmed_id: 21948594 title: 'ChEMBL: a large-scale bioactivity database for drug discovery.' - doi: 10.1093/nar/gky1075 pubmed_id: 30398643 title: 'ChEMBL: towards direct deposition of bioassay data.' - doi: 10.1093/nar/gkt1031 pubmed_id: 24214965 title: 'The ChEMBL bioactivity database: an update' - doi: 10.1093/nar/gkw1074 pubmed_id: 27899562 title: The ChEMBL database in 2017. repository: https://github.com/chembl/GLaDOS subjects: - Drug Discovery - Biochemistry - Genomics - Medicinal Chemistry twitter: chembl homepage: https://www.ebi.ac.uk/chembl mappings: cheminf: '000412' fairsharing: FAIRsharing.m3jtpg miriam: chembl prefixcommons: chembl re3data: r3d100010539 uniprot: DB-0174 miriam: deprecated: false description: ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature. homepage: https://www.ebi.ac.uk/chembl id: 00000799 name: ChEMBL namespaceEmbeddedInLui: false pattern: ^CHEMBL\d+$ prefix: chembl sampleId: CHEMBL4303805 uri_format: https://www.ebi.ac.uk/chembl/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 publications: - doi: 10.1093/nar/gky1075 pmc: PMC6323927 pubmed: '30398643' title: 'ChEMBL: towards direct deposition of bioassay data.' year: 2019 - doi: 10.1093/nar/gkw1074 pmc: PMC5210557 pubmed: '27899562' title: The ChEMBL database in 2017. year: 2016 - doi: 10.1093/nar/gkt1031 pmc: PMC3965067 pubmed: '24214965' title: 'The ChEMBL bioactivity database: an update.' year: 2013 - doi: 10.1093/nar/gkr777 pmc: PMC3245175 pubmed: '21948594' title: 'ChEMBL: a large-scale bioactivity database for drug discovery.' year: 2011 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: abbreviation: ChEMBL category: Chemistry databases homepage: https://www.ebi.ac.uk/chembldb name: ChEMBL database of bioactive drug-like small molecules prefix: DB-0174 publications: - doi: 10.1093/nar/gkr777 pubmed: '21948594' 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 keywords: - bioactivities - cell lines 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 description: identifier from a chemical database of bioactive molecules with drug-like properties example: - CHEMBL113 - CHEMBL1200604 - CHEMBL417016 homepage: https://www.ebi.ac.uk/chembl miriam: chembl name: ChEMBL ID pattern: ^CHEMBL\d+$ prefix: P592 uri_format: https://www.ebi.ac.uk/chembl/compound_report_card/$1/ uri_format_rdf: - http://rdf.ebi.ac.uk/resource/chembl/molecule/$1 chembl.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/$1 fairsharing: abbreviation: ChemDB description: ChemDB is a chemical database containing nearly 5M commercially available small molecules, important for use as synthetic building blocks, probes in systems biology and as leads for the discovery of drugs and other useful compounds. homepage: http://cdb.ics.uci.edu license: http://opendatacommons.org/licenses/pddl/1.0 name: The UC Irvine ChemDB prefix: FAIRsharing.dstf7h publications: - doi: 10.1093/bioinformatics/bti683 pubmed_id: 16174682 title: 'ChemDB: a public database of small molecules and related chemoinformatics resources.' - doi: 10.1093/bioinformatics/btm341 pubmed_id: 17599932 title: ChemDB update--full-text search and virtual chemical space. subjects: - Biochemistry - Life Science - Biomedical Science - Systems Biology - Preclinical Studies mappings: biocontext: CHEMDB fairsharing: FAIRsharing.dstf7h miriam: chemdb n2t: chemdb prefixcommons: chemdb miriam: deprecated: false description: ChemDB is a chemical database containing commercially available small molecules, important for use as synthetic building blocks, probes in systems biology and as leads for the discovery of drugs and other useful compounds. homepage: http://cdb.ics.uci.edu/ id: 00000279 name: ChemDB namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: chemdb sampleId: '3966782' uri_format: http://cdb.ics.uci.edu/cgibin/ChemicalDetailWeb.py?chemical_id=$1 n2t: description: ChemDB is a chemical database containing commercially available small molecules, important for use as synthetic building blocks, probes in systems biology and as leads for the discovery of drugs and other useful compounds. example: '3966782' homepage: http://cdb.ics.uci.edu/ name: ChemDB at UC Irvine namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: chemdb uri_format: http://cdb.ics.uci.edu/cgibin/ChemicalDetailWeb.py?chemical_id=$1 prefixcommons: description: ChemDB is a chemical database containing nearly 5M commercially available small molecules, important for use as synthetic building blocks, probes in systems biology and as leads for the discovery of drugs and other useful compounds. example: '3965223' homepage: http://cdb.ics.uci.edu keywords: - small molecule name: The UC Irvine ChemDB pattern: ^\d+$ prefix: chemdb pubmed_ids: - '17599932' uri_format: http://cdb.ics.uci.edu/cgibin/ChemicalDetailWeb.py?chemical_id=$1 publications: - doi: 10.1093/bioinformatics/btm341 pmc: null pubmed: '17599932' title: ChemDB update--full-text search and virtual chemical space. year: 2007 - doi: 10.1093/bioinformatics/bti683 pmc: null pubmed: '16174682' title: 'ChemDB: a public database of small molecules and related chemoinformatics resources.' year: 2005 chemidplus: biocontext: is_identifiers: true is_obo: false prefix: CHEMIDPLUS uri_format: http://identifiers.org/chemidplus/$1 edam: description: Identifier of a chemical from the ChemIDplus database. name: Compound ID (ChemIDplus) obsolete: false prefix: '2658' fairsharing: abbreviation: ChemIDplus description: ChemIDplus is a web-based search system that provides access to structure and nomenclature authority files used for the identification of chemical substances cited in National Library of Medicine (NLM) databases. It also provides structure searching and direct links to many biomedical resources at NLM and on the Internet for chemicals of interest. homepage: https://chem.nlm.nih.gov/chemidplus/ name: ChemIDplus prefix: FAIRsharing.5949vn publications: - doi: 10.1300/J115v21n01_04 pubmed_id: 11989279 title: ChemIDplus-super source for chemical and drug information. subjects: - Chemistry - Biomedical Science mappings: biocontext: CHEMIDPLUS edam: '2658' fairsharing: FAIRsharing.5949vn miriam: chemidplus n2t: chemidplus prefixcommons: chemidplus miriam: deprecated: false description: ChemIDplus is a web-based search system that provides access to structure and nomenclature authority files used for the identification of chemical substances cited in National Library of Medicine (NLM) databases. It also provides structure searching and direct links to many biomedical resources at NLM and on the Internet for chemicals of interest. homepage: https://chem.nlm.nih.gov/chemidplus/chemidheavy.jsp id: 00000096 name: ChemIDplus namespaceEmbeddedInLui: false pattern: ^\d+\-\d+\-\d+$ 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 publications: - doi: 10.1300/j115v21n01_04 pmc: null pubmed: '11989279' title: ChemIDplus-super source for chemical and drug information. year: 2002 synonyms: - ChemIDplus cheminf: aberowl: description: Includes terms for the descriptors commonly used in cheminformatics software applications and the algorithms which generate them. download_owl: http://aber-owl.net/media/ontologies/CHEMINF/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 contact: email: egon.willighagen@gmail.com name: Egon Willighagen orcid: 0000-0001-7542-0286 description: The Chemical Information Ontology (CHEMINF) aims to establish a standard in representing chemical information. In particular, it aims to produce an ontology to represent chemical structure and to richly describe chemical properties, whether intrinsic or computed. homepage: https://github.com/semanticchemistry/semanticchemistry license: CC-BY-4.0 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.' repository: https://github.com/semanticchemistry/semanticchemistry/issues 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. domain: chemistry and biochemistry download.owl: http://purl.obolibrary.org/obo/cheminf.owl homepage: https://github.com/semanticchemistry/semanticchemistry license: CC0 1.0 license.url: http://creativecommons.org/publicdomain/zero/1.0/ name: Chemical Information Ontology preferredPrefix: CHEMINF prefix: cheminf publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/21991315 title: 'The chemical information ontology: provenance and disambiguation for chemical data on the biological semantic web' repository: https://github.com/semanticchemistry/semanticchemistry ols: 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/$1 cheminf: description: Database identifier used by ChemSpider. name: ChemSpider obsolete: false prefix: '000405' edam: description: Identifier of an entry from the ChemSpider database. name: ChemSpider obsolete: false prefix: '1173' fairsharing: abbreviation: ChemSpider description: ChemSpider is a freely available collection of compound data from across the web, which aggregates chemical structures and their associated information into a single searchable repository entry. These entries are supplemented with additional properties, related information and links back to original data sources. homepage: http://www.chemspider.com/ name: ChemSpider prefix: FAIRsharing.96f3gm publications: - doi: 10.1021/ed100697w pubmed_id: null title: 'ChemSpider: An Online Chemical Information Resource' subjects: - Chemistry - Life Science twitter: ChemSpider mappings: biocontext: CHEMSPIDER cheminf: '000405' edam: '1173' fairsharing: FAIRsharing.96f3gm miriam: chemspider n2t: chemspider prefixcommons: chemspider re3data: r3d100010205 wikidata: P661 miriam: deprecated: false description: ChemSpider is a collection of compound data from across the web, which aggregates chemical structures and their associated information into a single searchable repository entry. These entries are supplemented with additional properties, related information and links back to original data sources. homepage: http://www.chemspider.com/ id: 00000138 name: ChemSpider namespaceEmbeddedInLui: false pattern: ^\d+$ 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.$1.html publications: - doi: 10.1021/ed100697w pmc: null pubmed: null title: 'ChemSpider: An Online Chemical Information Resource' year: 2010 re3data: description: "ChemSpider is a free chemical structure database providing fast\ \ access to over 58 million structures, properties and associated information.\ \ By integrating and linking compounds from more than 400 data sources, ChemSpider\ \ enables researchers to discover the most comprehensive view of freely available\ \ chemical data from a single online search. It is owned by the Royal Society\ \ of Chemistry.\nChemSpider builds on the collected sources by adding additional\ \ properties, related information and links back to original data sources. ChemSpider\ \ offers text and structure searching to find compounds of interest and provides\ \ unique services to improve this data by curation and annotation and to integrate\ \ it with users\u2019 applications." homepage: http://www.chemspider.com/ name: ChemSpider prefix: r3d100010205 synonyms: - Search and share chemistry xrefs: nlx: '152101' scr: '006360' synonyms: - ChemSpiderID - Chemspider wikidata: database: Q2311683 description: identifier in a free chemical database, owned by the Royal Society of Chemistry example: - '10189562' - '1086' - '3953' homepage: https://www.chemspider.com/ name: ChemSpider ID pattern: ^[1-9]\d*$ prefix: P661 uri_format: https://www.chemspider.com/Chemical-Structure.$1.html uri_format_rdf: - http://rdf.chemspider.com/$1 chickenqtldb: biocontext: 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. domain: chemistry and biochemistry download.obo: http://purl.obolibrary.org/obo/chiro.obo download.owl: http://purl.obolibrary.org/obo/chiro.owl homepage: https://github.com/obophenotype/chiro license: CC0 1.0 license.url: http://creativecommons.org/publicdomain/zero/1.0/ name: CHEBI Integrated Role Ontology preferredPrefix: CHIRO prefix: chiro publications: - id: https://doi.org/10.26434/chemrxiv.12591221 title: Extension of Roles in the ChEBI Ontology repository: https://github.com/obophenotype/chiro ols: description: CHEBI provides a distinct role hierarchy. Chemicals in the structural hierarchy are connected via a 'has role' relation. CHIRO provides links from these roles to useful other classes in other ontologies. This will allow direct connection between chemical structures (small molecules, drugs) and what they do. This could be formalized using 'capable of', in the same way Uberon and the Cell Ontology link structures to processes. download: 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 publications: - doi: 10.26434/chemrxiv.12591221 pmc: null pubmed: null title: Extension of Roles in the ChEBI Ontology year: 2020 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). homepage: https://github.com/rsc-ontologies/rsc-cmo license: CC-BY-4.0 name: Chemical Methods Ontology prefix: FAIRsharing.9j4wh2 publications: [] repository: https://github.com/rsc-ontologies/rsc-cmo/issues 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 domain: health download.owl: http://purl.obolibrary.org/obo/chmo.owl homepage: https://github.com/rsc-ontologies/rsc-cmo license: CC BY 4.0 license.url: http://creativecommons.org/licenses/by/4.0/ name: Chemical Methods Ontology preferredPrefix: CHMO prefix: chmo repository: https://github.com/rsc-ontologies/rsc-cmo ols: contact: chemistry-ontologies@googlegroups.com description: CHMO, the chemical methods ontology, describes methods used to 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/33/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: 1.0.366 download_owl: https://github.com/CIDO-ontology/cido/raw/master/cido.owl example: '0000005' fairsharing: abbreviation: CIDO description: The Ontology of Coronavirus Infectious Disease (CIDO) is a community-driven open-source biomedical ontology in the area of coronavirus infectious disease. The CIDO is developed to provide standardized human- and computer-interpretable annotation and representation of various coronavirus infectious diseases, including their etiology, transmission, epidemiology, pathogenesis, diagnosis, prevention, and treatment. Its development follows the OBO Foundry Principles. homepage: https://github.com/cido-ontology/cido license: CC-BY-4.0 name: Coronavirus Infectious Disease Ontology prefix: FAIRsharing.aVmpKl publications: - doi: 10.1038/s41597-020-0523-6 pubmed_id: 32533075 title: CIDO, a community-based ontology for coronavirus disease knowledge and data integration, sharing, and analysis. repository: https://github.com/CIDO-ontology/cido/issues 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. domain: health download.owl: http://purl.obolibrary.org/obo/cido.owl homepage: https://github.com/cido-ontology/cido license: CC BY 4.0 license.url: http://creativecommons.org/licenses/by/4.0/ name: Coronavirus Infectious Disease Ontology preferredPrefix: CIDO prefix: cido publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/36271389 title: 'A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology' repository: https://github.com/cido-ontology/cido ols: contact: cido-discuss@googlegroups.com description: The Ontology of Coronavirus Infectious Disease (CIDO) is a community-driven open-source biomedical ontology in the area of coronavirus infectious disease. The CIDO is developed to provide standardized human- and computer-interpretable annotation and representation of various coronavirus infectious diseases, including their etiology, transmission, pathogenesis, diagnosis, prevention, and treatment. download: http://purl.obolibrary.org/obo/cido.owl homepage: https://github.com/cido-ontology/cido name: 'CIDO: Ontology of Coronavirus Infectious Disease' prefix: cido version: 1.0.337 ontobee: library: Library name: Coronavirus Infectious Disease Ontology prefix: CIDO pattern: ^\d{7}$ publications: - doi: 10.1186/s13326-022-00279-z pmc: PMC9585694 pubmed: '36271389' title: 'A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology.' year: 2022 - doi: 10.1038/s41597-020-0523-6 pmc: PMC7293349 pubmed: '32533075' title: CIDO, a community-based ontology for coronavirus disease knowledge and data integration, sharing, and analysis. year: 2020 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. homepage: https://github.com/BgeeDB/confidence-information-ontology license: CC0-1.0 name: Confidence Information Ontology prefix: FAIRsharing.e3t0yw publications: - doi: 10.1093/database/bav043 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. domain: information download.obo: http://purl.obolibrary.org/obo/cio.obo download.owl: http://purl.obolibrary.org/obo/cio.owl homepage: https://github.com/BgeeDB/confidence-information-ontology license: CC0 1.0 license.url: https://creativecommons.org/publicdomain/zero/1.0/ name: Confidence Information Ontology preferredPrefix: CIO prefix: cio publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/25957950 title: 'The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations' repository: https://github.com/BgeeDB/confidence-information-ontology ols: description: An ontology to capture confidence information about annotations. download: 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 contact: email: maria.taboada@usc.es name: Maria Taboada orcid: 0000-0002-2353-596X description: The ontology represents CTX phenotypes, genetic variants, and bidirectional relationships between them though a patient model. The CTX ontology was build reusing the Human Phenotype Ontology (HPO) and the Snomed ct ontologies. A set of temporal clinical manifestations are semantically annotated with a domain phenotype ontology and registered with a time-stamped value. homepage: http://bioportal.bioontology.org/ontologies/CTX 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 contact: email: silvio.peroni@unibo.it name: Silvio Peroni orcid: 0000-0003-0530-4305 description: 'The Citation Typing Ontology (CiTO) is an ontology that enables the characterization of the nature or type of citations, both factually and rhetorically. It is intended to allow authors (or others) to mark citation links and to capture citation intent when someone cites a particular publication. In particular, CiTO allows the creation of metadata describing citations that are distinct from metadata describing the cited works themselves, and permits the motives of an author when referring to another document to be captured. ' homepage: http://www.sparontologies.net/ontologies/cito license: CC-BY-4.0 name: 'Citation Typing Ontology ' prefix: FAIRsharing.b220d4 publications: - doi: 10.1016/j.websem.2012.08.001 pubmed_id: null title: 'FaBiO and CiTO: Ontologies for describing bibliographic resources and citations' repository: https://github.com/sparontologies/cito subjects: - Knowledge and Information Systems twitter: sparontologies homepage: http://www.sparontologies.net/ontologies/cito mappings: fairsharing: FAIRsharing.b220d4 name: Citation Typing Ontology preferred_prefix: CiTO publications: - doi: 10.1016/j.websem.2012.08.001 pmc: null pubmed: null title: 'FaBiO and CiTO: Ontologies for describing bibliographic resources and citations' year: 2012 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/$1 part_of: civic civic.did: mappings: miriam: civic.did miriam: deprecated: false description: Within the CIViC database, the disease should be the cancer or cancer subtype that is a result of the described variant. The disease selected should be as specific as possible should reflect the disease type used in the source that supports the evidence statement. homepage: https://civicdb.org/ id: 00000957 name: CIViC Disease namespaceEmbeddedInLui: false pattern: ^[0-9]+$ prefix: civic.did sampleId: '46' uri_format: https://civicdb.org/links/diseases/$1 part_of: civic civic.eid: mappings: miriam: civic.eid miriam: deprecated: false description: "Evidence Items are the central building block of the Clinical Interpretation\ \ of Variants in Cancer (CIViC) knowledgebase. The clinical Evidence Item is\ \ a piece of information that has been manually curated from trustable medical\ \ literature about a Variant or genomic \u2018event\u2019 that has implications\ \ in cancer Predisposition, Diagnosis (aka molecular classification), Prognosis,\ \ Predictive response to therapy, Oncogenicity or protein Function. For example,\ \ an Evidence Item might describe a line of evidence supporting the notion that\ \ tumors with a somatic BRAF V600 mutation generally respond well to the drug\ \ dabrafenib. A Variant may be a single nucleotide substitution, a small insertion\ \ or deletion, an RNA gene fusion, a chromosomal rearrangement, an RNA expression\ \ pattern (e.g. over-expression), etc. Each clinical Evidence statement corresponds\ \ to a single citable Source (a publication or conference abstract)." homepage: https://civicdb.org/ id: 00000839 name: CIViC Evidence namespaceEmbeddedInLui: false pattern: ^[0-9]+$ prefix: civic.eid sampleId: '1199' uri_format: https://civicdb.org/links/evidence/$1 part_of: civic civic.gid: mappings: miriam: civic.gid wikidata: P11277 miriam: deprecated: false description: "A CIViC Gene Summary is created to provide a high-level overview\ \ of clinical relevance of cancer variants for the gene. Gene Summaries in CIViC\ \ focus on emphasizing the clinical relevance from a molecular perspective rather\ \ than describing the biological function of the gene unless necessary to contextualize\ \ its clinical relevance in cancer. Gene Summaries include relevant cancer subtypes,\ \ specific treatments for the gene\u2019s associated variants, pathway interactions,\ \ functional alterations caused by the variants in the gene, and normal/abnormal\ \ functions of the gene with associated roles in oncogenesis" homepage: https://civicdb.org/ id: 00000907 name: CIViC Gene namespaceEmbeddedInLui: false pattern: ^[0-9]+$ prefix: civic.gid sampleId: '272' uri_format: https://civicdb.org/links/gene/$1 part_of: civic wikidata: database: Q27612411 description: identifier for a human gene in the CIViC database example: - '1134' - '14221' - '2' - '3' - '4' homepage: https://civic.genome.wustl.edu/#/home name: CIViC gene ID pattern: ^[1-9]\d*$ prefix: P11277 uri_format: https://civicdb.org/genes/$1/summary civic.sid: mappings: miriam: civic.sid miriam: deprecated: false description: In CIViC, each Evidence Item must be associated with a Source Type and Source ID, which link the Evidence Item to the original source of information supporting clinical claims. Currently, CIViC accepts publications indexed on PubMed OR abstracts published through the American Society of Clinical Oncology (ASCO). Each such source entered into CIViC is assigned a unique identifier and expert curators can curate guidance that assists future curators in the interpretation of information from this source. homepage: https://civicdb.org/ id: 00000953 name: CIViC Source namespaceEmbeddedInLui: false pattern: ^[0-9]+$ prefix: civic.sid sampleId: '62' uri_format: https://civicdb.org/links/sources/$1 part_of: civic civic.tid: mappings: miriam: civic.tid miriam: deprecated: false description: Therapies (often drugs) in CIViC are associated with Predictive Evidence Types, which describe sensitivity, resistance or adverse response to therapies when a given variant is present. The Therapy field may also be used to describe more general treatment types and regimes, such as FOLFOX or Radiation, as long as the literature derived Evidence Item makes a scientific association between the Therapy (treatment type) and the presence of the variant. homepage: https://civicdb.org/ id: 00000955 name: CIViC Therapy namespaceEmbeddedInLui: false pattern: ^[0-9]+$ prefix: civic.tid sampleId: '14' uri_format: https://civicdb.org/links/drugs/$1 part_of: civic civic.vid: mappings: miriam: civic.vid wikidata: P3329 miriam: deprecated: false description: "CIViC variants are usually genomic alterations, including single\ \ nucleotide variants (SNVs), insertion/deletion events (indels), copy number\ \ alterations (CNV\u2019s such as amplification or deletion), structural variants\ \ (SVs such as translocations and inversions), and other events that differ\ \ from the \u201Cnormal\u201D genome. In some cases a CIViC variant may represent\ \ events of the transcriptome or proteome. For example, \u2018expression\u2019\ \ or \u2018over-expression\u2019 is a valid variant. Regardless of the variant,\ \ it must have a Predictive, Prognostic, Predisposing, Diagnostic, Oncogenic,\ \ or Functional relevance that is clinical in nature to be entered in CIViC.\ \ i.e. There must be some rationale for why curation of this variant could ultimately\ \ aid clinical decision making." homepage: https://civicdb.org/ id: 00000909 name: CIViC Variant namespaceEmbeddedInLui: false pattern: ^[0-9]+$ prefix: civic.vid sampleId: '12' uri_format: https://civicdb.org/links/variant/$1 part_of: civic wikidata: database: Q27612411 description: identifier used in the CIViC database to identify specific variant example: - '12' homepage: https://civic.genome.wustl.edu/#/home name: CIViC variant ID pattern: ^[1-9]\d*$ prefix: P3329 uri_format: https://civic.genome.wustl.edu/links/variants/$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/92/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: '2023-01-09' 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: '2023-01-09' 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 contact: email: addiehl@buffalo.edu name: Alexander Diehl orcid: 0000-0001-9990-8331 description: The Cell Ontology (CL) is a candidate OBO Foundry ontology for the representation of cell types. First described in 2005, the CL integrates cell types from the prokaryotic, fungal, and eukaryotic organisms. As a core component of the OBO Foundry, the CL merges information contained in species-specific anatomical ontologies as well as referencing other OBO Foundry ontologies such as the Protein Ontology (PR) for uniquely expressed biomarkers and the Gene Ontology (GO) for the biological processes a cell type participates in. The CL is under continuous revision to expand representation of cell types and to better integrate with other biomedical ontologies. homepage: https://github.com/obophenotype/cell-ontology license: CC-BY-3.0 name: Cell Ontology prefix: FAIRsharing.j9y503 publications: - doi: 10.1186/1471-2105-12-6 pubmed_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.' repository: https://github.com/obophenotype/cell-ontology/blob/master/src/ontology/README.txt 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:$1 obofoundry: appears_in: - clo - ecao - go - mco - pcl - uberon - xpo - ehdaa2 contact: addiehl@buffalo.edu contact.github: addiehl contact.label: Alexander Diehl contact.orcid: 0000-0001-9990-8331 depends_on: - chebi - go - ncbitaxon - pato - pr - ro - uberon deprecated: false description: The Cell Ontology is a structured controlled vocabulary for cell types in animals. domain: anatomy and development download.obo: http://purl.obolibrary.org/obo/cl.obo download.owl: http://purl.obolibrary.org/obo/cl.owl homepage: https://obophenotype.github.io/cell-ontology/ license: CC BY 4.0 license.url: http://creativecommons.org/licenses/by/4.0/ name: Cell Ontology preferredPrefix: CL prefix: cl publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/27377652 title: 'The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability.' repository: https://github.com/obophenotype/cell-ontology ols: description: An ontology of cell types. download: http://purl.obolibrary.org/obo/cl.owl name: Cell Ontology prefix: cl version: '2022-12-15' version.iri: http://purl.obolibrary.org/obo/cl/releases/2022-12-15/cl.owl ontobee: library: Library name: Cell Ontology prefix: CL pattern: ^\d{7}$ 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/s13326-016-0088-7 pmc: PMC4932724 pubmed: '27377652' title: 'The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability.' year: 2016 - doi: 10.1186/1471-2105-12-6 pmc: PMC3024222 pubmed: '21208450' title: Logical development of the cell ontology. year: 2011 wikidata: database: Q55118285 description: ID in the Cell Ontology example: - CL_0000148 - CL_0000232 - CL_0000235 - CL_0000540 - CL_0002328 homepage: http://www.ontobee.org/ontology/CL miriam: cl name: Cell Ontology ID pattern: ^CL_[0-9]{7}$ prefix: P7963 uri_format: http://purl.obolibrary.org/obo/$1 uri_format_rdf: - 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).' domain: anatomy and development download.obo: http://purl.obolibrary.org/obo/clao.obo download.owl: http://purl.obolibrary.org/obo/clao.owl homepage: https://github.com/luis-gonzalez-m/Collembola license: CC0 1.0 license.url: http://creativecommons.org/publicdomain/zero/1.0/ name: Collembola Anatomy Ontology preferredPrefix: CLAO prefix: clao repository: https://github.com/luis-gonzalez-m/Collembola ols: description: 'CLAO is an ontology of anatomical terms employed in morphological descriptions for the Class Collembola (Arthropoda: Hexapoda).' download: 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$1 clb: mappings: miriam: clb miriam: deprecated: false description: ChecklistBank is an index and repository for taxonomic and nomenclatural datasets homepage: https://www.checklistbank.org id: 00000964 name: ChecklistBank namespaceEmbeddedInLui: false pattern: ^[0-9]+(LR)?$ prefix: clb sampleId: '1010' uri_format: https://www.checklistbank.org/dataset/$1 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=$1 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 contributor_extras: - email: null github: sierra-moxon name: Sierra Moxon orcid: 0000-0002-8719-7760 description: The allele registry provides and maintains identifiers for genetic variants example: CA981206459 homepage: https://reg.clinicalgenome.org keywords: - alleles - genetics - mutations mappings: biolink: CAID name: ClinGen Allele Registry pattern: ^CA\d+$ references: - https://github.com/biopragmatics/bioregistry/issues/647 synonyms: - CAID 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/$1 mappings: biocontext: CLINICALTRIALS miriam: clinicaltrials n2t: clinicaltrials prefixcommons: clinicaltrials wikidata: P3098 miriam: deprecated: false description: ClinicalTrials.gov provides free access to information on clinical studies for a wide range of diseases and conditions. Studies listed in the database are conducted in 175 countries homepage: https://clinicaltrials.gov/ id: '00000137' name: ClinicalTrials.gov namespaceEmbeddedInLui: false pattern: ^NCT\d{8}$ prefix: clinicaltrials sampleId: NCT00222573 uri_format: https://clinicaltrials.gov/ct2/show/$1 n2t: description: ClinicalTrials.gov provides free access to information on clinical studies for a wide range of diseases and conditions. Studies listed in the database are conducted in 175 countries example: NCT00222573 homepage: https://clinicaltrials.gov/ name: ClinicalTrials.gov at NIH namespaceEmbeddedInLui: false pattern: ^NCT\d{8}$ prefix: clinicaltrials uri_format: https://clinicaltrials.gov/ct2/show/$1 prefixcommons: description: ClinicalTrials.gov is a registry and results database of publicly and privately supported clinical studies of human participants conducted around the world. example: NCT00050895 homepage: http://clinicaltrials.gov/ keywords: - disease - drug - human name: ClinicalTrials.gov pattern: ^NCT\d{8}$ 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/$1 synonyms: - clinicaltrial wikidata: database: Q5133746 description: identifier in the ClinicalTrials.gov database example: - NCT00243178 - NCT04315948 name: ClinicalTrials.gov ID pattern: ^NCT(\d{8})$ prefix: P3098 uri_format: https://clinicaltrials.gov/show/$1 clinvar: biocontext: is_identifiers: false is_obo: false prefix: ClinVarVariant uri_format: http://www.ncbi.nlm.nih.gov/clinvar/variation/$1 biolink: is_identifiers: true is_obo: false prefix: CLINVAR uri_format: http://identifiers.org/clinvar$1 cellosaurus: category: Polymorphism and mutation databases homepage: https://www.ncbi.nlm.nih.gov/clinvar/ name: ClinVar prefix: ClinVar uri_format: https://www.ncbi.nlm.nih.gov/clinvar/variation/$1 fairsharing: abbreviation: ClinVar description: ClinVar is a freely accessible, public archive of reports of the relationships among human variations and phenotypes, with supporting evidence. ClinVar thus facilitates access to and communication about the relationships asserted between human variation and observed health status, and the history of that interpretation. ClinVar processes submissions reporting variants found in patient samples, assertions made regarding their clinical significance, information about the submitter, and other supporting data. The alleles described in submissions are mapped to reference sequences, and reported according to the HGVS standard. ClinVar then presents the data for interactive users as well as those wishing to use ClinVar in daily workflows and other local applications. ClinVar works in collaboration with interested organizations to meet the needs of the medical genetics community as efficiently and effectively as possible. homepage: http://www.ncbi.nlm.nih.gov/clinvar/ license: https://www.ncbi.nlm.nih.gov/home/about/policies name: ClinVar prefix: FAIRsharing.wx5r6f publications: - doi: 10.1093/nar/gkt1113 pubmed_id: 24234437 title: 'ClinVar: public archive of relationships among sequence variation and human phenotype.' subjects: - Genomics - Clinical Studies - Biomedical Science - Preclinical Studies hl7: description: 'ClinVar processes submissions reporting variants found in patient samples, assertions made regarding their clinical significance, information about the submitter, and other supporting data. The alleles described in submissions are mapped to reference sequences, and reported according to the HGVS standard. The ClinVar records have a field for Allele ID and for Variant ID. All simple variants have an Allele ID. At present, all complex and most simple variants also have a Variant ID, and by the end of 2016, all variants will have a variant ID. This coding system uses the variant ID as the code and the variant name ( field TBD) from the "variant_summary" file as the code print string. The "variant_summary" file caries more than 20 fields , including the seperate components of the variant nane, the cytogenomic locatiaon, the genomic reference etc. Many of these attributes have been indexed to assist users and applications that need to find the ID for a particular variant. ' homepage: https://lhncbc.nlm.nih.gov/ name: ClinVar Variant ID organization: National Lister Hill Center of Biomedical Communications, National Library of Medicine preferred_prefix: clinVar-V prefix: 2.16.840.1.113883.6.319 status: Complete mappings: biocontext: ClinVarVariant biolink: CLINVAR cellosaurus: ClinVar fairsharing: FAIRsharing.wx5r6f hl7: 2.16.840.1.113883.6.319 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 publications: - doi: 10.1093/nar/gkt1113 pmc: PMC3965032 pubmed: '24234437' title: 'ClinVar: public archive of relationships among sequence variation and human phenotype.' year: 2013 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 synonyms: - clinvar.variant - clinvar.variation wikidata: database: Q20023123 description: identifier in the ClinVar database for human genomic variation example: - '7105' homepage: https://www.ncbi.nlm.nih.gov/clinvar/ name: ClinVar Variation ID prefix: P1929 uri_format: https://www.ncbi.nlm.nih.gov/clinvar/variation/$1/ 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: contact: email: yongqunh@med.umich.edu name: Oliver He description: The Cell Line Ontology (CLO) is a community-based ontology in domain of biological cell lines with a focus on permanent cell lines from culture collections. Upper ontology structures that frame the skeleton of CLO include Basic Formal Ontology and Relation Ontology. Cell lines contained in CLO are associated with terms from other ontologies such as Cell Type Ontology, NCBI Taxonomy, and Ontology for Biomedical Investigation. A common design pattern for the cell line is used to model cell lines and their attributes, the Jurkat cell line provides ane xample. Currently CLO contains over 36,000 cell line entries obtained from ATCC, HyperCLDB, Coriell, and bymanual curation. The cell lines are derived from 194 cell types, 656 anatomical entries, and 217 organisms. The OWL-based CLO is machine-readable and can be used in various applications. homepage: http://www.clo-ontology.org/ name: Cell Line Ontology prefix: CLO publication: http://www.jbiomedsem.com/content/5/1/37 version: 2.1.178 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/$1 example: 0000091 fairsharing: abbreviation: CLO contact: email: Sirarat.Sarntivijai@fda.hhs.gov name: Sirarat Sarntivijai orcid: 0000-0002-2548-641X description: The Cell Line Ontology (CLO) is a community-driven ontology that is developed to standardize and integrate cell line information and support computer-assisted reasoning. Thousands of cell lines have been artificially developed and used for different applications. Integration of data from multiple sources is a challenge, confounded by lack of consistent naming conventions, contamination of cell lines, and provision of the same cell lines by multiple commercial sources but with different biological attributes. CLO is a community-based effort to represent all cell lines in a standard ontology approach. homepage: http://www.clo-ontology.org/ license: CC-BY-3.0 name: Cell Line Ontology prefix: FAIRsharing.4dvtcz publications: - doi: 10.1186/2041-1480-5-37 pubmed_id: 25852852 title: 'CLO: The cell line ontology.' repository: https://github.com/CLO-ontology/CLO/issues subjects: - Life Science - Cell Biology mappings: aberowl: CLO biocontext: CLO bioportal: CLO cellosaurus: CLO fairsharing: FAIRsharing.4dvtcz miriam: clo obofoundry: clo ols: clo ontobee: CLO prefixcommons: clo wikidata: P2158 miriam: deprecated: false description: The Cell Line Ontology is a community-based ontology of cell lines. The CLO is developed to unify publicly available cell line entry data from multiple sources to a standardized logically defined format based on consensus design patterns. homepage: https://www.ebi.ac.uk/ols/ontologies/clo id: 00000983 name: Cell Line Ontology namespaceEmbeddedInLui: false pattern: ^\d{7}$ prefix: clo providers: - code: bioportal description: Our vision is that all biomedical knowledge and data are disseminated on the Internet using principled ontologies in such a way that the knowledge and data are semantically interoperable and useful for furthering biomedical science and clinical care. Our mission is to create software and support services for the application of principled ontologies in biomedical science and clinical care, ranging from tools for application developers to software for end-users. homepage: https://bioportal.bioontology.org name: Center for Biomedical Informatics Research, Stanford uri_format: https://bioportal.bioontology.org/ontologies/CLO/?p=classes&conceptid=http://purl.obolibrary.org/obo/CLO_$1 sampleId: 0000091 uri_format: https://www.ebi.ac.uk/ols/ontologies/clo/terms?short_form=CLO_$1 obofoundry: appears_in: - mco contact: siiraa@umich.edu contact.github: siiraa contact.label: Sirarat Sarntivijai contact.orcid: 0000-0002-2548-641X depends_on: - cl - doid - ncbitaxon - uberon deprecated: false description: An ontology to standardize and integrate cell line information and to support computer-assisted reasoning. domain: anatomy and development download.owl: http://purl.obolibrary.org/obo/clo.owl homepage: http://www.clo-ontology.org license: CC BY 3.0 license.url: http://creativecommons.org/licenses/by/3.0/ name: Cell Line Ontology preferredPrefix: CLO prefix: clo publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/25852852 title: 'CLO: The Cell Line Ontology' repository: https://github.com/CLO-Ontology/CLO ols: description: The Cell Line Ontology (CLO) is a community-based ontology of cell lines. The CLO is developed to unify publicly available cell line entry data from multiple sources to a standardized logically defined format based on consensus design patterns. download: http://purl.obolibrary.org/obo/clo.owl homepage: http://www.clo-ontology.org name: 'CLO: Cell Line Ontology' prefix: clo version: 2.1.178 ontobee: library: Library name: Cell Line Ontology prefix: CLO pattern: ^\d{7}$ 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: 10.1186/2041-1480-5-37 pmc: PMC4387853 pubmed: '25852852' title: 'CLO: The cell line ontology.' year: 2014 - doi: 10.1186/gb-2005-6-2-r21 pmc: PMC551541 pubmed: '15693950' title: An ontology for cell types. year: 2005 synonyms: - CLO wikidata: database: Q21039006 description: identifier for the Cell Line Ontology which describes anatomic origin and nature of eukaryotic cell lines example: - CLO_0007043 homepage: http://www.clo-ontology.org/ name: Cell Line Ontology ID pattern: ^CLO_\d{7}$ prefix: P2158 uri_format: http://purl.obolibrary.org/obo/$1 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. domain: anatomy and development download.obo: http://purl.obolibrary.org/obo/clyh.obo download.owl: http://purl.obolibrary.org/obo/clyh.owl homepage: https://github.com/EBISPOT/clyh_ontology license: CC BY 3.0 license.url: http://creativecommons.org/licenses/by/3.0/ name: Clytia hemisphaerica Development and Anatomy Ontology preferredPrefix: CLYH prefix: clyh repository: https://github.com/EBISPOT/clyh_ontology ols: description: Anatomy, development and life cycle stages - planula, polyp, medusa/jellyfish - of the cnidarian hydrozoan species, Clytia hemiphaerica. download: 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 keywords: - ecology - marine ecology 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 domain: health 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: name: Clinical Measurement Ontology prefix: CMO example: '0001350' fairsharing: abbreviation: CMO contact: email: shimoyama@mcw.edu name: Mary Shimoyama orcid: 0000-0003-1176-0796 description: The Clinical Measurement Ontology is designed to be used to standardize morphological and physiological measurement records generated from clinical and model organism research and health programs. homepage: http://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=CMO:0000000 license: CC0-1.0 name: Clinical Measurement Ontology prefix: FAIRsharing.dq78pn publications: - doi: 10.3389/fgene.2012.00087 pubmed_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. domain: health download.obo: http://purl.obolibrary.org/obo/cmo.obo download.owl: http://purl.obolibrary.org/obo/cmo.owl homepage: http://rgd.mcw.edu/rgdweb/ontology/search.html license: CC0 1.0 license.url: http://creativecommons.org/publicdomain/zero/1.0/ 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: 10.1186/2041-1480-4-26 pmc: PMC3882879 pubmed: '24103152' title: 'The clinical measurement, measurement method and experimental condition ontologies: expansion, improvements and new applications.' year: 2013 - doi: 10.3389/fgene.2012.00087 pmc: PMC3361058 pubmed: '22654893' title: Three ontologies to define phenotype measurement data. year: 2012 twitter: ratgenome cmpo: aberowl: description: The Cellular Microscopy Phenotype Ontology (CMPO) is a species neutral ontology for describing general phenotypic observations relating to the whole cell, cellular components, cellular processes and cell populations. CMPO is an application ontology developed in OWL that contains precomposed phenotypes descriptions that are defined using the Gene Ontology (GO) and the Phenotype Trait Ontology (PATO). download_owl: http://aber-owl.net/media/ontologies/CMPO/14/cmpo.owl homepage: https://github.com/EBISPOT/CMPO name: Cellular microscopy phenotype ontology prefix: CMPO version: '1.3' bioportal: contact: email: jupp@ebi.ac.uk name: Simon Jupp description: The Cellular Microscopy Phenotype Ontology (CMPO) is a species neutral ontology for describing general phenotypic observations relating to the whole cell, cellular components, cellular processes and cell populations. CMPO is an application ontology developed in OWL that contains precomposed phenotypes descriptions that are defined using the Gene Ontology (GO) and the Phenotype Trait Ontology (PATO). homepage: https://github.com/EBISPOT/CMPO name: Cellular microscopy phenotype ontology prefix: CMPO version: '1.3' contact: email: jupp@ebi.ac.uk github: null name: Simon Jupp orcid: 0000-0002-0643-3144 example: '0000435' fairsharing: abbreviation: CMPO 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 homepage: http://www.ebi.ac.uk/cmpo/ license: Apache 2.0 License 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. repository: https://github.com/EBISPOT/CMPO 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_$1 cnrs: comment: Motivated to add because of appearance in ROR contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: identifier for an academic research group issued by the CNRS example: UMR7315 homepage: https://annuaire.cnrs.fr mappings: wikidata: P4550 name: French National Center for Scientific Research - Research Group Identifier pattern: ^(UMR|UMS|UMI|UPR|URA|USR|GDR|EA|FR|SNC|ERL|FRC|FRE|IFR|MOY)\d+$ uri_format: https://web-ast.dsi.cnrs.fr/l3c/owa/structure.infos_admin?&p_lab=$1&p_origine_appel=u 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 repository: https://github.com/Planteome/CO_320-rice-traits AND/OR https://forgemia.inra.fr/urgi-is/ontologies/-/tree/develop/Rice 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." homepage: https://cropontology.org/term/CO_320:ROOT license: CC-BY-4.0 name: Rice Ontology prefix: FAIRsharing.2jkxp5 publications: [] subjects: - Botany - Agriculture - Life Science license: CC-BY-4.0 mappings: agroportal: CO_320 cropoct: CO_320 fairsharing: FAIRsharing.2jkxp5 ols: co_320 ols: contact: helpdesk@cropontology-curationtool.org description: Rice Trait Dictionary in template v 5.0 - IRRI - March 2016 - Based on SES, RD, UPOV variables and on variables used by CIAT, FLAR and the GRISP Phenotyping Network variables download: https://cropontology.org/ontology/CO_320/Rice/owl homepage: https://cropontology.org/ontology/CO_320/Rice name: Rice ontology prefix: co_320 version: '2019-10-09' pattern: ^\d{7}$ preferred_prefix: CO_320 repository: https://github.com/bioversity/Crop-Ontology uri_format: https://cropontology.org/rdf/CO_320:$1 co_321: agroportal: contact: email: helpdesk@cropontology-curationtool.org name: Crop Ontology Helpdesk description: Wheat Trait Dictionary in template v5. example_uri: http://www.cropontology.org/rdf/CO_321:0000238 homepage: http://www.cropontology.org/ license: CC-BY-4.0 name: Wheat Ontology prefix: CO_321 publication: https://doi.org/10.1093/aobpla/plq008 repository: https://github.com/Planteome/CO_321-wheat-traits AND/OR? https://forgemia.inra.fr/urgi-is/ontologies/-/tree/develop/Wheat 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 contact: email: R.Shrestha2@cgiar.org name: Rosemary Shrestha orcid: 0000-0002-9399-8003 description: This ontology defines traits of the International Wheat Information System (IWIS) database and wheat descriptor. The Wheat Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe the data. The use of ontology terms to describe agronomic phenotypes and the accurate mapping of these descriptions into databases is important in comparative phenotypic and genotypic studies across species and gene-discovery experiments as it provides harmonized description of the data and therefore facilitates the retrieval of information. homepage: https://cropontology.org/term/CO_321:ROOT license: CC-BY-4.0 name: Wheat Ontology prefix: FAIRsharing.czzmpg publications: - doi: 10.1093/aobpla/plq008 pubmed_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 license: CC-BY-4.0 mappings: agroportal: CO_321 cropoct: CO_321 fairsharing: FAIRsharing.czzmpg ols: co_321 ols: contact: helpdesk@cropontology-curationtool.org description: July 2018 download: https://cropontology.org/ontology/CO_321/Wheat/owl homepage: https://cropontology.org/ontology/CO_321/Wheat name: Wheat ontology prefix: co_321 version: '2019-10-09' pattern: ^\d{7}$ preferred_prefix: CO_321 publications: - doi: 10.1093/aobpla/plq008 pmc: PMC3000699 pubmed: '22476066' title: 'Multifunctional crop trait ontology for breeders'' data: field book, annotation, data discovery and semantic enrichment of the literature.' year: 2010 repository: https://github.com/bioversity/Crop-Ontology uri_format: https://cropontology.org/rdf/CO_321:$1 co_322: agroportal: contact: email: helpdesk@cropontology-curationtool.org name: Crop Ontology Helpdesk description: 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 repository: https://github.com/Planteome/CO_322-maize-traits AND/OR https://forgemia.inra.fr/urgi-is/ontologies/-/tree/develop/Maize 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. homepage: https://cropontology.org/term/CO_322:ROOT license: CC-BY-4.0 name: Maize Ontology prefix: FAIRsharing.eeyne8 publications: [] subjects: - Botany - Agriculture - Life Science license: CC-BY-4.0 mappings: agroportal: CO_322 cropoct: CO_322 fairsharing: FAIRsharing.eeyne8 ols: co_322 ols: contact: helpdesk@cropontology-curationtool.org description: Maize Trait Dictionary in template 5 - CIMMYT- September 2016 download: https://cropontology.org/ontology/CO_322/Maize/owl homepage: https://cropontology.org/ontology/CO_322/Maize name: Maize ontology prefix: co_322 version: '2019-10-09' pattern: ^\d{7}$ preferred_prefix: CO_322 repository: https://github.com/bioversity/Crop-Ontology uri_format: https://cropontology.org/rdf/CO_322:$1 co_323: agroportal: contact: email: r.verma@cgiar.org name: Ramesh Verna description: Reference Plant Ontologies are being developed in the context of the Plantome project and are being integrated with the Crop Ontology, which provides harmonized breeder's trait names, measurement methods, scales, and standard variables for many crops. The barley Ontology is one of these reference plant ontologies integrated within the Crop Ontology. example_uri: http://www.cropontology.org/rdf/CO_323:0000005/4 homepage: http://www.cropontology.org/ license: CC-BY-4.0 name: Barley Ontology prefix: CO_323 repository: https://github.com/Planteome/CO_323-barley-traits version: '1.2' cropoct: description: ICARDA - TDv5 - Sept 2018 download_owl: https://cropontology.org/ontology/CO_323/Barley/owl homepage: https://cropontology.org/term/CO_323:ROOT name: Barley ontology prefix: CO_323 example: '0000252' fairsharing: abbreviation: CO_323 description: "Reference Plant Ontologies are being developed in the context of\ \ the Planteome project and are being integrated with the Crop Ontology, which\ \ provides harmonized breeders\u2019 trait names, measurement methods, scales\ \ and standard variables for many crops. The Barley Ontology is one of these\ \ reference plant ontologies integrated within the Crop Ontology. Its focus\ \ is on traits and variable used in field trials for breeding." homepage: https://cropontology.org/term/CO_323:ROOT license: CC-BY-4.0 name: Barley Ontology prefix: FAIRsharing.f69084 publications: [] subjects: - Botany - Agriculture license: CC-BY-4.0 mappings: agroportal: CO_323 cropoct: CO_323 fairsharing: FAIRsharing.f69084 ols: co_323 ols: contact: helpdesk@cropontology-curationtool.org description: ICARDA - TDv5 - Sept 2018 download: https://cropontology.org/ontology/CO_323/Barley/owl homepage: https://cropontology.org/ontology/CO_323/Barley name: Barley ontology prefix: co_323 version: '2019-11-20' pattern: ^\d{7}$ preferred_prefix: CO_323 repository: https://github.com/bioversity/Crop-Ontology uri_format: https://cropontology.org/rdf/CO_323:$1 co_324: agroportal: contact: email: helpdesk@cropontology-curationtool.org name: Crop Ontology Helpdesk description: Sorghum TDv5 Ontology example_uri: http://www.cropontology.org/rdf/CO_324:0000660 homepage: http://www.cropontology.org/ license: CC-BY-4.0 name: Sorghum Ontology prefix: CO_324 repository: https://github.com/Planteome/CO_324-sorghum-traits version: '1.0' cropoct: description: Sorghum TDv5 - Oct 2019 download_owl: https://cropontology.org/ontology/CO_324/Sorghum/owl homepage: https://cropontology.org/term/CO_324:ROOT name: Sorghum ontology prefix: CO_324 example: '0000111' fairsharing: abbreviation: CO_324 description: The Sorghum Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe the data. The use of ontology terms to describe agronomic phenotypes and the accurate mapping of these descriptions into databases is important in comparative phenotypic and genotypic studies across species and gene-discovery experiments as it provides harmonized description of the data and therefore facilitates the retrieval of information. homepage: https://cropontology.org/term/CO_324:ROOT license: CC-BY-4.0 name: Sorghum Ontology prefix: FAIRsharing.dxx0c publications: [] subjects: - Botany - Agriculture license: CC-BY-4.0 mappings: agroportal: CO_324 cropoct: CO_324 fairsharing: FAIRsharing.dxx0c ols: co_324 ols: contact: helpdesk@cropontology-curationtool.org description: Sorghum TDv5 - Oct 2019 download: https://cropontology.org/ontology/CO_324/Sorghum/owl homepage: https://cropontology.org/ontology/CO_324/Sorghum name: Sorghum ontology prefix: co_324 version: '2019-10-09' pattern: ^\d{7}$ preferred_prefix: CO_324 repository: https://github.com/bioversity/Crop-Ontology uri_format: https://cropontology.org/rdf/CO_324:$1 co_325: agroportal: contact: email: helpdesk@cropontology-curationtool.org name: Crop Ontology Helpdesk description: Banana Trait Dictionary in template 5 - characterization and breeding variables, drought experiment variables. example_uri: http://www.cropontology.org/rdf/CO_325:0000267 homepage: http://www.cropontology.org/ license: CC-BY-4.0 name: Banana Ontology prefix: CO_325 repository: https://github.com/Planteome/CO_325-banana-traits version: April 2019 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 contact: email: e.arnaud@cgiar.org name: Elizabeth Arnaud orcid: 0000-0002-6020-5919 description: The Banana Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe the data. The use of ontology terms to describe agronomic phenotypes and the accurate mapping of these descriptions into databases is important in comparative phenotypic and genotypic studies across species and gene-discovery experiments as it provides harmonized description of the data and therefore facilitates the retrieval of information. homepage: https://cropontology.org/term/CO_325:ROOT license: CC-BY-4.0 name: Banana Ontology prefix: FAIRsharing.gdszhh publications: [] subjects: - Agriculture - Life Science license: CC-BY-4.0 mappings: agroportal: CO_325 cropoct: CO_325 fairsharing: FAIRsharing.gdszhh ols: co_325 ols: contact: helpdesk@cropontology-curationtool.org description: Banana Trait Dictionary in template 5 - Bioversity & IITA - April 2019 download: https://cropontology.org/ontology/CO_325/Banana/owl homepage: https://cropontology.org/ontology/CO_325/Banana name: Banana ontology prefix: co_325 version: '2019-10-09' pattern: ^\d{7}$ preferred_prefix: CO_325 repository: https://github.com/bioversity/Crop-Ontology uri_format: https://cropontology.org/rdf/CO_325:$1 co_326: cropoct: download_owl: https://cropontology.org/ontology/CO_326/Coconut/owl homepage: https://cropontology.org/term/CO_326:ROOT name: Coconut ontology prefix: CO_326 example: '0000254' license: CC-BY-4.0 mappings: cropoct: CO_326 ols: co_326 ols: contact: helpdesk@cropontology-curationtool.org description: Draft version download: https://cropontology.org/ontology/CO_326/Coconut/owl homepage: https://cropontology.org/ontology/CO_326/Coconut name: Coconut ontology prefix: co_326 pattern: ^\d{7}$ preferred_prefix: CO_326 repository: https://github.com/bioversity/Crop-Ontology uri_format: https://cropontology.org/rdf/CO_326:$1 co_327: agroportal: contact: email: helpdesk@cropontology-curationtool.org name: Crop Ontology Helpdesk description: Pearl millet Trait Dictionary in template 5. example_uri: http://www.cropontology.org/rdf/CO_327:0000185 homepage: http://www.cropontology.org/ license: CC-BY-4.0 name: Pearl Millet Ontology prefix: CO_327 repository: https://github.com/Planteome/CO_327-pearl-millet-traits version: April 2016 cropoct: description: Pearl millet Trait Dictionary in template 5 - ICRISAT/INERA - April 2016 download_owl: https://cropontology.org/ontology/CO_327/Pearl millet/owl homepage: https://cropontology.org/term/CO_327:ROOT name: Pearl millet ontology prefix: CO_327 example: 0000095 fairsharing: abbreviation: CO_327 description: The goal of the CGIAR Pearl Millet Ontology is to help improve food security for subsistence smallholder farmers in East and West Africa with productive and nutritious pearl millet food and fodder production technologies. homepage: https://cropontology.org/term/CO_327:ROOT license: CC-BY-4.0 name: Pearl Millet Ontology prefix: FAIRsharing.4e3qh9 publications: [] subjects: - Botany - Agriculture license: CC-BY-4.0 mappings: agroportal: CO_327 cropoct: CO_327 fairsharing: FAIRsharing.4e3qh9 ols: co_327 ols: contact: helpdesk@cropontology-curationtool.org description: Pearl millet Trait Dictionary in template 5 - ICRISAT/INERA - April 2016 download: http://www.cropontology.org/ontology/CO_327/Pearl%20millet/owl homepage: http://www.cropontology.org/ontology/CO_327/Pearl%20millet name: Pearl millet ontology prefix: co_327 pattern: ^\d{7}$ preferred_prefix: CO_327 repository: https://github.com/bioversity/Crop-Ontology uri_format: https://cropontology.org/rdf/CO_327:$1 co_330: agroportal: contact: email: helpdesk@cropontology-curationtool.org name: Crop Ontology Helpdesk description: Potato Ontology example_uri: http://www.cropontology.org/rdf/CO_330:0000056/2 homepage: http://www.cropontology.org/ license: CC-BY-4.0 name: Potato Ontology prefix: CO_330 repository: https://github.com/Planteome/CO_330-potato-traits version: december 2017 cropoct: description: CIP - potato ontology - december 2018 download_owl: https://cropontology.org/ontology/CO_330/Potato/owl homepage: https://cropontology.org/term/CO_330:ROOT name: Potato ontology prefix: CO_330 example: '0000106' fairsharing: abbreviation: CO_330 description: "Reference Plant Ontologies are being developed in the context of\ \ the Planteome project and are being integrated with the Crop Ontology, which\ \ provides harmonized breeders\u2019 trait names, measurement methods, scales\ \ and standard variables for many crops. The Potato Ontology is one of these\ \ reference plant ontologies integrated within the Crop Ontology." homepage: https://cropontology.org/term/CO_330:ROOT license: CC-BY-4.0 name: Potato Ontology prefix: FAIRsharing.4fa657 publications: [] subjects: - Botany - Agriculture - Life Science license: CC-BY-4.0 mappings: agroportal: CO_330 cropoct: CO_330 fairsharing: FAIRsharing.4fa657 ols: co_330 ols: contact: helpdesk@cropontology-curationtool.org description: CIP - potato ontology - december 2018 download: https://cropontology.org/ontology/CO_330/Potato/owl homepage: https://cropontology.org/ontology/CO_330/Potato name: Potato ontology prefix: co_330 version: '2019-10-09' pattern: ^\d{7}$ preferred_prefix: CO_330 repository: https://github.com/bioversity/Crop-Ontology uri_format: https://cropontology.org/rdf/CO_330:$1 co_331: agroportal: contact: email: helpdesk@cropontology-curationtool.org name: Crop Ontology Helpdesk description: Sweet Potato Trait Dictionary in template v5 example_uri: http://www.cropontology.org/rdf/CO_331:0000601/1 homepage: http://www.cropontology.org/ license: CC-BY-4.0 name: Sweet Potato Ontology prefix: CO_331 repository: https://github.com/Planteome/CO_331-sweetpotato-traits version: June 2016 cropoct: description: Sweetpotato Trait Dictionary in template v5 - CIP - November 2019 download_owl: https://cropontology.org/ontology/CO_331/Sweet Potato/owl homepage: https://cropontology.org/term/CO_331:ROOT name: Sweet Potato ontology prefix: CO_331 example: 0000088 fairsharing: abbreviation: CO_331 contact: email: V.Hualla@cgiar.org name: Vilma Hualla Mamani orcid: 0000-0003-0595-5271 description: "Reference Plant Ontologies are being developed in the context of\ \ the Planteome project and are being integrated with the Crop Ontology, which\ \ provides harmonized breeders\u2019 trait names, measurement methods, scales\ \ and standard variables for many crops. The Sweet Potato Ontology is one of\ \ these reference plant ontologies integrated within the Crop Ontology." homepage: https://cropontology.org/term/CO_331:ROOT license: CC-BY-4.0 name: Sweet Potato Ontology prefix: FAIRsharing.4g5qcw publications: [] subjects: - Botany - Agriculture - Life Science license: CC-BY-4.0 mappings: agroportal: CO_331 cropoct: CO_331 fairsharing: FAIRsharing.4g5qcw ols: co_331 ols: contact: helpdesk@cropontology-curationtool.org description: Sweet Potato Trait Dictionary in template v5 - CIP - November 2019 download: http://www.cropontology.org/ontology/CO_331/Sweet%20Potato/owl homepage: http://www.cropontology.org/ontology/CO_331/Sweet%20Potato name: Sweet Potato ontology prefix: co_331 pattern: ^\d{7}$ preferred_prefix: CO_331 repository: https://github.com/bioversity/Crop-Ontology uri_format: https://cropontology.org/rdf/CO_331:$1 co_333: agroportal: contact: email: helpdesk@cropontology-curationtool.org name: Crop Ontology Helpdesk description: "This ontology was built as part of the AKER project. It describes\ \ variables used in beet phenotyping (experimental properties and measurement\ \ scale) for each institution (INRA, Geves, ITB, 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 repository: https://forgemia.inra.fr/urgi-is/ontologies/-/tree/develop/Beet 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." homepage: https://cropontology.org/term/CO_333:ROOT license: CC-BY-4.0 name: Beet Ontology prefix: FAIRsharing.af5655 publications: [] subjects: - Botany - Plant Breeding - Agriculture - Life Science license: CC-BY-4.0 mappings: agroportal: CO_333 cropoct: CO_333 fairsharing: FAIRsharing.af5655 ols: co_333 ols: contact: helpdesk@cropontology-curationtool.org description: 'This ontology was built as part of the AKER project. It describes variables used in beet phenotyping (experimental properties and measurement scale) for each institution (INRAE, Geves, ITB) and breeding companies (Florimond Desprez). Curator: Dorothee Charruaud (ADRINORD - URGI) Daphne Verdelet (Florimond Desprez) - First submission in November 2017.' download: http://www.cropontology.org/ontology/CO_333/Beet%20Ontology/owl homepage: http://www.cropontology.org/ontology/CO_333/Beet%20Ontology name: Beet Ontology ontology prefix: co_333 pattern: ^\d+$ preferred_prefix: CO_333 repository: https://github.com/bioversity/Crop-Ontology uri_format: https://cropontology.org/rdf/CO_333:$1 co_334: agroportal: contact: email: helpdesk@cropontology-curationtool.org name: Crop Ontology Helpdesk description: 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/ repository: https://github.com/Planteome/CO_334-cassava-traits 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. homepage: https://cropontology.org/term/CO_334:ROOT license: CC-BY-4.0 name: IBP Cassava Trait Ontology prefix: FAIRsharing.v06c4q publications: [] repository: https://github.com/Planteome/ibp-cassava-traits subjects: - Botany - Agriculture - Nutritional Science license: CC-BY-4.0 mappings: agroportal: CO_334 cropoct: CO_334 fairsharing: FAIRsharing.v06c4q ols: co_334 ols: contact: helpdesk@cropontology-curationtool.org description: Cassava Trait Dictionary in template 5 - IITA - July 2015, updated in February 2016 download: https://cropontology.org/ontology/CO_334/Cassava/owl homepage: https://cropontology.org/ontology/CO_334/Cassava name: Cassava ontology prefix: co_334 version: '2019-10-09' pattern: ^\d{7}$ preferred_prefix: CO_334 repository: https://github.com/bioversity/Crop-Ontology uri_format: https://cropontology.org/rdf/CO_334:$1 co_335: agroportal: contact: email: helpdesk@cropontology-curationtool.org name: Crop Ontology Helpdesk description: Common bean trait dictionary example_uri: http://www.cropontology.org/rdf/CO_335:0000475/4 homepage: http://www.cropontology.org/ license: CC-BY-4.0 name: Common Bean Ontology prefix: CO_335 repository: https://github.com/Planteome/CO_335-common-bean-traits version: August 2014 cropoct: description: CIAT Common bean trait dictionary - version Oct 2021 download_owl: https://cropontology.org/ontology/CO_335/Common Bean/owl homepage: https://cropontology.org/term/CO_335:ROOT name: Common Bean ontology prefix: CO_335 example: 0000189 fairsharing: abbreviation: CO_335 description: "Reference Plant Ontologies are being developed in the context of\ \ the Planteome project and are being integrated with the Crop Ontology, which\ \ provides harmonized breeders\u2019 trait names, measurement methods, scales\ \ and standard variables for many crops. The Common Bean Ontology is one of\ \ these reference plant ontologies integrated within the Crop Ontology." homepage: https://cropontology.org/term/CO_335:ROOT license: CC-BY-4.0 name: Common Bean Ontology prefix: FAIRsharing.a14123 publications: [] subjects: - Botany - Agriculture license: CC-BY-4.0 mappings: agroportal: CO_335 cropoct: CO_335 fairsharing: FAIRsharing.a14123 ols: co_335 ols: contact: helpdesk@cropontology-curationtool.org description: CIAT Common bean trait dictionary - version August 2014 download: http://www.cropontology.org/ontology/CO_335/Common%20Bean/owl homepage: http://www.cropontology.org/ontology/CO_335/Common%20Bean name: Common Bean ontology prefix: co_335 pattern: ^\d{7}$ preferred_prefix: CO_335 repository: https://github.com/bioversity/Crop-Ontology uri_format: https://cropontology.org/rdf/CO_335:$1 co_336: agroportal: contact: email: helpdesk@cropontology-curationtool.org name: Crop Ontology Helpdesk description: Soybean Trait Dictionary in template v5 example_uri: http://www.cropontology.org/rdf/CO_336:0000230/2 homepage: http://www.cropontology.org/ license: CC-BY-4.0 name: Soybean Ontology prefix: CO_336 repository: https://github.com/Planteome/CO_336-soybean-traits version: July 2015 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 contact: email: e.arnaud@cgiar.org name: Elizabeth Arnaud orcid: 0000-0002-6020-5919 description: The Soybean Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe the data. The use of ontology terms to describe agronomic phenotypes and the accurate mapping of these descriptions into databases is important in comparative phenotypic and genotypic studies across species and gene-discovery experiments as it provides harmonized description of the data and therefore facilitates the retrieval of information. homepage: https://cropontology.org/term/CO_336:ROOT license: CC-BY-4.0 name: Soybean Ontology prefix: FAIRsharing.j75srj publications: [] subjects: - Agriculture - Life Science license: CC-BY-4.0 mappings: agroportal: CO_336 cropoct: CO_336 fairsharing: FAIRsharing.j75srj ols: co_336 ols: contact: helpdesk@cropontology-curationtool.org description: Soybean Trait Dictionary in template v5 - IITA - July 2015 download: https://cropontology.org/ontology/CO_336/Soybean/owl homepage: https://cropontology.org/ontology/CO_336/Soybean name: Soybean ontology prefix: co_336 pattern: ^\d{7}$ preferred_prefix: CO_336 repository: https://github.com/bioversity/Crop-Ontology uri_format: https://cropontology.org/rdf/CO_336:$1 co_337: agroportal: contact: email: tm.shah@cgiar.org name: Trushar Shah description: 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 repository: https://github.com/Planteome/CO_337-groundnut-traits 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. homepage: https://cropontology.org/term/CO_337:ROOT license: CC-BY-4.0 name: Groundnut Ontology prefix: FAIRsharing.ge8y23 publications: [] subjects: - Botany - Agriculture - Life Science license: CC-BY-4.0 mappings: agroportal: CO_337 cropoct: CO_337 fairsharing: FAIRsharing.ge8y23 ols: co_337 ols: contact: helpdesk@cropontology-curationtool.org description: Groundnut Trait Dictionary in template v5 - ICRISAT/ISRA/DARS - Sept 2015 download: https://cropontology.org/ontology/CO_337/Groundnut/owl homepage: https://cropontology.org/ontology/CO_337/Groundnut name: Groundnut ontology prefix: co_337 version: '2019-10-09' pattern: ^\d{7}$ preferred_prefix: CO_337 repository: https://github.com/bioversity/Crop-Ontology uri_format: https://cropontology.org/rdf/CO_337:$1 co_338: agroportal: contact: email: tm.shah@cgiar.org name: Trushar Shah description: 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 repository: https://github.com/Planteome/CO_338-chickpea-traits 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. homepage: https://cropontology.org/term/CO_338:ROOT license: CC-BY-4.0 name: Chickpea Ontology prefix: FAIRsharing.js20q3 publications: [] subjects: - Botany - Agriculture license: CC-BY-4.0 mappings: agroportal: CO_338 cropoct: CO_338 fairsharing: FAIRsharing.js20q3 ols: co_338 ols: contact: helpdesk@cropontology-curationtool.org description: Chickpea Trait Dictionary in template v5 - ICRISAT - July 2015 download: https://cropontology.org/ontology/CO_338/Chickpea/owl homepage: https://cropontology.org/ontology/CO_338/Chickpea name: Chickpea ontology prefix: co_338 version: '2019-10-09' pattern: ^\d{7}$ preferred_prefix: CO_338 repository: https://github.com/bioversity/Crop-Ontology uri_format: https://cropontology.org/rdf/CO_338:$1 co_339: agroportal: contact: email: helpdesk@cropontology-curationtool.org name: Crop Ontology Helpdesk description: 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 repository: https://github.com/Planteome/CO_339-lentil-traits AND/OR https://forgemia.inra.fr/urgi-is/ontologies/-/tree/develop/Lentil 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. homepage: https://cropontology.org/term/CO_339:ROOT license: CC-BY-4.0 name: Lentil Ontology prefix: FAIRsharing.ry1ezg publications: [] subjects: - Botany - Agriculture - Life Science license: CC-BY-4.0 mappings: agroportal: CO_339 cropoct: CO_339 fairsharing: FAIRsharing.ry1ezg ols: co_339 ols: contact: helpdesk@cropontology-curationtool.org description: Lentil Trait Dictionary in template v5 - ICARDA - July 2015 download: https://cropontology.org/ontology/CO_339/Lentil/owl homepage: https://cropontology.org/ontology/CO_339/Lentil name: Lentil ontology prefix: co_339 version: '2019-10-09' pattern: ^\d{7}$ preferred_prefix: CO_339 repository: https://github.com/bioversity/Crop-Ontology uri_format: https://cropontology.org/rdf/CO_339:$1 co_340: agroportal: contact: email: helpdesk@cropontology-curationtool.org name: Crop Ontology Helpdesk description: 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/ repository: https://github.com/Planteome/CO_340-cowpea-traits 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. homepage: https://cropontology.org/term/CO_340:ROOT license: CC-BY-4.0 name: IBP Cowpea Trait Ontology prefix: FAIRsharing.31apg2 publications: - doi: 10.3389/fphys.2012.00326 pubmed_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 license: CC-BY-4.0 mappings: agroportal: CO_340 cropoct: CO_340 fairsharing: FAIRsharing.31apg2 ols: co_340 ols: contact: helpdesk@cropontology-curationtool.org description: Cowpea Trait Dictionary in template v5 - IITA - August 2015 download: https://cropontology.org/ontology/CO_340/Cowpea/owl homepage: https://cropontology.org/ontology/CO_340/Cowpea name: Cowpea ontology prefix: co_340 version: '2019-10-09' pattern: ^\d{7}$ preferred_prefix: CO_340 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 repository: https://github.com/bioversity/Crop-Ontology uri_format: https://cropontology.org/rdf/CO_340:$1 co_341: agroportal: contact: email: helpdesk@cropontology-curationtool.org name: Crop Ontology Helpdesk description: Pigeonpea Trait Dictionary in template v5 example_uri: http://www.cropontology.org/rdf/CO_341:0000015 homepage: http://www.cropontology.org/ license: CC-BY-4.0 name: Pigeon Pea Ontology prefix: CO_341 repository: https://github.com/Planteome/CO_341-pigeonpea-traits version: July 2015 cropoct: description: Pigeonpea Trait Dictionary in template v5 - ICRISAT - July 2015 download_owl: https://cropontology.org/ontology/CO_341/Pigeonpea/owl homepage: https://cropontology.org/term/CO_341:ROOT name: Pigeonpea ontology prefix: CO_341 example: '0000140' fairsharing: abbreviation: CO_341 contact: email: e.arnaud@cgiar.org name: Elizabeth Arnaud orcid: 0000-0002-6020-5919 description: "Reference Plant Ontologies are being developed in the context of\ \ the Planteome project and are being integrated with the Crop Ontology, which\ \ provides harmonized breeders\u2019 trait names, measurement methods, scales\ \ and standard variables for many crops. The Pigeon Pea Ontology is one of these\ \ reference plant ontologies integrated within the Crop Ontology." homepage: https://cropontology.org/term/CO_341:ROOT license: CC-BY-4.0 name: Pigeon Pea Ontology prefix: FAIRsharing.ehe3yp publications: [] subjects: - Botany - Agriculture - Life Science license: CC-BY-4.0 mappings: agroportal: CO_341 cropoct: CO_341 fairsharing: FAIRsharing.ehe3yp ols: co_341 ols: contact: helpdesk@cropontology-curationtool.org description: Pigeonpea Trait Dictionary in template v5 - ICRISAT - July 2015 download: https://cropontology.org/ontology/CO_341/Pigeonpea/owl homepage: https://cropontology.org/ontology/CO_341/Pigeonpea name: Pigeonpea ontology prefix: co_341 version: '2019-11-18' pattern: ^\d{7}$ preferred_prefix: CO_341 repository: https://github.com/bioversity/Crop-Ontology uri_format: https://cropontology.org/rdf/CO_341:$1 co_343: agroportal: contact: email: helpdesk@cropontology-curationtool.org name: Crop Ontology Helpdesk description: Yam trait ontology example_uri: http://www.cropontology.org/rdf/CO_343:0000357 homepage: http://www.cropontology.org/ license: CC-BY-4.0 name: Yam Ontology prefix: CO_343 repository: https://github.com/Planteome/CO_343-yam-traits version: Feb 2017 cropoct: description: version 2019 - pvs download_owl: https://cropontology.org/ontology/CO_343/Yam/owl homepage: https://cropontology.org/term/CO_343:ROOT name: Yam ontology prefix: CO_343 example: '0100010' fairsharing: abbreviation: CO_343 description: "Reference Plant Ontologies are being developed in the context of\ \ the Planteome project and are being integrated with the Crop Ontology, which\ \ provides harmonized breeders\u2019 trait names, measurement methods, scales\ \ and standard variables for many crops. The Yam Ontology is one of these reference\ \ plant ontologies integrated within the Crop Ontology." homepage: https://cropontology.org/term/CO_343:ROOT license: CC-BY-4.0 name: Yam Ontology prefix: FAIRsharing.7e9cff publications: [] subjects: - Botany - Agriculture - Life Science license: CC-BY-4.0 mappings: agroportal: CO_343 cropoct: CO_343 fairsharing: FAIRsharing.7e9cff ols: co_343 ols: contact: helpdesk@cropontology-curationtool.org description: version 2019 - pvs download: https://cropontology.org/ontology/CO_343/Yam/owl homepage: https://cropontology.org/ontology/CO_343/Yam name: Yam ontology prefix: co_343 version: '2019-10-09' pattern: ^\d{7}$ preferred_prefix: CO_343 repository: https://github.com/bioversity/Crop-Ontology uri_format: https://cropontology.org/rdf/CO_343:$1 co_345: agroportal: contact: email: helpdesk@cropontology-curationtool.org name: Crop Ontology Helpdesk description: Brachiaria (forages) ontology TD v5 example_uri: http://www.cropontology.org/rdf/CO_345:0000044 homepage: http://www.cropontology.org/ license: CC-BY-4.0 name: Brachiaria Ontology prefix: CO_345 repository: https://github.com/Planteome/CO_345-brachiaria-traits version: Oct 2016 cropoct: description: Brachiaria (forages) ontology TD v5 - Version Oct 2016 download_owl: https://cropontology.org/ontology/CO_345/Brachiaria/owl homepage: https://cropontology.org/term/CO_345:ROOT name: Brachiaria ontology prefix: CO_345 example: '0000127' fairsharing: abbreviation: CO_345 description: "Reference Plant Ontologies are being developed in the context of\ \ the Planteome project and are being integrated with the Crop Ontology, which\ \ provides harmonized breeders\u2019 trait names, measurement methods, scales\ \ and standard variables for many crops. The Brachiaria Ontology is one of these\ \ reference plant ontologies integrated within the Crop Ontology." homepage: https://cropontology.org/term/CO_345:ROOT license: CC-BY-4.0 name: Brachiaria Ontology prefix: FAIRsharing.9e9683 publications: [] subjects: - Botany - Agriculture - Life Science license: CC-BY-4.0 mappings: agroportal: CO_345 cropoct: CO_345 fairsharing: FAIRsharing.9e9683 ols: co_345 ols: contact: helpdesk@cropontology-curationtool.org description: Brachiaria (forages) ontology TD v5 - Version Oct 2016 download: https://cropontology.org/ontology/CO_345/Brachiaria/owl homepage: https://cropontology.org/ontology/CO_345/Brachiaria name: Brachiaria ontology prefix: co_345 version: '2019-10-09' pattern: ^\d{7}$ preferred_prefix: CO_345 repository: https://github.com/bioversity/Crop-Ontology uri_format: https://cropontology.org/rdf/CO_345:$1 co_346: agroportal: contact: email: helpdesk@cropontology-curationtool.org name: Crop Ontology Helpdesk description: Mungbean Ontology example_uri: http://www.cropontology.org/rdf/CO_346:0000095 homepage: http://www.cropontology.org/ license: CC-BY-4.0 name: Mungbean Ontology prefix: CO_346 repository: https://agroportal.lirmm.fr/ontologies/CO_346 version: Oct 2016 cropoct: description: oct 2016 download_owl: https://cropontology.org/ontology/CO_346/Mungbean/owl homepage: https://cropontology.org/term/CO_346:ROOT name: Mungbean ontology prefix: CO_346 example: 0000199 fairsharing: abbreviation: CO_346 description: The Mungbean Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe data. homepage: https://cropontology.org/term/CO_346:ROOT license: CC-BY-4.0 name: Mungbean Ontology prefix: FAIRsharing.fgd5gq publications: [] subjects: - Agriculture - Life Science license: CC-BY-4.0 mappings: agroportal: CO_346 cropoct: CO_346 fairsharing: FAIRsharing.fgd5gq ols: co_346 ols: contact: helpdesk@cropontology-curationtool.org description: oct 2016 download: https://cropontology.org/ontology/CO_346/Mungbean/owl homepage: https://cropontology.org/ontology/CO_346/Mungbean name: Mungbean ontology prefix: co_346 version: '2019-10-09' pattern: ^\d{7}$ preferred_prefix: CO_346 repository: https://github.com/bioversity/Crop-Ontology uri_format: https://cropontology.org/rdf/CO_346:$1 co_347: agroportal: contact: email: helpdesk@cropontology-curationtool.org name: Crop Ontology Helpdesk description: Castor Bean Ontology example_uri: http://www.cropontology.org/rdf/CO_347:0000108 homepage: http://www.cropontology.org/ license: CC-BY-4.0 name: Castor Bean Ontology prefix: CO_347 repository: https://github.com/Planteome/CO_347-castorbean-traits version: March 2017 cropoct: description: 'March 2017 version ' download_owl: https://cropontology.org/ontology/CO_347/Castor bean/owl homepage: https://cropontology.org/term/CO_347:ROOT name: Castor bean ontology prefix: CO_347 example: 0000108 fairsharing: abbreviation: CO_347 description: The Castor Bean Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe data. homepage: https://cropontology.org/term/CO_347:ROOT license: CC-BY-4.0 name: Castor Bean Ontology prefix: FAIRsharing.qrrvyk publications: [] subjects: - Botany - Agriculture - Life Science license: CC-BY-4.0 mappings: agroportal: CO_347 cropoct: CO_347 fairsharing: FAIRsharing.qrrvyk ols: co_347 ols: contact: helpdesk@cropontology-curationtool.org description: 'March 2017 version ' download: http://www.cropontology.org/ontology/CO_347/Castor%20bean/owl homepage: http://www.cropontology.org/ontology/CO_347/Castor%20bean name: Castor bean ontology prefix: co_347 pattern: ^\d{7}$ preferred_prefix: CO_347 repository: https://github.com/bioversity/Crop-Ontology uri_format: https://cropontology.org/rdf/CO_347:$1 co_348: agroportal: contact: email: helpdesk@cropontology-curationtool.org name: helpdesk cropontology description: Brassica Trait Ontology (BRaTO) hosts trait information to describe brassica crop data. Terms are collected from various projects including OREGIN, RIPR (UK) and Rapsodyn (France). BRATO development is conducted by Earlham Institute (UK), Southern Cross University (Australia) and INRA (France). example_uri: http://www.cropontology.org/rdf/CO_348:1000012 homepage: http://www.cropontology.org/ license: CC-BY-4.0 name: Brassica Ontology prefix: CO_348 repository: https://github.com/Brassica-Trait-Ontology/brato AND/OR https://forgemia.inra.fr/urgi-is/ontologies/-/tree/develop/Brassica 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." homepage: https://cropontology.org/term/CO_348:ROOT license: CC-BY-4.0 name: Brassica Ontology prefix: FAIRsharing.af7a2d publications: [] repository: https://github.com/Brassica-Trait-Ontology/brato subjects: - Botany - Agriculture - Life Science license: CC-BY-4.0 mappings: agroportal: CO_348 cropoct: CO_348 fairsharing: FAIRsharing.af7a2d ols: co_348 ols: contact: helpdesk@cropontology-curationtool.org description: Brassica Trait Ontology (BRaTO) hosts trait information to describe brassica crop data. Terms are collected from various projects including OREGIN, RIPR (UK) and Rapsodyn (France). BRATO development is conducted by Earlham Institute (UK), Southern Cross University (Australia) and INRA (France). download: https://cropontology.org/ontology/CO_348/Brassica/owl homepage: https://cropontology.org/ontology/CO_348/Brassica name: Brassica ontology prefix: co_348 version: '2019-11-29' pattern: ^\d+$ preferred_prefix: CO_348 repository: https://github.com/bioversity/Crop-Ontology uri_format: https://cropontology.org/rdf/CO_348:$1 co_350: agroportal: contact: email: helpdesk@cropontology-curationtool.org name: Crop Ontology Helpdesk description: Oat trait dictionary commissioned by Oat Global (http://oatglobal.org/) to hold the traits used in the T3/Oat database (http://triticeaetoolbox.org/oat/). example_uri: http://www.cropontology.org/rdf/CO_350:0000091 homepage: http://www.cropontology.org/ license: CC-BY-4.0 name: Oat Ontology prefix: CO_350 repository: https://github.com/Planteome/CO_350-oat-traits version: '1.0' cropoct: description: Oat trait dictionary started by Oat Global (http://oatglobal.org/) and improved by NIAB and PepsiCo download_owl: 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 contact: email: jeanluc.work@gmail.com name: Jean-Luc Jannink orcid: 0000-0003-4849-628X description: "Reference Plant Ontologies are being developed in the context of\ \ the Planteome project and are being integrated with the Crop Ontology, which\ \ provides harmonized breeders\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/)." homepage: https://cropontology.org/term/CO_350:ROOT license: CC-BY-4.0 name: Oat Trait Ontology prefix: FAIRsharing.35e1c3 publications: [] subjects: - Botany - Agriculture - Life Science license: CC-BY-4.0 mappings: agroportal: CO_350 cropoct: CO_350 fairsharing: FAIRsharing.35e1c3 ols: co_350 ols: contact: helpdesk@cropontology-curationtool.org description: Oat trait dictionary started by Oat Global (http://oatglobal.org/) and improved by NIAB and PepsiCo download: https://cropontology.org/ontology/CO_350/Oat/owl homepage: https://cropontology.org/ontology/CO_350/Oat name: Oat ontology prefix: co_350 version: '2019-10-09' pattern: ^\d{7}$ preferred_prefix: CO_350 repository: https://github.com/bioversity/Crop-Ontology uri_format: https://cropontology.org/rdf/CO_350:$1 co_356: agroportal: contact: email: helpdesk@cropontology-curationtool.org name: Crop Ontology Helpdesk description: Grape Ontology including OIV and bioversity descriptors. INRA July 2017 example_uri: http://www.cropontology.org/rdf/CO_356:1000182 homepage: http://www.cropontology.org/ license: CC-BY-4.0 name: Vitis Ontology prefix: CO_356 repository: https://forgemia.inra.fr/urgi-is/ontologies/-/tree/develop/Vitis version: '2019-11-29' cropoct: description: Grape Ontology including OIV and bioversity descriptors. INRA July 2017 download_owl: https://cropontology.org/ontology/CO_356/Vitis/owl homepage: https://cropontology.org/term/CO_356:ROOT name: Vitis ontology prefix: CO_356 example: '4000027' fairsharing: abbreviation: CO_356 description: "Reference Plant Ontologies are being developed in the context of\ \ the Planteome project and are being integrated with the Crop Ontology, which\ \ provides harmonized breeders\u2019 trait names, measurement methods, scales\ \ and standard variables for many crops. The Vitis Ontology is one of these\ \ reference plant ontologies integrated within the Crop Ontology." homepage: https://cropontology.org/term/CO_356:ROOT license: CC BY-SA 4.0 name: Vitis Ontology prefix: FAIRsharing.c7f4d7 publications: [] subjects: - Botany - Agriculture - Life Science license: CC-BY-4.0 mappings: agroportal: CO_356 cropoct: CO_356 fairsharing: FAIRsharing.c7f4d7 ols: co_356 ols: contact: helpdesk@cropontology-curationtool.org description: Grape Ontology including OIV and bioversity descriptors. INRA July 2017 download: https://cropontology.org/ontology/CO_356/Vitis/owl homepage: https://cropontology.org/ontology/CO_356/Vitis name: Vitis ontology prefix: co_356 version: '2019-11-29' pattern: ^\d+$ preferred_prefix: CO_356 repository: https://github.com/bioversity/Crop-Ontology uri_format: https://cropontology.org/rdf/CO_356:$1 co_357: agroportal: contact: email: celia.michotey@inrae.fr name: "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 repository: https://forgemia.inra.fr/urgi-is/ontologies/-/tree/develop/Tree 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 (ITQB NOVA/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." homepage: https://cropontology.org/term/CO_357:ROOT license: CC-BY-4.0 name: Woody Plant Ontology prefix: FAIRsharing.2b04ae publications: [] subjects: - Botany - Life Science license: CC-BY-4.0 mappings: agroportal: CO_357 cropoct: CO_357 fairsharing: FAIRsharing.2b04ae ols: co_357 ols: contact: helpdesk@cropontology-curationtool.org description: 'This ontology lists all variables used for woody plant observations. Terms are collected from various sources (past and ongoing projects at national and international levels). Curators: Celia Michotey (INRAE) & Ines Chaves (IBET) - Version 2 submitted on Jun 2020 by INRAE.' download: http://www.cropontology.org/ontology/CO_357/Woody%20Plant%20Ontology/owl homepage: http://www.cropontology.org/ontology/CO_357/Woody%20Plant%20Ontology name: Woody Plant Ontology ontology prefix: co_357 pattern: ^\d+$ preferred_prefix: CO_357 repository: https://github.com/bioversity/Crop-Ontology uri_format: https://cropontology.org/rdf/CO_357:$1 co_358: agroportal: contact: email: helpdesk@cropontology-curationtool.org name: Crop Ontology Helpdesk description: Cotton ontology from CottonGen database - June 2019 example_uri: http://www.cropontology.org/rdf/CO_358:0000215 homepage: http://www.cropontology.org/ license: CC-BY-4.0 name: Cotton Ontology prefix: CO_358 repository: https://github.com/Planteome/CO_358-cotton-traits version: '2020-01-03' cropoct: description: Cotton ontology from CottonGen database - June 2019 download_owl: https://cropontology.org/ontology/CO_358/Cotton/owl homepage: https://cropontology.org/term/CO_358:ROOT name: Cotton ontology prefix: CO_358 example: 0000139 license: CC-BY-4.0 mappings: agroportal: CO_358 cropoct: CO_358 ols: co_358 ols: contact: helpdesk@cropontology-curationtool.org description: Cotton ontology from CottonGen database - June 2019 download: https://cropontology.org/ontology/CO_358/Cotton/owl homepage: https://cropontology.org/ontology/CO_358/Cotton name: Cotton ontology prefix: co_358 version: '2020-01-03' pattern: ^\d{7}$ preferred_prefix: CO_358 repository: https://github.com/bioversity/Crop-Ontology uri_format: https://cropontology.org/rdf/CO_358:$1 co_359: agroportal: contact: email: helpdesk@cropontology-curationtool.org name: Crop Ontology Helpdesk description: Created in December 2019. example_uri: https://cropontology.org/rdf/CO_359:0000568 homepage: https://www.cropontology.org/ license: CC-BY-4.0 name: Sunflower Ontology prefix: CO_359 repository: https://github.com/Planteome/CO_359-sunflower-traits version: '2019-12-16' cropoct: description: December 2019 download_owl: https://cropontology.org/ontology/CO_359/Sunflower/owl homepage: https://cropontology.org/term/CO_359:ROOT name: Sunflower ontology prefix: CO_359 example: 0000947 license: CC-BY-4.0 mappings: agroportal: CO_359 cropoct: CO_359 ols: co_359 ols: contact: helpdesk@cropontology-curationtool.org description: December 2019 download: https://cropontology.org/ontology/CO_359/Sunflower/owl homepage: https://cropontology.org/ontology/CO_359/Sunflower name: Sunflower ontology prefix: co_359 pattern: ^\d{7}$ preferred_prefix: CO_359 repository: https://github.com/bioversity/Crop-Ontology uri_format: https://cropontology.org/rdf/CO_359:$1 co_360: agroportal: contact: email: helpdesk@cropontology-curationtool.org name: Crop Ontology Helpdesk description: Sugar Kelp trait ontology example_uri: http://www.cropontology.org/rdf/CO_360:0000085 homepage: http://www.cropontology.org/ license: CC-BY-4.0 name: Sugar Kelp Ontology prefix: CO_360 repository: https://github.com/Planteome/CO_360-sugar-kelp-traits version: June 2019 cropoct: description: Sugar Kelp trait ontology download_owl: https://cropontology.org/ontology/CO_360/Sugar Kelp trait/owl homepage: https://cropontology.org/term/CO_360:ROOT name: Sugar Kelp trait ontology prefix: CO_360 example: '0000071' fairsharing: abbreviation: CO_360 description: "Reference Plant Ontologies are being developed in the context of\ \ the Planteome project and are being integrated with the Crop Ontology, which\ \ provides harmonized breeders\u2019 trait names, measurement methods, scales\ \ and standard variables for many crops. The Sugar Kelp Trait Ontology is one\ \ of these reference plant ontologies integrated within the Crop Ontology." homepage: https://cropontology.org/term/CO_360:ROOT license: CC-BY-4.0 name: Sugar Kelp Trait Ontology prefix: FAIRsharing.1c1738 publications: [] subjects: - Botany - Life Science license: CC-BY-4.0 mappings: agroportal: CO_360 cropoct: CO_360 fairsharing: FAIRsharing.1c1738 ols: co_360 ols: contact: helpdesk@cropontology-curationtool.org description: Sugar Kelp trait ontology download: http://www.cropontology.org/ontology/CO_360/Sugar%20Kelp%20trait/owl homepage: http://www.cropontology.org/ontology/CO_360/Sugar%20Kelp%20trait name: Sugar Kelp trait ontology prefix: co_360 pattern: ^\d{7}$ preferred_prefix: CO_360 repository: https://github.com/bioversity/Crop-Ontology uri_format: https://cropontology.org/rdf/CO_360:$1 co_365: agroportal: contact: email: ICARDA-ethiopia@cgiar.org name: ICARDA Ethiopia description: developed by ICARDA - Dec 2018 example_uri: http://www.cropontology.org/rdf/CO_365:0000146 homepage: http://www.cropontology.org license: CC-BY-4.0 name: Fababean Ontology prefix: CO_365 repository: https://github.com/Planteome/CO_365-faba-bean-traits version: '2019-10-15' cropoct: description: developed by ICARDA - Dec 2018 download_owl: https://cropontology.org/ontology/CO_365/Fababean/owl homepage: https://cropontology.org/term/CO_365:ROOT name: Fababean ontology prefix: CO_365 example: '0000205' license: CC-BY-4.0 mappings: agroportal: CO_365 cropoct: CO_365 ols: co_365 ols: contact: helpdesk@cropontology-curationtool.org description: developed by ICARDA - Dec 2018 download: https://cropontology.org/ontology/CO_365/Fababean/owl homepage: https://cropontology.org/ontology/CO_365/Fababean name: Fababean ontology prefix: co_365 version: '2019-10-15' pattern: ^\d{7}$ preferred_prefix: CO_365 repository: https://github.com/bioversity/Crop-Ontology uri_format: https://cropontology.org/rdf/CO_365:$1 co_366: agroportal: contact: email: helpdesk@cropontology-curationtool.org name: Crop Ontology Helpdesk description: version Dec 2019 example_uri: http://www.cropontology.org/rdf/CO_366:0000253/9 homepage: http://www.cropontology.org license: CC-BY-4.0 name: Bambara Groundnut Ontology prefix: CO_366 publication: https://doi.org/10.1093/database/baab028 repository: https://github.com/Planteome/CO_366-bambara-goundnut-traits version: '2019-12-23' cropoct: description: version Dec 2019 download_owl: https://cropontology.org/ontology/CO_366/Bambara groundnut/owl homepage: https://cropontology.org/term/CO_366:ROOT name: Bambara groundnut ontology prefix: CO_366 example: '0000072' license: CC-BY-4.0 mappings: agroportal: CO_366 cropoct: CO_366 ols: co_366 ols: contact: helpdesk@cropontology-curationtool.org description: version Dec 2019 download: http://www.cropontology.org/ontology/CO_366/Bambara%20groundnut/owl homepage: http://www.cropontology.org/ontology/CO_366/Bambara%20groundnut name: Bambara groundnut ontology prefix: co_366 pattern: ^\d{7}$ preferred_prefix: CO_366 repository: https://github.com/bioversity/Crop-Ontology uri_format: https://cropontology.org/rdf/CO_366:$1 co_367: cropoct: description: 'Curator name: Clara S. Stanschewski; Curator Affiliation: King Abdullah University of Science and Technology; Contributing Scientists or Crop expert group: The Salt Lab and the Quinoa Phenotyping Consortium Creation Date: 23.05.2021' download_owl: https://cropontology.org/ontology/CO_367/Quinoa Ontology/owl homepage: https://cropontology.org/term/CO_367:ROOT name: Quinoa Ontology ontology prefix: CO_367 example: '0000004' license: CC-BY-4.0 mappings: cropoct: CO_367 pattern: ^\d{7}$ preferred_prefix: CO_367 repository: https://github.com/bioversity/Crop-Ontology uri_format: https://cropontology.org/rdf/CO_367:$1 co_370: agroportal: contact: email: ekaterina.chuprikova@eurac.edu name: Ekaterina Chuprikova description: Apple (Malus domestica) defines crop traits and variables to support the standardisation of apple breeding databases providing description of agronomic, morphological, physiological, quality traits, its methods and scales. example_uri: https://cropontology.org/rdf/CO_370:0001028 homepage: http://www.cropontology.org/ license: CC-BY-4.0 name: Apple Ontology prefix: CO_370 version: '1.1' cropoct: description: Apple (Malus domestica) defines crop traits and variables to support the standardisation of apple breeding databases providing description of agronomic, morphological, physiological, quality traits, its methods and scales. download_owl: https://cropontology.org/ontology/CO_370/Apple/owl homepage: https://cropontology.org/term/CO_370:ROOT name: Apple ontology prefix: CO_370 example: 0000890 license: CC-BY-4.0 mappings: agroportal: CO_370 cropoct: CO_370 pattern: ^\d{7}$ preferred_prefix: CO_370 repository: https://github.com/bioversity/Crop-Ontology uri_format: https://cropontology.org/rdf/CO_370:$1 cob: aberowl: description: COB brings together key terms from a wide range of OBO projects to improve interoperability. download_owl: http://aber-owl.net/media/ontologies/COB/8/cob.owl homepage: https://obofoundry.org/COB/ name: Core Ontology for Biology and Biomedicine prefix: COB bioportal: contact: email: bpeters@lji.org name: Bjoern Peters description: The Core Ontology for Biology and Biomedicine (COB) brings together key terms from a wide range of OBO projects into a single, small ontology. The goal is to improve interoperabilty and reuse across the OBO community through better coordination of key terms. homepage: https://github.com/OBOFoundry/COB name: Core Ontology for Biology and Biomedicine prefix: COB version: '2022-11-02' example: 0000080 mappings: aberowl: COB bioportal: COB obofoundry: cob ols: cob ontobee: COB obofoundry: contact: bpeters@lji.org contact.github: bpeters42 contact.label: Bjoern Peters contact.orcid: 0000-0002-8457-6693 deprecated: false description: COB brings together key terms from a wide range of OBO projects to improve interoperability. domain: upper download.owl: http://purl.obolibrary.org/obo/cob.owl homepage: https://obofoundry.org/COB/ license: CC0 1.0 license.url: https://creativecommons.org/publicdomain/zero/1.0/ name: Core Ontology for Biology and Biomedicine preferredPrefix: COB prefix: cob repository: https://github.com/OBOFoundry/COB ols: description: COB brings together key terms from a wide range of OBO projects to improve interoperability. download: http://purl.obolibrary.org/obo/cob.owl homepage: https://obofoundry.org/COB/ name: Core Ontology for Biology and Biomedicine prefix: cob version: '2022-05-02' version.iri: http://purl.obolibrary.org/obo/cob/releases/2022-05-02/cob.owl ontobee: library: Library name: Core Ontology for Biology and Biomedicine prefix: COB pattern: ^\d{7}$ 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 keywords: - chemistry - natural producs - organic chemistry 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/$1 codelink: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: 'GE Healthcare/Amersham Biosciences CodeLink? Human Whole Genome Bioarray targets most of the known and predictive genes of the human genome as it is described today in the public domain. It is comprised of approximately 55,000 30-mer probes designed to conserved exons across the transcripts of targeted genes. These 55,000 probes represent well annotated, full length, and partial human gene sequences from major public databases. GE Healthcare/Amersham Biosciences CodeLink? Human Whole Genome Bioarray probe sequences were selected from the NCBI UniGene build #165, RefSeq database (January 5, 2004 release) and dbEST database (January 8, 2004 release).' example: GE86325 homepage: https://www.ebi.ac.uk/arrayexpress/files/A-GEHB-1/A-GEHB-1.adf.txt keywords: - microarray - transcriptomics name: GE Healthcare/Amersham Biosciences CodeLink Human Whole Genome Bioarray pattern: ^GE\d+$ 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 contact: email: koonin@ncbi.nlm.nih.gov name: Eugene V Koonin orcid: 0000-0003-3943-8299 description: Clusters of Orthologous Groups of proteins (COGs) were delineated by comparing protein sequences encoded in complete genomes, representing major phylogenetic lineages. Each COG consists of individual proteins or groups of paralogs from at least 3 lineages and thus corresponds to an ancient conserved domain. homepage: https://www.ncbi.nlm.nih.gov/research/cog/ license: http://opendatacommons.org/licenses/pddl/1.0 name: 'Clusters of Orthologous Groups of Proteins: Phylogenetic classification of proteins encoded in complete genomes' prefix: FAIRsharing.djsbw2 publications: - doi: 10.1126/science.278.5338.631 pubmed_id: 9381173 title: A genomic perspective on protein families. - doi: 10.1093/nar/gku1223 pubmed_id: 25428365 title: Expanded microbial genome coverage and improved protein family annotation in the COG database. subjects: - Life Science go: homepage: http://www.ncbi.nlm.nih.gov/COG/ name: NCBI COG cluster prefix: COG_Cluster uri_format: 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 publications: - doi: 10.1126/science.278.5338.631 pmc: null pubmed: '9381173' title: A genomic perspective on protein families. year: 1997 - doi: 10.1093/nar/gku1223 pmc: PMC4383993 pubmed: '25428365' title: Expanded microbial genome coverage and improved protein family annotation in the COG database. year: 2014 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/ keywords: - pathways 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 keywords: - clinical data - clinical trials - health - health sciences name: MIMIC III Database no_own_terms: true repository: https://github.com/MIT-LCP/mimic-omop col: bartoc: abbreviation: CoL description: 'The Catalogue of Life (CoL) is the nearest thing to a comprehensive catalogue of all known species of organisms on Earth. Continuous progress is made towards completion, and this edition contains 1,639,016 living and 5,763 extinct species. Please note that this is probably just over three quarters of the world''s known species. This means that for many groups it continues to be deficient, and users will notice that many species are still missing from the Catalogue. The present Catalogue is compiled with sectors provided by 157 taxonomic databases from around the world. Many of these contain taxonomic data and opinions from extensive networks of specialists, so that the complete work contains contributions from more than 3,000 specialists from throughout the taxonomic profession. Species 2000 and ITIS teams peer review databases, select appropriate sectors and integrate the sectors into a single coherent catalogue with a single hierarchical classification.' homepage: http://www.catalogueoflife.org/col/ name: Catalogue of Life prefix: '1915' wikidata_database: Q38840 mappings: bartoc: '1915' miriam: col miriam: deprecated: false description: Identifier of a taxon or synonym in the Catalogue of Life homepage: https://www.checklistbank.org id: 00000969 name: Catalogue of Life namespaceEmbeddedInLui: false pattern: ^[23456789BCDFGHJKLMNPQRSTVWXYZ]{1,6}$ prefix: col providers: - code: col description: The Catalogue of Life website providing a view onto the latest release of the COL Checklist. homepage: https://www.catalogueoflife.org name: Catalogue of Life (COL) uri_format: https://www.catalogueoflife.org/data/taxon/$1 sampleId: 4QHKG uri_format: https://www.checklistbank.org/dataset/3LR/taxon/$1 col.taiwan: contributor: email: meghan.balk@gmail.com github: megbalk name: Meghan Balk orcid: 0000-0003-2699-3066 description: Identifier (name code) for a taxon in the catalogue of life in taiwan example: '431472' github_request_issue: 466 homepage: http://taibnet.sinica.edu.tw/home.php mappings: wikidata: P3088 name: Catalogue of Life in Taiwan pattern: ^[1-9]\d{5}$ 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=$1 wikidata: database: Q26218155 description: identifier (name code) for a taxon in the Catalogue of Life in Taiwan example: - '421738' - '431472' homepage: https://taibnet.sinica.edu.tw/home.php name: Catalogue of Life in Taiwan ID pattern: ^([1-9]\d{5})$ prefix: P3088 uri_format: https://taibnet.sinica.edu.tw/eng/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: '2022-08-25' 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. domain: anatomy and development download.obo: http://purl.obolibrary.org/obo/colao.obo download.owl: http://purl.obolibrary.org/obo/colao.owl homepage: https://github.com/insect-morphology/colao license: CC BY 4.0 license.url: https://creativecommons.org/licenses/by/4.0/ name: Coleoptera Anatomy Ontology (COLAO) preferredPrefix: COLAO prefix: colao repository: https://github.com/insect-morphology/colao ols: description: The Coleoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of beetles in biodiversity research. download: 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 (COLAO) prefix: COLAO pattern: ^\d{7}$ collagenmutdb: mappings: prefixcommons: cmd prefixcommons: description: This database aims to record all published accounts of variants resulting in osteogenesis imperfecta. Such variants occur in the COL1A1, COL1A2, CRTAP, FKBP10, LEPRE1 and PPIB genes. example: COL3A1 homepage: http://www.le.ac.uk/genetics/collagen/ keywords: - gene name: Collagen Mutation Database pattern: ^[A-Z,0-9]+$ prefix: cmd uri_format: https://eds.gene.le.ac.uk/home.php?select_db=$1 provides: hgnc.symbol reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 colonatlas: cellosaurus: category: Cell line databases/resources homepage: http://www.coloncanceratlas.org name: Colorectal Cancer Atlas prefix: ColonAtlas uri_format: http://www.coloncanceratlas.org/search_cell_line?cell_line=$1 example: ALA mappings: cellosaurus: ColonAtlas 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: sed-ml.level-1.version-1 uri_format: https://github.com/combine-org/combine-specifications/blob/main/specifications/$1.md n2t: description: The 'COmputational Modeling in BIology' NEtwork (COMBINE) is an initiative to coordinate the development of the various community standards and formats for computational models, initially in Systems Biology and related fields. This collection pertains to specifications of the standard formats developed by the Computational Modeling in Biology Network. example: sbgn.er.level-1.version-1.2 homepage: https://co.mbine.org/standards/ name: COMBINE at EBI namespaceEmbeddedInLui: false pattern: ^\w+(\-|\.|\w)*$ prefix: combine.specifications uri_format: https://co.mbine.org/specifications/$1 come: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: COMe (Co-Ordination of Metals) at the EBI represents an ontology for bioinorganic and other small molecule centres in complex proteins, using a classification system based on the concept of a bioinorganic motif. example: MOL000160 homepage: https://www.flymine.org/come mappings: prefixcommons: come name: The Bioinorganic Motif Database prefixcommons: description: COMe is an attempt to classify metalloproteins and some other complex proteins using the concept of bioinorganic motif. example: BIM000347 homepage: http://www.flymine.org/come/ keywords: - protein name: COMe pattern: ^BIM\d+$ prefix: come uri_format: http://www.flymine.org/come/entry?gn=$1 uri_format: https://www.flymine.org/come/entry?gn=$1 commoncoreontology: contact: email: mpjensen@buffalo.edu github: mark-jensen name: Mark Jensen orcid: 0000-0001-9228-8838 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: 'The Common Core Ontologies (CCO) comprise twelve ontologies that are designed to represent and integrate taxonomies of generic classes and relations across all domains of interest. CCO is a mid-level extension of Basic Formal Ontology (BFO), an upper-level ontology framework widely used to structure and integrate ontologies in the biomedical domain (Arp, et al., 2015). BFO aims to represent the most generic categories of entity and the most generic types of relations that hold between them, by defining a small number of classes and relations. CCO then extends from BFO in the sense that every class in CCO is asserted to be a subclass of some class in BFO, and that CCO adopts the generic relations defined in BFO (e.g., has_part) (Smith and Grenon, 2004). Accordingly, CCO classes and relations are heavily constrained by the BFO framework, from which it inherits much of its basic semantic relationships.' example: DirectiveInformationContentEntity homepage: http://www.ontologyrepository.com keywords: - ontology - upper-level ontology license: CC-BY-4.0 name: Common Core Ontologies repository: https://github.com/CommonCoreOntology/CommonCoreOntologies uri_format: http://www.ontologyrepository.com/CommonCoreOntologies/$1 complexportal: biocontext: is_identifiers: true is_obo: false prefix: COMPLEXPORTAL uri_format: http://identifiers.org/complexportal/$1 biolink: is_identifiers: false is_obo: false prefix: ComplexPortal uri_format: https://www.ebi.ac.uk/complexportal/complex/$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/$1 mappings: biocontext: COMPLEXPORTAL biolink: ComplexPortal go: ComplexPortal miriam: complexportal n2t: complexportal re3data: r3d100013295 uniprot: DB-0228 wikidata: P7718 miriam: deprecated: false description: A database that describes manually curated macromolecular complexes and provides links to details about these complexes in other databases. homepage: https://www.ebi.ac.uk/complexportal id: '00000657' name: Complex Portal namespaceEmbeddedInLui: false pattern: ^CPX-[0-9]+$ prefix: complexportal sampleId: CPX-2158 uri_format: https://www.ebi.ac.uk/complexportal/complex/$1 n2t: description: A database that describes manually curated macromolecular complexes and provides links to details about these complexes in other databases. example: CPX-2158 homepage: https://www.ebi.ac.uk/complexportal name: Complex Portal namespaceEmbeddedInLui: false pattern: ^CPX-[0-9]+$ prefix: complexportal uri_format: https://www.ebi.ac.uk/complexportal/complex/$1 name: Complex Portal publications: - doi: 10.1093/nar/gku975 pmc: PMC4384031 pubmed: '25313161' title: The complex portal--an encyclopaedia of macromolecular complexes. year: 2014 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: abbreviation: ComplexPortal category: Protein-protein interaction databases homepage: https://www.ebi.ac.uk/complexportal/ name: ComplexPortal prefix: DB-0228 publications: - doi: 10.1093/nar/gku975 pubmed: '25313161' 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/$1 wikidata: database: Q54774134 description: DSSTox substance identifier (DTXSID) used in the Environmental Protection Agency CompTox Dashboard example: - DTXSID3039242 - DTXSID5020108 - DTXSID6046761 - DTXSID7020182 - DTXSID8031865 - DTXSID9020112 name: DSSTox substance ID pattern: ^DTXSID\d{7,9}$ prefix: P3117 uri_format: https://comptox.epa.gov/dashboard/chemical/details/$1 compulyeast: biocontext: is_identifiers: true is_obo: false prefix: COMPULYEAST uri_format: http://identifiers.org/compulyeast/$1 fairsharing: abbreviation: Compulyeast description: Compluyeast-2D-DB is a two-dimensional polyacrylamide gel electrophoresis federated database. This collection references a subset of Uniprot, and contains general information about the protein record. homepage: http://compluyeast2dpage.dacya.ucm.es license: http://opendatacommons.org/licenses/pddl/1.0 name: Compulyeast prefix: FAIRsharing.rbjs3e publications: [] subjects: [] mappings: biocontext: COMPULYEAST fairsharing: FAIRsharing.rbjs3e miriam: compulyeast n2t: compulyeast prefixcommons: compluyeast2dpage miriam: deprecated: false description: Compluyeast-2D-DB is a two-dimensional polyacrylamide gel electrophoresis federated database. This collection references a subset of Uniprot, and contains general information about the protein record. homepage: http://compluyeast2dpage.dacya.ucm.es/ id: 00000198 name: Compulyeast namespaceEmbeddedInLui: false pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$ 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=$1 name: Compluyeast-2D-DB prefixcommons: description: Compluyeast-2D-DB is a Two-dimensional polyacrilamide gel electrophoresis federated database built with the Make2DDB package and integrated at the WORLD-2DPAGE of the ExPASy proteomics web server. example: P20029 homepage: http://compluyeast2dpage.dacya.ucm.es/ keywords: - protein name: CompluYeast 2D-PAGE pattern: ^P\d+$ prefix: compluyeast2dpage uri_format: http://compluyeast2dpage.dacya.ucm.es/cgi-bin/2d/2d.cgi?ac=$1 provides: uniprot confident.event: contact: email: Philip.Stroemert@tib.eu github: StroemPhi name: "Philip Str\xF6mert" orcid: 0000-0002-1595-3213 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Confident makes descriptive metadata on conferences and other formats of scientific events permanently accessible in a high quality through automated processes and scientific data curating. example: 37af84f2-bfd7-4653-b608-eaff44febba6 github_request_issue: 519 homepage: https://www.confident-conference.org/index.php/Category:Event keywords: - conferences - meetings - metascience name: ConfIDent Event pattern: ^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$ 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 keywords: - conferences - grouping - meetings - metascience 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/$1 fairsharing: abbreviation: ConoServer contact: email: d.craik@imb.uq.edu.au name: David Craik orcid: 0000-0003-0007-6796 description: ConoServer is a database specializing in sequences and structures of peptides expressed by marine cone snails. The database gives access to protein sequences, nucleic acid sequences and structural information on conopeptides. ConoServer's data are first collected from the peer reviewed literature and from publicly available databases, including UniProtKB/Swiss-Prot, NCBI nucleotide (nt), and the World Wide Protein Data Bank. The data are then curated manually, which include the addition of references, the analysis of sequence regions, the identification of cysteine frameworks and gene superfamilies, and the identification of mature peptides in the precusor sequences. homepage: http://www.conoserver.org license: http://www.conoserver.org name: ConoServer prefix: FAIRsharing.y00hz4 publications: - doi: 10.1016/j.toxicon.2010.03.002 pubmed_id: 20211197 title: 'Conopeptide characterization and classifications: an analysis using ConoServer.' - doi: 10.1152/physrev.00020.2003 pubmed_id: 14715910 title: 'Conus venoms: a rich source of novel ion channel-targeted peptides.' - doi: 10.1021/cb700091j pubmed_id: 17649970 title: Chemical modification of conotoxins to improve stability and activity. - doi: 10.1093/bioinformatics/btm596 pubmed_id: 18065428 title: ConoServer, a database for conopeptide sequences and structures. subjects: - Neurophysiology - Statistics - Life Science - Synthetic Biology mappings: biocontext: CONOSERVER fairsharing: FAIRsharing.y00hz4 miriam: conoserver n2t: conoserver uniprot: DB-0156 miriam: deprecated: false description: ConoServer is a database specialized in the sequence and structures of conopeptides, which are peptides expressed by carnivorous marine cone snails. homepage: http://www.conoserver.org/ id: '00000254' name: Conoserver namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: conoserver sampleId: '2639' uri_format: http://www.conoserver.org/?page=card&table=protein&id=$1 n2t: description: ConoServer is a database specialized in the sequence and structures of conopeptides, which are peptides expressed by carnivorous marine cone snails. example: '2639' homepage: http://www.conoserver.org/ name: ConoServer at University of Queensland namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: conoserver uri_format: http://www.conoserver.org/?page=card&table=protein&id=$1 name: ConoServer publications: - doi: 10.1016/j.toxicon.2010.03.002 pmc: null pubmed: '20211197' title: 'Conopeptide characterization and classifications: an analysis using ConoServer.' year: 2010 - doi: 10.1093/bioinformatics/btm596 pmc: null pubmed: '18065428' title: ConoServer, a database for conopeptide sequences and structures. year: 2007 - doi: 10.1021/cb700091j pmc: null pubmed: '17649970' title: Chemical modification of conotoxins to improve stability and activity. year: 2007 - doi: 10.1152/physrev.00020.2003 pmc: null pubmed: '14715910' title: 'Conus venoms: a rich source of novel ion channel-targeted peptides.' year: 2004 uniprot: abbreviation: ConoServer category: Organism-specific databases homepage: http://www.conoserver.org/ name: ConoServer prefix: DB-0156 publications: - doi: 10.1093/bioinformatics/btm596 pubmed: '18065428' uri_format: http://www.conoserver.org/?page=card&table=protein&id=$1 conso: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: An ontology describing phenomena encountered in the literature surrounding neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, Huntington's disease, tauopathies, and related protein aggregation diseases. example: CONSO00010 homepage: https://pharmacome.github.io/conso/ keywords: - biology - life science - neurodegeneration - neuroscience - ontology name: Curation of Neurodegeneration Supporting Ontology pattern: ^CONSO\d{5}$ 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=$1 corrdb: fairsharing: abbreviation: CorrDB contact: email: zhu@iastate.edu name: Zhiliang Hu orcid: 0000-0002-6704-7538 description: A genetic correlation is the proportion of shared variance between two traits that is due to genetic causes; a phenotypic correlation is the degree to which two traits co-vary among individuals in a population. In the genomics era, while gene expression, genetic association, and network analysis provide unprecedented means to decode the genetic basis of complex phenotypes, it is important to recognize the possible effects genetic progress in one trait can have on other traits. This database is designed to collect all published livestock genetic/phenotypic trait correlation data, aimed at facilitating genetic network analysis or systems biology studies homepage: https://www.animalgenome.org/cgi-bin/CorrDB/index name: Animal Trait Correlation Database prefix: FAIRsharing.IziuCK publications: [] subjects: - Animal Genetics - Genetics - Life Science - Systems Biology mappings: fairsharing: FAIRsharing.IziuCK miriam: corrdb re3data: r3d100011496 miriam: deprecated: false description: A genetic correlation is the proportion of shared variance between two traits that is due to genetic causes; a phenotypic correlation is the degree to which two traits co-vary among individuals in a population. In the genomics era, while gene expression, genetic association, and network analysis provide unprecedented means to decode the genetic basis of complex phenotypes, it is important to recognize the possible effects genetic progress in one trait can have on other traits. This database is designed to collect all published livestock genetic/phenotypic trait correlation data, aimed at facilitating genetic network analysis or systems biology studies. homepage: https://www.animalgenome.org id: 00000831 name: CorrDB namespaceEmbeddedInLui: false pattern: ^[0-9]+$ prefix: corrdb sampleId: '37232' uri_format: https://www.animalgenome.org/CorrDB/q/?id=CorrID:$1 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 contact: email: andreas.ruepp@helmholtz-muenchen.de name: Andreas Ruepp orcid: 0000-0003-1705-3515 description: CORUM is a database that provides a manually curated repository of experimentally characterized protein complexes from mammalian organisms, mainly human (64%), mouse (16%) and rat (12%). Each protein complex is described by a protein complex name, subunit composition, function as well as the literature reference that characterizes the respective protein complex. homepage: https://mips.helmholtz-muenchen.de/corum/ name: ' Comprehensive Resource of Mammalian protein complexes' prefix: FAIRsharing.ohbpNw publications: - doi: 10.1093/nar/gky973 pubmed_id: 30357367 title: 'CORUM: the comprehensive resource of mammalian protein complexes-2019.' subjects: - Bioinformatics - Biology go: homepage: https://mips.helmholtz-muenchen.de/corum/ name: CORUM - the Comprehensive Resource of Mammalian protein complexes prefix: CORUM uri_format: https://mips.helmholtz-muenchen.de/corum/?id=$1 mappings: biocontext: CORUM fairsharing: FAIRsharing.ohbpNw go: CORUM miriam: corum n2t: corum prefixcommons: corum uniprot: DB-0224 miriam: deprecated: false description: The CORUM database provides a resource of manually annotated protein complexes from mammalian organisms. Annotation includes protein complex function, localization, subunit composition, literature references and more. All information is obtained from individual experiments published in scientific articles, data from high-throughput experiments is excluded. homepage: https://mips.helmholtz-muenchen.de/genre/proj/corum/ id: '00000440' name: CORUM namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: corum sampleId: '100' uri_format: https://mips.helmholtz-muenchen.de/corum/?id=$1 n2t: description: The CORUM database provides a resource of manually annotated protein complexes from mammalian organisms. Annotation includes protein complex function, localization, subunit composition, literature references and more. All information is obtained from individual experiments published in scientific articles, data from high-throughput experiments is excluded. example: '100' homepage: https://mips.helmholtz-muenchen.de/genre/proj/corum/ name: CORUM at Institute for Bioinformatics and Systems Biology (Germany) namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: corum uri_format: https://mips.helmholtz-muenchen.de/corum/?id=$1 name: Comprehensive Resource of Mammalian protein complexes prefixcommons: description: The CORUM database provides a resource of manually annotated protein complexes from mammalian organisms. Annotation includes protein complex function, localization, subunit composition, literature references and more. example: '56' homepage: http://mips.gsf.de/genre/proj/corum keywords: - protein name: the Comprehensive Resource of Mammalian protein complexes pattern: ^\d+$ prefix: corum uri_format: http://mips.helmholtz-muenchen.de/genre/proj/corum/complexdetails.html?id=$1 publications: - doi: 10.1093/nar/gky973 pmc: PMC6323970 pubmed: '30357367' title: 'CORUM: the comprehensive resource of mammalian protein complexes-2019.' year: 2019 uniprot: abbreviation: CORUM category: Protein-protein interaction databases homepage: http://mips.helmholtz-muenchen.de/corum/ name: CORUM comprehensive resource of mammalian protein complexes prefix: DB-0224 publications: - doi: 10.1093/nar/gky973 pubmed: '30357367' 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=$1 edam: description: Identifier of a COSMIC database entry. name: COSMIC obsolete: false prefix: '3264' fairsharing: abbreviation: COSMIC description: The Catalogue of Somatic Mutations in Cancer (COSMIC) is a database of manually-curated somatic mutation information relating to human cancers. The COSMIC database combines manually-curated data and genome-wide screen data. homepage: http://cancer.sanger.ac.uk name: Catalogue of Somatic Mutations in Cancer prefix: FAIRsharing.s5zmbp publications: - doi: 10.1093/nar/gku1075 pubmed_id: 25355519 title: 'COSMIC: exploring the world''s knowledge of somatic mutations in human cancer.' - doi: 10.1093/nar/gkq929 pubmed_id: 20952405 title: 'COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer.' - doi: 10.1038/sj.bjc.6601894 pubmed_id: 15188009 title: The COSMIC (Catalogue of Somatic Mutations in Cancer) database and website. - doi: 10.1093/nar/gky1015 pubmed_id: 30371878 title: 'COSMIC: the Catalogue Of Somatic Mutations In Cancer.' subjects: - Genetics - Biomedical Science mappings: biocontext: COSMIC cellosaurus: Cosmic edam: '3264' fairsharing: FAIRsharing.s5zmbp miriam: cosmic n2t: cosmic miriam: deprecated: false description: COSMIC is a comprehensive global resource for information on somatic mutations in human cancer, combining curation of the scientific literature with tumor resequencing data from the Cancer Genome Project at the Sanger Institute, U.K. This collection references genes. homepage: http://cancer.sanger.ac.uk/cosmic/ id: '00000601' name: COSMIC Gene namespaceEmbeddedInLui: false pattern: ^[A-Z0-9]+$ 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 publications: - doi: 10.1093/nar/gky1015 pmc: PMC6323903 pubmed: '30371878' title: 'COSMIC: the Catalogue Of Somatic Mutations In Cancer.' year: 2019 - doi: 10.1093/nar/gku1075 pmc: PMC4383913 pubmed: '25355519' title: 'COSMIC: exploring the world''s knowledge of somatic mutations in human cancer.' year: 2014 - doi: 10.1093/nar/gkq929 pmc: PMC3013785 pubmed: '20952405' title: 'COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer.' year: 2010 - doi: 10.1038/sj.bjc.6601894 pmc: PMC2409828 pubmed: '15188009' title: The COSMIC (Catalogue of Somatic Mutations in Cancer) database and website. year: 2004 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/$1 covoc: contact: email: zmp@ebi.ac.uk github: zoependlington name: "Zo\xEB May Pendlington" orcid: 0000-0002-4071-8397 download_json: https://github.com/EBISPOT/covoc/releases/download/current/covoc.json download_obo: https://github.com/EBISPOT/covoc/releases/download/current/covoc.obo download_owl: https://github.com/EBISPOT/covoc/releases/download/current/covoc.owl example: '0010034' homepage: https://github.com/EBISPOT/covoc mappings: ols: covoc ols: description: The COVID-19 Vocabulary (COVoc) is an ontology containing terms related to the research of the COVID-19 pandemic. This includes host organisms, pathogenicity, gene and gene products, barrier gestures, treatments and more. download: https://github.com/EBISPOT/covoc/releases/download/current/covoc.owl homepage: https://github.com/EBISPOT/covoc name: CoVoc Coronavirus Vocabulary prefix: covoc version: '2020-08-28' version.iri: http://purl.obolibrary.org/obo/covoc/releases/2020-08-28/covoc.owl pattern: ^\d{7}$ 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/$1 fairsharing: abbreviation: CPC description: The Climate Prediction Center (CPC) produces operational predictions of climate variability, real-time monitoring of climate and the required data bases, and assessments of the origins of major climate anomalies. These cover time scales from a week to seasons, extending into the future as far as technically feasible, and cover the land, the ocean, and the atmosphere, extending into the stratosphere. homepage: https://www.cpc.ncep.noaa.gov/ name: Climate Prediction Center prefix: FAIRsharing.e08886 publications: [] subjects: - Hydrogeology - Geography - Meteorology - Geodesy - Earth Science - Atmospheric Science mappings: biocontext: CPC fairsharing: FAIRsharing.e08886 miriam: cpc n2t: cpc miriam: deprecated: false description: The Cooperative Patent Classification (CPC) is a patent classification system, developed jointly by the European Patent Office (EPO) and the United States Patent and Trademark Office (USPTO). It is based on the previous European classification system (ECLA), which itself was a version of the International Patent Classification (IPC) system. The CPC patent classification system has been used by EPO and USPTO since 1st January, 2013. homepage: https://worldwide.espacenet.com/classification id: 00000539 name: Cooperative Patent Classification namespaceEmbeddedInLui: false pattern: ^([A-H,Y]|[A-H, Y]\d{2}|[A-H, Y]\d{2}[A-Z]|[A-H, Y]\d{2}[A-Z]\d{1,3}|[A-H, Y]\d{2}[A-Z]\d{1,3}(\/)?\d{2,})$ prefix: cpc sampleId: A01M1/026 uri_format: https://worldwide.espacenet.com/classification?locale=en_EP#!/CPC=$1 n2t: description: The Cooperative Patent Classification (CPC) is a patent classification system, developed jointly by the European Patent Office (EPO) and the United States Patent and Trademark Office (USPTO). It is based on the previous European classification system (ECLA), which itself was a version of the International Patent Classification (IPC) system. The CPC patent classification system has been used by EPO and USPTO since 1st January, 2013. example: A01M1/026 homepage: https://worldwide.espacenet.com/classification name: Cooperative Patent Classification at Espace namespaceEmbeddedInLui: false pattern: ^([A-H,Y]|[A-H, Y]\d{2}|[A-H, Y]\d{2}[A-Z]|[A-H, Y]\d{2}[A-Z]\d{1,3}|[A-H, Y]\d{2}[A-Z]\d{1,3}(\/)?\d{2,})$ prefix: cpc uri_format: https://worldwide.espacenet.com/classification?locale=en_EP#!/CPC=$1 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/$1 bioportal: contact: email: Intellectual.PropertyServices@ama-assn.org name: American Medical Association description: CPT is a list of descriptive terms and identifying numeric codes for medical services and procedures that are provided by physicians and health care professionals. homepage: https://www.ama-assn.org/practice-management/cpt-current-procedural-terminology name: CPT - Current Procedural Terminology prefix: CPT version: 2020AB contributor: email: null github: sierra-moxon name: Sierra Moxon orcid: 0000-0002-8719-7760 contributor_extras: - email: null github: colleenXu name: Colleen Xu orcid: 0000-0003-2975-882X description: "Current Procedural Terminology, more commonly known as CPT\xAE, refers\ \ to a medical code set created and maintained by the American Medical Association\ \ \u2014 and used by physicians, allied health professionals, nonphysician practitioners,\ \ hospitals, outpatient facilities, and laboratories to represent the services\ \ and procedures they perform. No provider of outpatient services gets paid without\ \ reporting the proper CPT\xAE codes. [Description taken from this site](https://www.aapc.com/codes/cpt-codes-range/)]" example: '00103' fairsharing: abbreviation: CPT description: Current Procedural Terminology is a medical nomenclature used to report medical procedures and services under public and private health insurance programs. homepage: http://www.ama-assn.org/go/cpt name: Current Procedural Terminology prefix: FAIRsharing.wpxab1 publications: - doi: 10.1136/neurintsurg-2014-011156 pubmed_id: 24589819 title: Current procedural terminology; a primer. - doi: 10.1016/j.jacr.2007.10.004 pubmed_id: 18359442 title: 'CPT: an open system that describes all that you do.' subjects: - Medicine - Health Science - Biomedical Science github_request_issue: 357 homepage: https://www.aapc.com mappings: aberowl: CPT biolink: CPT bioportal: CPT fairsharing: FAIRsharing.wpxab1 name: Current Procedural Terminology pattern: ^\d+$ publications: - doi: 10.1136/neurintsurg-2014-011156 pmc: null pubmed: '24589819' title: Current procedural terminology; a primer. year: 2014 - doi: 10.1016/j.jacr.2007.10.004 pmc: null pubmed: '18359442' title: 'CPT: an open system that describes all that you do.' year: 2008 references: - https://github.com/biopragmatics/bioregistry/pull/358 - https://github.com/biolink/biolink-model/pull/993 reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 synonyms: - ama-cpt uri_format: https://www.aapc.com/codes/cpt-codes/$1 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 fairsharing: abbreviation: CRediT contact: email: info@casrai.org name: Liz Allen orcid: 0000-0002-9298-3168 description: "CRediT (Contributor Roles Taxonomy) is a high-level taxonomy, including\ \ 14 roles, that can be used to represent the roles typically played by contributors\ \ to scientific scholarly output. The roles describe each contributor\u2019\ s specific contribution to the scholarly output." homepage: https://doi.org/10.3789/ansi.niso.z39.104-2022 license: https://creativecommons.org/licenses/by-nd/2.0/uk name: Contributor Roles Taxonomy prefix: FAIRsharing.fe4816 publications: - doi: 10.1038/508312a pubmed_id: null title: 'Publishing: Credit where credit is due' - doi: 10.3789/ansi.niso.z39.104-2022 pubmed_id: null title: ANSI/NISO Z39.104-2022, CRediT, Contributor Roles Taxonomy - doi: 10.1002/leap.1210 pubmed_id: null title: How can we ensure visibility and diversity in research contributions? How the Contributor Role Taxonomy (CRediT) is helping the shift from authorship to contributorship - doi: 10.1087/20150211 pubmed_id: null title: 'Beyond authorship: attribution, contribution, collaboration, and credit' - doi: 10.1038/d41586-019-01715-4 pubmed_id: null title: Credit data generators for data reuse subjects: - Data Quality - Subject Agnostic - Ontology and Terminology twitter: contrib_roles homepage: https://casrai.org/credit/ mappings: fairsharing: FAIRsharing.fe4816 name: CASRAI Contributor Roles Taxonomy publications: - doi: 10.1038/d41586-019-01715-4 pmc: null pubmed: '31164773' title: Credit data generators for data reuse. year: 2019 - doi: 10.1038/508312a pmc: null pubmed: '24745070' title: 'Publishing: Credit where credit is due.' year: 2014 - doi: 10.3789/ansi.niso.z39.104-2022 pmc: null pubmed: null title: ANSI/NISO Z39.104-2022, CRediT, Contributor Roles Taxonomy year: null - doi: 10.1087/20150211 pmc: null pubmed: null title: 'Beyond authorship: attribution, contribution, collaboration, and credit' year: 2015 - doi: 10.1002/leap.1210 pmc: null pubmed: null title: How can we ensure visibility and diversity in research contributions? How the Contributor Role Taxonomy (CRediT) is helping the shift from authorship to contributorship year: 2019 crisprdb: biocontext: is_identifiers: true is_obo: false prefix: CRISPRDB uri_format: http://identifiers.org/crisprdb/$1 fairsharing: abbreviation: CRISPRdb contact: email: Christine.Pourcel@u-psud.fr name: Christine Pourcel orcid: 0000-0002-8951-466X description: CRISPRdb acts as a gateway to a publicly accessible database and software. It enables the easy detection of CRISPR sequences in locally-produced data and the consultation of CRISPR sequence data present in the database. It also gives information on the presence of CRISPR-associated (cas) genes when they have been annotated as such. homepage: http://crispr.i2bc.paris-saclay.fr/ name: CRISPRdb prefix: FAIRsharing.7sfedh publications: - doi: 10.1186/1471-2105-8-172 pubmed_id: 17521438 title: The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats. - doi: 10.1093/nar/gkm360 pubmed_id: 17537822 title: 'CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats.' - doi: 10.1093/nar/gkn228 pubmed_id: 18442988 title: 'CRISPRcompar: a website to compare clustered regularly interspaced short palindromic repeats.' subjects: - Life Science mappings: biocontext: CRISPRDB fairsharing: FAIRsharing.7sfedh miriam: crisprdb n2t: crisprdb miriam: deprecated: false description: Repeated CRISPR ("clustered regularly interspaced short palindromic repeats") elements found in archaebacteria and eubacteria are believed to defend against viral infection, potentially targeting invading DNA for degradation. CRISPRdb is a database that stores information on CRISPRs that are automatically extracted from newly released genome sequence data. homepage: http://crispr.i2bc.paris-saclay.fr/ id: '00000626' name: CRISPRdb namespaceEmbeddedInLui: false pattern: ^[0-9]+$ 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 publications: - doi: 10.1093/nar/gkn228 pmc: PMC2447796 pubmed: '18442988' title: 'CRISPRcompar: a website to compare clustered regularly interspaced short palindromic repeats.' year: 2008 - doi: 10.1093/nar/gkm360 pmc: PMC1933234 pubmed: '17537822' title: 'CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats.' year: 2007 - doi: 10.1186/1471-2105-8-172 pmc: PMC1892036 pubmed: '17521438' title: The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats. year: 2007 cro: aberowl: description: A classification of the diverse roles performed in the work leading to a published research output in the sciences. Its purpose to provide transparency in contributions to scholarly published work, to enable improved systems of attribution, credit, and accountability. download_owl: http://aber-owl.net/media/ontologies/CRO/5/cro.owl homepage: https://github.com/data2health/contributor-role-ontology name: Contributor Role Ontology prefix: CRO biocontext: 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. domain: information download.owl: http://purl.obolibrary.org/obo/cro.owl homepage: https://github.com/data2health/contributor-role-ontology license: CC BY 2.0 license.url: https://creativecommons.org/licenses/by/2.0/ name: Contributor Role Ontology preferredPrefix: CRO prefix: cro repository: https://github.com/data2health/contributor-role-ontology ols: description: A classification of the diverse roles performed in the work leading to a published research output in the sciences. Its purpose to provide transparency in contributions to scholarly published work, to enable improved systems of attribution, credit, and accountability. download: 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/$1 cryoem: aberowl: description: Ontology that describes data types and image processing operations in Cryo Electron Microscopy of Single Particles download_owl: http://aber-owl.net/media/ontologies/CRYOEM/4/cryoem.owl homepage: http://scipion.i2pc.es/ontology/cryoem name: Cryo Electron Microscopy prefix: CRYOEM version: '2021-03-09' bioportal: contact: email: coss@cnb.csic.es name: Carlos Oscar Sorzano description: Ontology that describes data types and image processing operations in Cryo Electron Microscopy of Single Particles homepage: http://scipion.i2pc.es/ontology/cryoem name: Cryo Electron Microscopy prefix: CRYOEM version: '2021-03-09' example: '0000052' fairsharing: abbreviation: CryoEM contact: email: coss@cnb.csic.es name: Carlos Oscar S. Sorzano orcid: 0000-0002-9473-283X description: The CryoEM Ontology for describing objects and workflows in Single Particle Analysis by Cryo Electron Microscopy. homepage: http://scipion.i2pc.es/ontology/cryoem license: CC-BY-3.0 name: CryoEM Ontology prefix: FAIRsharing.q47I0t publications: [] subjects: - Structural Biology mappings: aberowl: CRYOEM bioportal: CRYOEM fairsharing: FAIRsharing.q47I0t ols: cryoem ols: contact: isanchez@cnb.csic.es description: Ontology that describes data types and image processing operations in Cryo Electron Microscopy of Single Particles download: http://scipion.i2pc.es/ontology/cryoem.owl homepage: http://scipion.i2pc.es/ontology/cryoem name: Cryo Electron Microscopy ontology prefix: cryoem version: '2021-03-09' version.iri: http://scipion.i2pc.es/ontology/cryoem/releases/2021-03-09/cryoem.owl pattern: ^\d{7}$ 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 contact: email: jkissing@uga.edu name: Jessica Kissinger orcid: 0000-0003-4446-6200 description: CryptoDB serves as the functional genomics database for Cryptosporidium and related species. CryptoDB is a free, online resource for accessing and exploring genome sequence and annotation, functional genomics data, isolate sequences, and orthology profiles across organisms. It also includes supplemental bioinformatics analyses and a web interface for data-mining. homepage: https://cryptodb.org/cryptodb/app name: CryptoDB prefix: FAIRsharing.t3nprm publications: - doi: 10.1093/nar/gkj078 pubmed_id: 16381902 title: 'CryptoDB: a Cryptosporidium bioinformatics resource update.' - doi: 10.1007/978-1-4939-9748-0_10 pubmed_id: 31452162 title: Accessing Cryptosporidium Omic and Isolate Data via CryptoDB.org. subjects: - Functional Genomics - Genomics - Parasitology twitter: VEuPathDB 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: 10.1007/978-1-4939-9748-0_10 pmc: null pubmed: '31452162' title: Accessing Cryptosporidium Omic and Isolate Data via CryptoDB.org. year: 2020 - doi: 10.1093/nar/gkj078 pmc: PMC1347441 pubmed: '16381902' title: 'CryptoDB: a Cryptosporidium bioinformatics resource update.' year: 2006 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/$1 fairsharing: abbreviation: CSA contact: email: nickf@ebi.ac.uk name: Nicholas Furnham orcid: 0000-0002-7532-1269 description: The Catalytic Site Atlas (CSA) is a database documenting enzyme active sites and catalytic residues in enzymes of 3D structure. It uses a defined classification for catalytic residues which includes only those residues thought to be directly involved in some aspect of the reaction catalysed by an enzyme. homepage: http://www.ebi.ac.uk/thornton-srv/databases/CSA/ license: http://opendatacommons.org/licenses/pddl/1.0 name: Catalytic Site Atlas prefix: FAIRsharing.2ajtcf publications: - doi: 10.1093/nar/gkh028 pubmed_id: 14681376 title: 'The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data.' - doi: 10.1093/nar/gkt1243 pubmed_id: 24319146 title: 'The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues identified in enzymes.' subjects: - Life Science mappings: biocontext: CSA fairsharing: FAIRsharing.2ajtcf miriam: csa n2t: csa prefixcommons: csa miriam: deprecated: false description: The Catalytic Site Atlas (CSA) is a database documenting enzyme active sites and catalytic residues in enzymes of 3D structure. It uses a defined classification for catalytic residues which includes only those residues thought to be directly involved in some aspect of the reaction catalysed by an enzyme. homepage: https://www.ebi.ac.uk/thornton-srv/databases/CSA/ id: '00000144' name: CSA namespaceEmbeddedInLui: false pattern: ^[0-9][A-Za-z0-9]{3}$ 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=$1 publications: - doi: 10.1093/nar/gkt1243 pmc: PMC3964973 pubmed: '24319146' title: 'The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues identified in enzymes.' year: 2013 - doi: 10.1093/nar/gkh028 pmc: PMC308762 pubmed: '14681376' title: 'The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data.' year: 2004 csd: fairsharing: abbreviation: CSD contact: email: support@ccdc.cam.ac.uk name: Support Email orcid: 0000-0002-6062-7492 description: Established in 1965, the Cambridge Structural Database (CSD) is the a repository for small-molecule organic and metal-organic crystal 3D structures. Database records are automatically checked and manually curated by one of our expert in-house scientific editors. Every structure is enriched with chemical representations, as well as bibliographic, chemical and physical property information, adding further value to the raw structural data. homepage: http://www.ccdc.cam.ac.uk/solutions/csd-system/components/csd/ license: https://www.ccdc.cam.ac.uk/access-structures-terms name: The Cambridge Structural Database prefix: FAIRsharing.vs7865 publications: - doi: 10.1107/S0108768102003890 pubmed_id: 12037359 title: 'The Cambridge Structural Database: a quarter of a million crystal structures and rising' - doi: 10.1107/S2052520616003954 pubmed_id: 27048719 title: The Cambridge Structural Database. subjects: - Organic Chemistry - Biochemistry - Organic Molecular Chemistry - Chemistry twitter: ccdc_cambridge mappings: fairsharing: FAIRsharing.vs7865 miriam: csd re3data: r3d100010197 miriam: deprecated: false description: The Cambridge Stuctural Database (CSD) is the world's most comprehensive collection of small-molecule crystal structures. Entries curated into the CSD are identified by a CSD Refcode. homepage: https://www.ccdc.cam.ac.uk/ id: 00000820 name: Cambridge Structural Database namespaceEmbeddedInLui: false pattern: ^[A-Z]{6}(\d{2})?$ prefix: csd sampleId: PELNAW uri_format: https://www.ccdc.cam.ac.uk/services/structures?pid=csd:$1&sid=IDORG publications: - doi: 10.1107/s2052520616003954 pmc: PMC4822653 pubmed: '27048719' title: The Cambridge Structural Database. year: 2016 - doi: 10.1107/s0108768102003890 pmc: null pubmed: '12037359' title: 'The Cambridge Structural Database: a quarter of a million crystal structures and rising.' year: 2002 re3data: description: "Established in 1965, the CSD is the world\u2019s repository for\ \ small-molecule organic and metal-organic crystal structures. Containing the\ \ results of over one million x-ray and neutron diffraction analyses this unique\ \ database of accurate 3D structures has become an essential resource to scientists\ \ around the world. The CSD records bibliographic, chemical and crystallographic\ \ information for:organic molecules, metal-organic compounds whose 3D structures\ \ have been determined using X-ray diffraction, neutron diffraction. The CSD\ \ records results of: single crystal studies, powder diffraction studies which\ \ yield 3D atomic coordinate data for at least all non-H atoms. In some cases\ \ the CCDC is unable to obtain coordinates, and incomplete entries are archived\ \ to the CSD. \nThe CSD includes crystal structure data arising from: publications\ \ in the open literature and Private Communications to the CSD (via direct data\ \ deposition). \nThe CSD contains directly deposited data that are not available\ \ anywhere else, known as CSD Communications." homepage: https://www.ccdc.cam.ac.uk/solutions/csd-system/components/csd/ name: The Cambridge Structural Database prefix: r3d100010197 synonyms: - CSD - Cambridge Crystallographic Data Centre xrefs: fairsharing: FAIRsharing.vs7865 nif: 0000-00174 scr: '007310' 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: 2022AB deprecated: true example: 2004-2820 fairsharing: abbreviation: CRISP description: CRISP is a terminology used for indexing biomedical information. CRISP contains over 8,000 preferred terms that are grouped hierarchically into 11 domains. homepage: http://bioportal.bioontology.org/ontologies/1526 name: Computer Retrieval of Information on Scientific Projects Thesaurus prefix: FAIRsharing.1evfpc publications: - doi: null pubmed_id: 8718842 title: Taking a bite out of CRISP. Strategies on using and conducting searches in the Computer Retrieval of Information on Scientific Projects database. subjects: - Anatomy - Social Science - Medicine - Chemical Biology - Biomedical Science - Biology hl7: description: 'Computer Retrieval of Information on Scientific Projects (CRISP). Bethesda (MD): National Institutes of Health, Division of Research Grants, Research Documentation Section, 2004. http://crisp.cit.nih.gov/The CRISP system has been replaced by the RePORT Expenditures and Results (RePORTER) query tool.' homepage: http://www.nih.gov/ name: CRISP Thesaurus organization: National Institutes of Health preferred_prefix: csp prefix: 2.16.840.1.113883.6.120 status: Complete homepage: https://web.archive.org/web/20091223034048/http://crisp.cit.nih.gov/Thesaurus/index.htm mappings: aberowl: CRISP bioportal: CRISP fairsharing: FAIRsharing.1evfpc hl7: 2.16.840.1.113883.6.120 name: Computer Retrieval of Information on Science Projects Thesaurus publications: - doi: null pmc: null pubmed: '8718842' title: Taking a bite out of CRISP. Strategies on using and conducting searches in the Computer Retrieval of Information on Scientific Projects database. year: 1996 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/$1 fairsharing: abbreviation: CST description: A small pathway portal for showcasing Cell Signaling Technology phospho-antibody products. Contains pathway diagrams that are clickable and link to more information about each protein and the commercial products that are available for that protein. homepage: http://www.cellsignal.com/ name: Cell Signaling Technology Pathway Database prefix: FAIRsharing.n8pxvx publications: [] subjects: - Life Science - Biomedical Science hl7: description: COSTART name: CST preferred_prefix: CST prefix: 2.16.840.1.113883.6.62 status: Pending mappings: biocontext: CST fairsharing: FAIRsharing.n8pxvx hl7: 2.16.840.1.113883.6.62 miriam: cst n2t: cst miriam: deprecated: false description: Cell Signaling Technology is a commercial organisation which provides a pathway portal to showcase their phospho-antibody products. This collection references pathways. homepage: http://www.cellsignal.com/pathways/index.html id: 00000429 name: Cell Signaling Technology Pathways namespaceEmbeddedInLui: false pattern: ^[A-Za-z0-9_-]+$ 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=$1 mappings: biocontext: CTD.GENE biolink: CTD.GENE miriam: ctd.gene n2t: ctd.gene uniprot: DB-0140 miriam: deprecated: false description: The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences. homepage: http://ctdbase.org/ id: '00000100' name: CTD Gene namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: ctd.gene sampleId: '101' uri_format: http://ctdbase.org/detail.go?type=gene&acc=$1 n2t: description: The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences. example: '101' homepage: http://ctdbase.org/ name: Comparative Toxicogenomics Database (Gene) namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: ctd.gene uri_format: http://ctdbase.org/detail.go?type=gene&acc=$1 part_of: ctd provides: ncbigene publications: - doi: 10.1093/nar/gkaa891 pmc: PMC7779006 pubmed: '33068428' title: 'Comparative Toxicogenomics Database (CTD): update 2021.' year: 2021 uniprot: abbreviation: CTD category: Organism-specific databases homepage: https://ctdbase.org/ name: Comparative Toxicogenomics Database prefix: DB-0140 publications: - doi: 10.1093/nar/gkaa891 pubmed: '33068428' uri_format: https://ctdbase.org/detail.go?type=gene&db=GENE&acc=$1 cteno: aberowl: description: An anatomical and developmental ontology for ctenophores (Comb Jellies) download_owl: http://aber-owl.net/media/ontologies/CTENO/2/cteno.owl homepage: https://github.com/obophenotype/ctenophore-ontology name: Ctenophore Ontology prefix: CTENO biocontext: is_identifiers: false is_obo: true prefix: CTENO uri_format: http://purl.obolibrary.org/obo/CTENO_$1 bioportal: contact: email: cjmungall@lbl.gov name: Chris Mungall description: An anatomical and developmental ontology for ctenophores (Comb Jellies) homepage: https://github.com/obophenotype/ctenophore-ontology name: Ctenophore Ontology prefix: CTENO download_obo: https://raw.githubusercontent.com/obophenotype/ctenophore-ontology/master/cteno.obo example: '0000047' fairsharing: abbreviation: CTENO description: An anatomical and developmental ontology for ctenophores (Comb Jellies). Please note that, while available, this ontology has not been updated since 2016. homepage: https://github.com/obophenotype/ctenophore-ontology license: CC-BY-3.0 name: Ctenophore Ontology prefix: FAIRsharing.mgxgza publications: [] subjects: - Anatomy - Developmental Biology mappings: aberowl: CTENO biocontext: CTENO bioportal: CTENO fairsharing: FAIRsharing.mgxgza obofoundry: cteno ols: cteno ontobee: CTENO obofoundry: contact: cjmungall@lbl.gov contact.github: cmungall contact.label: Chris Mungall contact.orcid: 0000-0002-6601-2165 depends_on: - ro - uberon deprecated: false description: An anatomical and developmental ontology for ctenophores (Comb Jellies) domain: anatomy and development download.owl: http://purl.obolibrary.org/obo/cteno.owl homepage: https://github.com/obophenotype/ctenophore-ontology license: CC BY 3.0 license.url: http://creativecommons.org/licenses/by/3.0/ name: Ctenophore Ontology preferredPrefix: CTENO prefix: cteno repository: https://github.com/obophenotype/ctenophore-ontology ols: description: An anatomical and developmental ontology for ctenophores (Comb Jellies) download: http://purl.obolibrary.org/obo/cteno.owl homepage: https://github.com/obophenotype/ctenophore-ontology name: Ctenophore Ontology prefix: cteno version: '2016-10-19' version.iri: http://purl.obolibrary.org/obo/cteno/releases/2016-10-19/cteno.owl ontobee: library: Library name: Ctenophore Ontology prefix: CTENO pattern: ^\d{7}$ 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: 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 contact: email: erfan.younesi@scai.fraunhofer.de name: Dr. Erfan Younesi orcid: 0000-0001-8793-2692 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). homepage: http://bioportal.bioontology.org/ontologies/CTO 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. domain: health download.owl: http://purl.obolibrary.org/obo/cto.owl homepage: https://github.com/ClinicalTrialOntology/CTO/ license: CC BY 4.0 license.url: http://creativecommons.org/licenses/by/4.0/ name: 'CTO: Core Ontology of Clinical Trials' preferredPrefix: CTO prefix: cto repository: https://github.com/ClinicalTrialOntology/CTO ols: description: The core Ontology of Clinical Trials (CTO) will serve as a structured resource integrating basic terms and concepts in the context of clinical trials. Thereby covering clinicaltrails.gov. CoreCTO will serve as a basic ontology to generate extended versions for specific applications such as annotation of variables in study documents from clinical trials. download: http://purl.obolibrary.org/obo/cto.owl homepage: https://github.com/BFO-ontology/BFO name: 'CTO: Core Ontology of Clinical Trials' prefix: cto version: 1.0.0 ontobee: library: Library name: 'CTO: Core Ontology of Clinical Trials' prefix: CTO pattern: ^\d{7}$ 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/$1/ cutg: mappings: prefixcommons: cutg prefixcommons: description: Codon usage in individual genes has been calculated using the nucleotide sequence data obtained from the GenBank Genetic Sequence Database. The compilation of codon usage is synchronized with each major release of GenBank. example: '9606' homepage: http://www.kazusa.or.jp/codon/ keywords: - gene - DNA name: Codon Usage Tabulated from GenBank pattern: ^\d+$ prefix: cutg uri_format: http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=$1 provides: ncbitaxon reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 cvdo: aberowl: description: An ontology to describe entities related to cardiovascular diseases download_owl: http://aber-owl.net/media/ontologies/CVDO/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). homepage: https://github.com/OpenLHS/CVDO license: CC-BY-4.0 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 domain: health download.owl: http://purl.obolibrary.org/obo/cvdo.owl homepage: https://github.com/OpenLHS/CVDO license: CC BY 4.0 license.url: https://creativecommons.org/licenses/by/4.0/ name: Cardiovascular Disease Ontology preferredPrefix: CVDO prefix: cvdo repository: https://github.com/OpenLHS/CVDO ols: description: An ontology to describe entities related to cardiovascular diseases download: 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=$1 dandi: fairsharing: abbreviation: DANDI contact: email: yoh@dartmouth.edu name: Yaroslav Halchenko orcid: 0000-0003-3456-2493 description: The Distributed Archives for Neurophysiology Data Integration (DANDI) is a platform for publishing, sharing, and processing neurophysiology data funded by the BRAIN Initiative. The archive accepts cellular neurophysiology data including electrophysiology, optophysiology, and behavioral time-series, and images from immunostaining experiments. homepage: https://www.dandiarchive.org license: CC0-1.0 name: Distributed Archives for Neurophysiology Data Integration prefix: FAIRsharing.f2c119 publications: [] repository: https://github.com/dandi/dandiarchive subjects: - Neurophysiology twitter: dandiarchive mappings: fairsharing: FAIRsharing.f2c119 miriam: dandi re3data: r3d100013638 miriam: deprecated: false description: 'DANDI works with BICCN and other BRAIN Initiative awardees to curate data using community data standards such as NWB and BIDS, and to make data and software for cellular neurophysiology FAIR (Findable, Accessible, Interoperable, and Reusable). DANDI references electrical and optical cellular neurophysiology recordings and associated MRI and/or optical imaging data. These data will help scientists uncover and understand cellular level mechanisms of brain function. Scientists will study the formation of neural networks, how cells and networks enable functions such as learning and memory, and how these functions are disrupted in neurological disorders.' homepage: https://dandiarchive.org/ id: 00000786 name: 'DANDI: Distributed Archives for Neurophysiology Data Integration' namespaceEmbeddedInLui: false pattern: ^\d{6}(\/\d+\.\d+\.\d+)?$ prefix: dandi sampleId: '000017' uri_format: https://dandiarchive.org/dandiset/$1 name: Distributed Archives for Neurophysiology Data Integration 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/$1 fairsharing: abbreviation: DARC description: The Database for Aligned Ribosomal Complexes (DARC) site provides a resource for directly comparing the structures of available ribosomal complexes. homepage: http://darcsite.genzentrum.lmu.de/darc/ name: Database of Aligned Ribosomal Complexes prefix: FAIRsharing.evfe2s publications: - doi: 10.1093/nar/gkr824 pubmed_id: 22009674 title: 'The DARC site: a database of aligned ribosomal complexes.' subjects: - Life Science mappings: biocontext: DARC fairsharing: FAIRsharing.evfe2s miriam: darc n2t: darc miriam: deprecated: false description: DARC (Database of Aligned Ribosomal Complexes) stores available cryo-EM (electron microscopy) data and atomic coordinates of ribosomal particles from the PDB, which are aligned within a common coordinate system. The aligned coordinate system simplifies direct visualization of conformational changes in the ribosome, such as subunit rotation and head-swiveling, as well as direct comparison of bound ligands, such as antibiotics or translation factors. homepage: http://darcsite.genzentrum.lmu.de/darc/index.php id: '00000366' name: DARC namespaceEmbeddedInLui: false pattern: ^\d+$ 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 publications: - doi: 10.1093/nar/gkr824 pmc: PMC3245104 pubmed: '22009674' title: 'The DARC site: a database of aligned ribosomal complexes.' year: 2011 dashr: biocontext: is_identifiers: true is_obo: false prefix: DASHR uri_format: http://identifiers.org/dashr/$1 fairsharing: abbreviation: DASHR contact: email: dashr@lisanwanglab.org name: Li-San Wang orcid: 0000-0002-3684-0031 description: Integrated annotation and sequencing-based expression data for all major classes of human small non-coding RNAs (sncRNAs) for both full sncRNA transcripts and mature sncRNA products derived from these larger RNAs. homepage: http://lisanwanglab.org/DASHR name: Database of small human non-coding RNAs prefix: FAIRsharing.ztvs34 publications: - doi: 10.1093/nar/gkv1188 pubmed_id: 26553799 title: 'DASHR: database of small human noncoding RNAs.' subjects: - Life Science mappings: biocontext: DASHR fairsharing: FAIRsharing.ztvs34 miriam: dashr n2t: dashr miriam: deprecated: false description: DASHR reports the annotation, expression and evidence for specific RNA processing (cleavage specificity scores/entropy) of human sncRNA genes, precursor and mature sncRNA products across different human tissues and cell types. DASHR integrates information from multiple existing annotation resources for small non-coding RNAs, including microRNAs (miRNAs), Piwi-interacting (piRNAs), small nuclear (snRNAs), nucleolar (snoRNAs), cytoplasmic (scRNAs), transfer (tRNAs), tRNA fragments (tRFs), and ribosomal RNAs (rRNAs). These datasets were obtained from non-diseased human tissues and cell types and were generated for studying or profiling small non-coding RNAs. This collection references RNA records. homepage: http://lisanwanglab.org/DASHR/ id: '00000564' name: DASHR namespaceEmbeddedInLui: false pattern: ^(hsa-(let|mir)-\w+(-\w+)?)|(piR-\d+)|(chr\w+.tRNA\d+-\w+)|(chr\w+.tRNA\d+-\w+-tRF\d)|((SNORD|SNORA|ACA|HBII|HBI|U)(-)?\w+)|(HY\d\+(-L\d+)?)|((LSU|SSU|5S)(-rRNA_Hsa)?(-L\d+)?)$ prefix: dashr sampleId: hsa-mir-200a uri_format: http://lisanwanglab.org/DASHR/entry/$1 n2t: description: DASHR reports the annotation, expression and evidence for specific RNA processing (cleavage specificity scores/entropy) of human sncRNA genes, precursor and mature sncRNA products across different human tissues and cell types. DASHR integrates information from multiple existing annotation resources for small non-coding RNAs, including microRNAs (miRNAs), Piwi-interacting (piRNAs), small nuclear (snRNAs), nucleolar (snoRNAs), cytoplasmic (scRNAs), transfer (tRNAs), tRNA fragments (tRFs), and ribosomal RNAs (rRNAs). These datasets were obtained from non-diseased human tissues and cell types and were generated for studying or profiling small non-coding RNAs. This collection references RNA records. example: hsa-mir-200a homepage: http://lisanwanglab.org/DASHR/ name: DASHR at University of Pennsylvania namespaceEmbeddedInLui: false pattern: ^(hsa-(let|mir)-\w+(-\w+)?)|(piR-\d+)|(chr\w+.tRNA\d+-\w+)|(chr\w+.tRNA\d+-\w+-tRF\d)|((SNORD|SNORA|ACA|HBII|HBI|U)(-)?\w+)|(HY\d\+(-L\d+)?)|((LSU|SSU|5S)(-rRNA_Hsa)?(-L\d+)?)$ prefix: dashr uri_format: http://lisanwanglab.org/DASHR/entry/$1 name: Database of small human noncoding RNAs publications: - doi: 10.1093/nar/gkv1188 pmc: PMC4702848 pubmed: '26553799' title: 'DASHR: database of small human noncoding RNAs.' year: 2015 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 contact: email: silvio.peroni@unibo.it name: Silvio Peroni orcid: 0000-0003-0530-4305 description: The DataCite Ontology (DataCite) is an ontology that enables the metadata properties of the DataCite Metadata Schema Specification (i.e., a list of metadata properties for the accurate and consistent identification of a resource for citation and retrieval purposes) to be described in RDF. homepage: http://www.sparontologies.net/ontologies/datacite license: CC-BY-4.0 name: 'DataCite Ontology ' prefix: FAIRsharing.c06f1e publications: [] repository: https://github.com/sparontologies/datacite subjects: - Subject Agnostic twitter: sparontologies homepage: http://www.sparontologies.net/ontologies/datacite mappings: aberowl: DATACITE bioportal: DATACITE fairsharing: FAIRsharing.c06f1e name: DataCite Ontology preferred_prefix: DataCite repository: https://github.com/sparontologies/datacite twitter: 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/$1 edam: description: Identifier of a dbEST database entry. name: dbEST obsolete: false prefix: '1105' fairsharing: abbreviation: dbEST description: The dbEST contains sequence data and other information on "single-pass" cDNA sequences, or "Expressed Sequence Tags", from a number of organisms. NCBI is in the process of merging EST and GSS records into the Nucleotide database, and the process is expected to be completed 2019. Accession.version and GI identifiers will not change during this process. For more information please see https://ncbiinsights.ncbi.nlm.nih.gov/2018/07/30/upcoming-changes-est-gss-databases/ homepage: https://www.ncbi.nlm.nih.gov/genbank/dbest/ license: http://opendatacommons.org/licenses/pddl/1.0 name: Expressed Sequence Tags database prefix: FAIRsharing.v9fya8 publications: - doi: 10.1038/ng0893-332 pubmed_id: 8401577 title: dbEST--database for "expressed sequence tags". subjects: - Bioinformatics - Life Science mappings: biocontext: DBEST edam: '1105' fairsharing: FAIRsharing.v9fya8 miriam: dbest n2t: dbest ncbi: dbEST prefixcommons: dbest re3data: r3d100010648 miriam: deprecated: false description: The dbEST contains sequence data and other information on "single-pass" cDNA sequences, or "Expressed Sequence Tags", from a number of organisms. homepage: https://www.ncbi.nlm.nih.gov/nucest id: 00000159 name: dbEST namespaceEmbeddedInLui: false pattern: ^([A-Z]+)?\d+(\.\d+)?$ prefix: dbest providers: - code: ebi description: dbEST through European Nucleotide Archive (ENA) homepage: https://www.ebi.ac.uk/ena name: dbEST through European Nucleotide Archive (ENA) uri_format: https://www.ebi.ac.uk/ena/data/view/$1 - code: 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 publications: - doi: 10.1038/ng0893-332 pmc: null pubmed: '8401577' title: dbEST--database for "expressed sequence tags". year: 1993 re3data: description: 'dbEST is a division of GenBank that contains sequence data and other information on "single-pass" cDNA sequences, or "Expressed Sequence Tags", from a number of organisms. Expressed Sequence Tags (ESTs) are short (usually about 300-500 bp), single-pass sequence reads from mRNA (cDNA). Typically they are produced in large batches. They represent a snapshot of genes expressed in a given tissue and/or at a given developmental stage. They are tags (some coding, others not) of expression for a given cDNA library. Most EST projects develop large numbers of sequences. These are commonly submitted to GenBank and dbEST as batches of dozens to thousands of entries, with a great deal of redundancy in the citation, submitter and library information. To improve the efficiency of the submission process for this type of data, we have designed a special streamlined submission process and data format. dbEST also includes sequences that are longer than the traditional ESTs, or are produced as single sequences or in small batches. Among these sequences are products of differential display experiments and RACE experiments. The thing that these sequences have in common with traditional ESTs, regardless of length, quality, or quantity, is that there is little information that can be annotated in the record. If a sequence is later characterized and annotated with biological features such as a coding region, 5''UTR, or 3''UTR, it should be submitted through the regular GenBank submissions procedure (via BankIt or Sequin), even if part of the sequence is already in dbEST. dbEST is reserved for single-pass reads. Assembled sequences should not be submitted to dbEST. GenBank will accept assembled EST submissions for the forthcoming TSA (Transcriptome Shotgun Assembly) division. The individual reads which make up the assembly should be submitted to dbEST, the Trace archive or the Short Read Archive (SRA) prior to the submission of the assemblies.' homepage: https://www.ncbi.nlm.nih.gov/genbank/dbest/ name: Expressed Sequence Tags database prefix: r3d100010648 synonyms: - NCBI EST - dbEST xrefs: fairsharing: FAIRsharing.v9fya8 miriam: 00000159 scr: 016578 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 cellosaurus: category: Sequence databases homepage: https://www.ncbi.nlm.nih.gov/gap/ name: Database of Genotypes and Phenotypes prefix: dbGAP uri_format: https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=$1 fairsharing: abbreviation: dbGaP description: The Database of Genotypes and Phenotypes (dbGaP) archives and distributes the results of studies that have investigated the interaction of genotype and phenotype. Such studies include genome-wide association studies, medical sequencing, molecular diagnostic assays, as well as association between genotype and non-clinical traits. homepage: https://www.ncbi.nlm.nih.gov/gap/ name: Database of Genotypes and Phenotypes prefix: FAIRsharing.88v2k0 publications: - doi: 10.1038/ng1007-1181 pubmed_id: 17898773 title: The NCBI dbGaP database of genotypes and phenotypes. - doi: 10.1093/nar/gkt1211 pubmed_id: 24297256 title: 'NCBI''s Database of Genotypes and Phenotypes: dbGaP.' subjects: - Epigenetics - Genetics - Biomedical Science mappings: biocontext: DBGAP cellosaurus: dbGAP fairsharing: FAIRsharing.88v2k0 miriam: dbgap n2t: dbgap miriam: deprecated: false description: The database of Genotypes and Phenotypes (dbGaP) archives and distributes the results of studies that have investigated the interaction of genotype and phenotype. homepage: https://www.ncbi.nlm.nih.gov/projects/gap id: '00000602' name: dbGaP namespaceEmbeddedInLui: false pattern: ^phs[0-9]{6}(.v\d+.p\d+)?$ 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=$1 name: Database of Genotypes and Phenotypes publications: - doi: 10.1093/nar/gkt1211 pmc: PMC3965052 pubmed: '24297256' title: 'NCBI''s Database of Genotypes and Phenotypes: dbGaP.' year: 2013 - doi: 10.1038/ng1007-1181 pmc: PMC2031016 pubmed: '17898773' title: The NCBI dbGaP database of genotypes and phenotypes. year: 2007 dbmhc: appears_in: - cellosaurus cellosaurus: category: Cell line databases/resources homepage: https://www.ncbi.nlm.nih.gov/gv/mhc/ name: dbMHC database prefix: dbMHC deprecated: true example: '48439' mappings: cellosaurus: dbMHC name: Database of human Major Histocompatibility Complex pattern: ^\d+$ 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 keywords: - dbpedia - 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. homepage: https://www.ncbi.nlm.nih.gov/snp/ license: http://opendatacommons.org/licenses/pddl/1.0 name: Database of Single Nucleotide Polymorphism prefix: FAIRsharing.edxb58 publications: - doi: 10.1093/nar/29.1.308 pubmed_id: 11125122 title: 'dbSNP: the NCBI database of genetic variation.' repository: https://github.com/ncbi/dbsnp/tree/master/tutorials subjects: - Life Science go: homepage: http://www.ncbi.nlm.nih.gov/projects/SNP name: NCBI dbSNP prefix: dbSNP uri_format: http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=$1 hl7: description: 'In collaboration with the National Human Genome Research Institute, The National Center for Biotechnology Information has established the dbSNP database to serve as a central repository for both single base nucleotide substitutions and short deletion and insertion polymorphisms. The entries in the dbSNP database can be used with the HL7 coded data type. For example, in the HL7 messages specified according to the HL7 V2 Clinical Genomics Fully LOINC-Qualified Genetic Variation Model, dbSNP entries can be used to as the observation values for DNA sequence variation identifiers. For example, OBX|1|CWE|48004-6^DNA Sequence Variation Identifier^LN||rs55538123^^dbSNPVersioning is identified by the build id. A new build is released approximately every six months or every year. The latest build id is 130, and the dbSNP web query for built 130 was available on Apr 30, 2009.dbSNP is a database that can be used freely by the public.More information may be fouond at: http://www.ncbi.nlm.nih.gov/projects/SNP/' homepage: https://lhncbc.nlm.nih.gov/ name: The Short Genetic Variations database organization: National Center for Biotechnology Information,National Center for Biotechnology Information preferred_prefix: dbSNP prefix: 2.16.840.1.113883.6.284 status: Complete mappings: biocontext: dbSNP cellosaurus: dbSNP edam: '1106' fairsharing: FAIRsharing.edxb58 go: dbSNP hl7: 2.16.840.1.113883.6.284 miriam: dbsnp n2t: dbsnp ncbi: dbSNP prefixcommons: dbsnp re3data: r3d100010652 uniprot: DB-0013 wikidata: P6861 miriam: deprecated: false description: The dbSNP database is a repository for both single base nucleotide subsitutions and short deletion and insertion polymorphisms. homepage: https://www.ncbi.nlm.nih.gov/snp/ id: '00000161' name: dbSNP namespaceEmbeddedInLui: false pattern: ^rs\d+$ prefix: dbsnp providers: - code: sib description: SNP2TFBS homepage: https://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/gkl1031 pmc: PMC1781113 pubmed: '17170002' title: Database resources of the National Center for Biotechnology Information. year: 2006 - doi: 10.1093/nar/29.1.308 pmc: PMC29783 pubmed: '11125122' title: 'dbSNP: the NCBI database of genetic variation.' year: 2001 re3data: description: 'The NCBI Short Genetic Variations database, commonly known as dbSNP, catalogs short variations in nucleotide sequences from a wide range of organisms. These variations include single nucleotide variations, short nucleotide insertions and deletions, short tandem repeats and microsatellites. Short Genetic Variations may be common, thus representing true polymorphisms, or they may be rare. Some rare human entries have additional information associated withthem, including disease associations, genotype information and allele origin, as some variations are somatic rather than germline events. ***NCBI will phase out support for non-human organism data in dbSNP and dbVar beginning on September 1, 2017***' homepage: https://www.ncbi.nlm.nih.gov/snp/ name: dbSNP prefix: r3d100010652 synonyms: - Database for short genetic variations - SNV xrefs: fairsharing: FAIRsharing.edxb58 nif: 0000-02734 omics: '00264' scr: 002338 uniprot: abbreviation: dbSNP category: Genetic variation databases homepage: https://www.ncbi.nlm.nih.gov/snp/ name: Database of single nucleotide polymorphism prefix: DB-0013 publications: - doi: 10.1093/nar/gkl1031 pubmed: '17170002' uri_format: https://www.ncbi.nlm.nih.gov/snp/$1 wikidata: database: Q5243761 description: identifier used in dbSNP to uniquely identify a genetic variant example: - rs113488022 - rs121913355 - rs1488384581 homepage: https://civicdb.org/home miriam: dbsnp name: dbSNP Reference SNP number prefix: P6861 uri_format: https://www.ncbi.nlm.nih.gov/snp/$1 dbvar.study: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Studies in dbVar. example: nstd102 homepage: https://www.ncbi.nlm.nih.gov/dbvar name: Database of Genomic Structural Variation - Study 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 contact: email: kdurante@stanford.edu github: null name: Kim Durante orcid: 0000-0001-9052-2854 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: 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. homepage: http://dublincore.org/documents/dces/ license: CC-BY-3.0 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_$1 example: '0000003' mappings: biocontext: DC_CL obofoundry: dc_cl obofoundry: contact: Lindsay.Cowell@utsouthwestern.edu contact.label: Lindsay Cowell contact.orcid: 0000-0003-1617-8244 deprecated: true domain: anatomy and development homepage: http://www.dukeontologygroup.org/Projects.html name: Dendritic cell prefix: dc_cl pattern: ^\d{7}$ 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 contact: email: kdurante@stanford.edu github: null name: Kim Durante orcid: 0000-0001-9052-2854 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: DCAT is an RDF vocabulary designed to facilitate interoperability between data catalogs published on the Web example: Dataset fairsharing: abbreviation: DCAT contact: email: phila@w3.org name: Phil Archer orcid: 0000-0002-4989-0601 description: An RDF vocabulary designed to facilitate interoperability between data catalogs published on the Web. By using DCAT to describe datasets in data catalogs, publishers increase discoverability and enable applications easily to consume metadata from multiple catalogs. It further enables decentralized publishing of catalogs and facilitates federated dataset search across sites. Aggregated DCAT metadata can serve as a manifest file to facilitate digital preservation. homepage: https://www.w3.org/TR/vocab-dcat/ name: Data Catalog Vocabulary prefix: FAIRsharing.h4j3qm publications: [] repository: https://github.com/w3c/dxwg/ subjects: - Data Management - Subject Agnostic homepage: https://www.w3.org/ns/dcat 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. homepage: http://dublincore.org/documents/dcmi-terms/ license: CC-BY-3.0 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 Dictyostelium discoideum. 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 contact: email: pgaudet@northwestern.edu name: Pascale Gaudet orcid: 0000-0003-1813-6857 description: 'The Dictyostelium Anatomy Ontology ontology describes the anatomy of the slime mold. It defines the structural makeup of Dictyostelium and its composing parts including the different cell types, throughout its life cycle. It has two main goals: (1) promote the consistent annotation of Dictyostelium-specific events, such as phenotypes and gene expression information; and (2) encourage researchers to use the same terms with the same intended meaning.' homepage: http://dictybase.org/Dicty_Info/dicty_anatomy_ontology.html name: Dictyostelium Anatomy Ontology prefix: FAIRsharing.z656ab publications: - doi: 10.1186/1471-2164-9-130 pubmed_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 domain: anatomy and development download.obo: http://purl.obolibrary.org/obo/ddanat.obo download.owl: http://purl.obolibrary.org/obo/ddanat.owl homepage: http://dictybase.org/ license: CC0 1.0 license.url: https://creativecommons.org/publicdomain/zero/1.0/ name: Dictyostelium discoideum anatomy preferredPrefix: DDANAT prefix: ddanat publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/18366659 title: An anatomy ontology to represent biological knowledge in Dictyostelium discoideum repository: https://github.com/dictyBase/migration-data twitter: dictybase ols: description: A structured controlled vocabulary of 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 Dictyostelium discoideum. 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 keywords: - chemistry - drugs - relationships 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/$1 ddinter.interaction: contact: email: oriental-cds@163.com github: null name: Dongsheng Cao orcid: 0000-0003-3604-3785 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Ddinter is a comprehensive, professional, and open-access database specific to drug-drug interactions. it provides abundant annotations for each ddi association including mechanism description, risk levels, management strategies, alternative medications, etc. to improve clinical decision-making and patient safety. example: '1122888' github_request_issue: 492 homepage: http://ddinter.scbdd.com keywords: - chemistry - drug-drug interactions - drugs - relationships license: CC-BY-NC-SA-4.0 name: Curated Drug-Drug Interactions Database - Interaction pattern: ^\d+$ uri_format: http://ddinter.scbdd.com/ddinter/interact/$1 ddpheno: aberowl: description: A structured controlled vocabulary of phenotypes of the slime-mould Dictyostelium discoideum. 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 contact: email: pfey@northwestern.edu name: Petra Fey orcid: 00000-0002-2757-5950 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." homepage: https://github.com/dictyBase/migration-data/blob/master/ontologies/dicty_phenotypes.obo 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 Dictyostelium discoideum. domain: anatomy and development download.obo: http://purl.obolibrary.org/obo/ddpheno.obo download.owl: http://purl.obolibrary.org/obo/ddpheno.owl homepage: http://dictybase.org/ license: CC0 1.0 license.url: http://creativecommons.org/publicdomain/zero/1.0/ name: Dictyostelium discoideum phenotype ontology preferredPrefix: DDPHENO prefix: ddpheno publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/31840793 title: dictyBase and the Dicty Stock Center (version 2.0) - a progress report repository: https://github.com/obophenotype/dicty-phenotype-ontology twitter: dictybase ols: description: A structured controlled vocabulary of phenotypes of the slime-mould Dictyostelium discoideum. download: 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: 10.1387/ijdb.190226pf pmc: PMC7409682 pubmed: '31840793' title: dictyBase and the Dicty Stock Center (version 2.0) - a progress report. year: 2019 - doi: 10.1007/978-1-62703-302-2_4 pmc: PMC3762881 pubmed: '23494302' title: 'One stop shop for everything Dictyostelium: dictyBase and the Dicty Stock Center in 2012.' year: 2013 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 providers: - code: obo2 description: Because it's not possible to configure the base URI with ROBOT/OWLAPI, this pops out homepage: http://purl.obolibrary.org name: Placeholder OBO PURL uri_format: http://purl.obolibrary.org/obo/debio_$1 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_$1 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: CNV syndromes in the DECIPHER genomics database that are linked to Human Phenotype Ontology terms example: '1' fairsharing: abbreviation: DECIPHER description: DECIPHER (Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources) is an interactive web-based resource that incorporates a suite of tools designed to aid the interpretation of submicroscopic chromosomal imbalance, inversions, and translocations. homepage: https://decipher.sanger.ac.uk/ name: DatabasE of genomiC varIation and Phenotype in Humans using Ensembl Resources prefix: FAIRsharing.l8Sf5x publications: - doi: 10.1093/nar/gkt937 pubmed_id: 24150940 title: 'DECIPHER: database for the interpretation of phenotype-linked plausibly pathogenic sequence and copy-number variation.' - doi: 10.1016/j.ajhg.2009.03.010 pubmed_id: 19344873 title: 'DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources.' subjects: - Life Science - Biomedical Science homepage: https://www.deciphergenomics.org/ mappings: biocontext: DECIPHER fairsharing: FAIRsharing.l8Sf5x name: DECIPHER CNV Syndromes pattern: ^\d+$ publications: - doi: 10.1093/nar/gkt937 pmc: PMC3965078 pubmed: '24150940' title: 'DECIPHER: database for the interpretation of phenotype-linked plausibly pathogenic sequence and copy-number variation.' year: 2013 - doi: 10.1016/j.ajhg.2009.03.010 pmc: PMC2667985 pubmed: '19344873' title: 'DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources.' year: 2009 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 contact: email: silvio.peroni@unibo.it name: Silvio Peroni orcid: 0000-0003-0530-4305 description: The Discourse Elements Ontology (DEO) is an ontology that provides a structured vocabulary for rhetorical elements within documents (e.g., Introduction, Discussion, Acknowledgements, Reference List, Figures, Appendix). It is imported by DoCO. homepage: http://www.sparontologies.net/ontologies/deo license: CC-BY-4.0 name: Discourse Elements Ontology prefix: FAIRsharing.39fd58 publications: - doi: https://doi.org/10.3233/SW-150177 pubmed_id: null title: The Document Components Ontology (DoCO) repository: https://github.com/sparontologies/deo subjects: - Subject Agnostic twitter: sparontologies homepage: http://www.sparontologies.net/ontologies/deo mappings: fairsharing: FAIRsharing.39fd58 name: Discourse Elements Ontology preferred_prefix: DEO publications: - doi: 10.3233/sw-150177 pmc: null pubmed: null title: "The\_Document\_Components\_Ontology\_(DoCO)" year: 2016 repository: https://github.com/sparontologies/deo uri_format: http://purl.org/spar/deo/$1 depmap: cellosaurus: category: Cell line databases/resources homepage: https://depmap.org/portal/ name: Cancer Dependency Map prefix: DepMap uri_format: https://depmap.org/portal/cell_line/$1 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Cell lines used in the Dependency Map (DepMap). Highly related to CCLE Cells. example: ACH-000001 homepage: https://depmap.org/portal mappings: cellosaurus: DepMap name: DepMap Cell Lines pattern: ^ACH-\d+$ 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/$1 fairsharing: abbreviation: DEPOD contact: email: depod@embl.de name: General Enquiries orcid: 0000-0003-3562-7869 description: DEPOD - the human DEPhOsphorylation Database is a manually curated database collecting human active and inactive phosphatases, their experimentally verified protein and non-protein substrates, and dephosphorylation site information, and pathways in which they are involved. It also provides links to popular kinase databases and protein-protein interaction databases for these phosphatases and substrates. homepage: http://www.depod.org/ name: The human DEPhOsphorylation Database prefix: FAIRsharing.q9j2e3 publications: - doi: 10.1093/nar/gku1009 pubmed_id: 25332398 title: 'The human DEPhOsphorylation database DEPOD: a 2015 update.' - doi: 10.1126/scisignal.2003203 pubmed_id: 23674824 title: Elucidating human phosphatase-substrate networks. subjects: - Life Science mappings: biocontext: DEPOD fairsharing: FAIRsharing.q9j2e3 miriam: depod n2t: depod re3data: r3d100011936 uniprot: DB-0190 miriam: deprecated: false description: The human DEPhOsphorylation Database (DEPOD) contains information on known human active phosphatases and their experimentally verified protein and nonprotein substrates. Reliability scores are provided for dephosphorylation interactions, according to the type of assay used, as well as the number of laboratories that have confirmed such interaction. Phosphatase and substrate entries are listed along with the dephosphorylation site, bioassay type, and original literature, and contain links to other resources. homepage: http://www.depod.bioss.uni-freiburg.de id: 00000428 name: DEPOD namespaceEmbeddedInLui: false pattern: ^[A-Z0-9]+$ prefix: depod sampleId: PTPN1 uri_format: http://www.depod.bioss.uni-freiburg.de/showp.php?gene=$1 n2t: description: The human DEPhOsphorylation Database (DEPOD) contains information on known human active phosphatases and their experimentally verified protein and nonprotein substrates. Reliability scores are provided for dephosphorylation interactions, according to the type of assay used, as well as the number of laboratories that have confirmed such interaction. Phosphatase and substrate entries are listed along with the dephosphorylation site, bioassay type, and original literature, and contain links to other resources. example: PTPN1 homepage: http://www.depod.bioss.uni-freiburg.de name: DEPOD at EMBL namespaceEmbeddedInLui: false pattern: ^[A-Z0-9]+$ prefix: depod uri_format: http://www.depod.bioss.uni-freiburg.de/showp.php?gene=$1 name: Human Dephosphorylation Database provides: hgnc.symbol publications: - doi: 10.1093/database/baz133 pmc: PMC6911163 pubmed: '31836896' title: 'The human DEPhOsphorylation Database DEPOD: 2019 update.' year: 2019 - doi: 10.1093/nar/gku1009 pmc: PMC4383878 pubmed: '25332398' title: 'The human DEPhOsphorylation database DEPOD: a 2015 update.' year: 2014 - doi: 10.1126/scisignal.2003203 pmc: null pubmed: '23674824' title: Elucidating human phosphatase-substrate networks. year: 2013 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: abbreviation: DEPOD category: PTM databases homepage: http://depod.bioss.uni-freiburg.de name: DEPOD human dephosphorylation database prefix: DB-0190 publications: - doi: doi pubmed: '31836896' uri_format: http://depod.bioss.uni-freiburg.de/showp.php?name=$1 dermo: aberowl: description: Ontology of human dermatologic disease download_obo: http://aber-owl.net/media/ontologies/DERMO/10/dermo.obo name: Human Dermatological Disease Ontology prefix: DERMO version: '1.19' bioportal: contact: email: pns12@cam.ac.uk name: Paul Schofield description: Ontology of human dermatologic disease name: Human Dermatological Disease Ontology prefix: DERMO version: '1.19' contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: DermO is an ontology with broad coverage of the domain of dermatologic disease and we demonstrate here its utility for text mining and investigation of phenotypic relationships between dermatologic disorders example: '0000000' fairsharing: abbreviation: DERMO description: Ontology of human dermatologic disease homepage: http://bioportal.bioontology.org/ontologies/DERMO name: Human Dermatological Disease Ontology prefix: FAIRsharing.k008w7 publications: [] subjects: [] homepage: https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-016-0085-x mappings: aberowl: DERMO bioportal: DERMO fairsharing: FAIRsharing.k008w7 name: Human Dermatological Disease Ontology pattern: ^\d{7}$ 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 2023aAnnex D) homepage: http://dicom.nema.org/medical/dicom/current/output/chtml/part16/chapter_D.html name: DICOM Controlled Terminology prefix: DCM version: 2023a_20230123 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." homepage: http://medical.nema.org/ name: Digital Imaging and COmmunications in Medicine prefix: FAIRsharing.b7z8by publications: - doi: 10.1007/s10278-013-9577-8 pubmed_id: 23404629 title: 'Multi-series DICOM: an extension of DICOM that stores a whole study in a single object.' - doi: 10.1016/j.crad.2005.07.003 pubmed_id: 16223609 title: 'DICOM demystified: a review of digital file formats and their use in radiological practice.' subjects: - Anatomy - Medicine - Biomedical Science hl7: description: 'Coded concepts defined in PS 3.16 Digital Imaging andCommunications in Medicine (DICOM): Part 16: Content Mapping Resource,Annex D: DICOM Controlled Terminology Definition' homepage: http://medical.nema.org/ name: DICOM Controlled Terminology organization: DICOM Standards Committee preferred_prefix: DCM prefix: 1.2.840.10008.2.16.4 status: Complete mappings: bioportal: DCM fairsharing: FAIRsharing.b7z8by hl7: 1.2.840.10008.2.16.4 ols: dicom ols: contact: dclunie@dclunie.com description: DICOM Controlled Terminology download: 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+$ publications: - doi: 10.1007/s10278-013-9577-8 pmc: PMC3705029 pubmed: '23404629' title: 'Multi-series DICOM: an extension of DICOM that stores a whole study in a single object.' year: 2013 - doi: 10.1016/j.crad.2005.07.003 pmc: null pubmed: '16223609' title: 'DICOM demystified: a review of digital file formats and their use in radiological practice.' year: 2005 uri_format: http://dicom.nema.org/resources/ontology/DCM/$1 dictybase: biocontext: 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. homepage: http://www.dictybase.org name: dictyBase prefix: FAIRsharing.4shj9c publications: - doi: 10.1007/978-1-62703-302-2_4 pubmed_id: 23494302 title: 'One stop shop for everything Dictyostelium: dictyBase and the Dicty Stock Center in 2012.' - doi: 10.1093/nar/gks1064 pubmed_id: 23172289 title: 'DictyBase 2013: integrating multiple Dictyostelid species.' - doi: 10.1093/nar/gkh138 pubmed_id: 14681427 title: 'dictyBase: a new Dictyostelium discoideum genome database.' subjects: - Anatomy - Life Science - Comparative Genomics go: homepage: http://dictybase.org name: dictyBase prefix: dictyBase synonyms: - DDB - DictyBase uri_format: http://dictybase.org/gene/$1 mappings: biocontext: dictyBase fairsharing: FAIRsharing.4shj9c go: dictyBase ncbi: dictyBase prefixcommons: dictybase re3data: r3d100010586 uniprot: DB-0015 name: dictyBase ncbi: example: DDB0191090 homepage: http://dictybase.org/ name: Dictyostelium genome database prefix: dictyBase prefixcommons: description: Genome information, literature and experimental resources for Dictyostelium discoideum example: DBS0237308 homepage: http://dictybase.org/ keywords: - genome name: Dictyostelium discoideum online informatics resource pattern: ^DBS\d{7}$ prefix: dictybase publications: - doi: 10.1007/978-1-62703-302-2_4 pmc: PMC3762881 pubmed: '23494302' title: 'One stop shop for everything Dictyostelium: dictyBase and the Dicty Stock Center in 2012.' year: 2013 - doi: 10.1093/nar/gks1064 pmc: PMC3531180 pubmed: '23172289' title: 'DictyBase 2013: integrating multiple Dictyostelid species.' year: 2012 - doi: 10.1093/nar/gkh138 pmc: PMC308872 pubmed: '14681427' title: 'dictyBase: a new Dictyostelium discoideum genome database.' year: 2004 re3data: description: dictyBase is an integrated genetic and literature database that contains published Dictyostelium discoideum literature, genes, expressed sequence tags (ESTs), as well as the chromosomal and mitochondrial genome sequences. Direct access to the genome browser, a Blast search tool, the Dictyostelium Stock Center, research tools, colleague databases, and much much more are just a mouse click away. Dictybase is a genome portal for the Amoebozoa. dictyBase is funded by a grant from the National Institute for General Medical Sciences. 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: abbreviation: dictyBase category: Organism-specific databases homepage: http://dictybase.org/ name: Dictyostelium discoideum online informatics resource prefix: DB-0015 publications: - doi: 10.1093/nar/gks1064 pubmed: '23172289' uri_format: http://dictybase.org/db/cgi-bin/gene_page.pl?primary_id=$1 dictybase.est: biocontext: 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 contact: email: rdb20@pitt.edu name: Richard D. Boyce orcid: 0000-0002-2993-2085 description: 'A domain ontology for potential drug-drug interactions (PDDIs) that covers the material entities and processes in the domain of discourse for PDDI evidence and knowledge claims. The representation enables the integration of drug interaction mechanisms, effects, risk factors, severity, and management options with the chemical and pharmacological properties (e.g., chemical structure, function, pharmacokinetic and pharmacodynamic properties) of the interacting drugs. It also has a rich and detailed set evidence entities related to pharmacology. See below for publications about DIDEO. A description of the goals of the project can be found in the following workshop paper located in the docs/DIDEO-discussion-ICBO-Brochhausen-2014.pdf: Brochhausen, M., Schneider, J., Malone, D., Empey, PE., Hogan WR., and Boyce, RD. Towards a foundational representation of potential drug-drug interaction knowledge. The 1st International Drug-Drug Interaction Knowledge Representation Workshop (DIKR 2014). Collocated with the 2014 International Conference on Biomedical Ontology (ICBO 2014). October 6th, Houston, Texas. United States.' homepage: https://github.com/DIDEO/DIDEO license: CC-BY-4.0 name: The Potential Drug-drug Interaction and Potential Drug-drug Interaction Evidence Ontology prefix: FAIRsharing.9y8f0n publications: - doi: 10.1016/j.knosys.2016.10.006 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: - Biochemistry 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 domain: chemistry and biochemistry download.owl: http://purl.obolibrary.org/obo/dideo.owl homepage: https://github.com/DIDEO/DIDEO license: CC BY 4.0 license.url: https://creativecommons.org/licenses/by/4.0/ name: Drug-drug Interaction and Drug-drug Interaction Evidence Ontology preferredPrefix: DIDEO prefix: dideo repository: https://github.com/DIDEO/DIDEO ols: description: The Potential Drug-drug Interaction and Potential Drug-drug Interaction Evidence Ontology download: 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: 10.1186/s13326-018-0183-z pmc: PMC5944177 pubmed: '29743102' title: Extending the DIDEO ontology to include entities from the natural product drug interaction domain of discourse. year: 2018 - doi: null pmc: PMC5765984 pubmed: '29295242' title: Formalizing Evidence Type Definitions for Drug-Drug Interaction Studies to Improve Evidence Base Curation. year: 2017 - doi: 10.1016/j.knosys.2016.10.006 pmc: null pubmed: null title: 'Conceptual models of drug-drug interactions: A summary of recent efforts' year: 2016 - 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: contact: email: maria.herrero@kcl.ac.uk name: Maria Herrero description: DINTO is an OWL ontology that systematically organizes all drug-drug interaction (DDI) related information. Drug-drug interactions (DDIs) form a significant risk group for adverse effects associated with pharmaceutical treatment. These interactions are often reported in the literature, however, they are sparsely represented in machine-readable resources, such as online databases, thesauri or ontologies. DINTO is an ontology that describes and categorizes DDIs and all the possible mechanisms that can lead to them (including both pharmacodynamic and pharmacokinetic DDI mechanisms). homepage: http://labda.inf.uc3m.es/doku.php?id=es:labda_dinto name: The Drug-Drug Interactions Ontology prefix: DINTO version: '1.3' mappings: aberowl: DINTO biocontext: DINTO bioportal: DINTO obofoundry: dinto ontobee: DINTO obofoundry: contact: maria.herrero@kcl.ac.uk contact.label: Maria Herrero deprecated: true description: A formal represention for drug-drug interactions knowledge. domain: health download.owl: http://purl.obolibrary.org/obo/dinto.owl homepage: http://labda.inf.uc3m.es/doku.php?id=es:labda_dinto license: CC BY 3.0 license.url: https://creativecommons.org/licenses/by/3.0/ name: The Drug-Drug Interactions Ontology prefix: dinto publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/26147071 title: "DINTO: Using OWL Ontologies and SWRL Rules to Infer Drug\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/$1 edam: description: Unique identifier of an entry from the DIP database of protein-protein interactions. name: DIP obsolete: false prefix: '2616' fairsharing: abbreviation: DIP description: The database of interacting protein (DIP) database stores experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions. The data stored within the DIP database were curated, both manually by expert curators and automatically using computational approaches that utilize the the knowledge about the protein-protein interaction networks extracted from the core DIP data. homepage: https://dip.doe-mbi.ucla.edu/dip/Main.cgi license: CC BY-ND 3.0 name: Database of Interacting Proteins prefix: FAIRsharing.qje0v8 publications: - doi: 10.1093/nar/29.1.239 pubmed_id: 11125102 title: 'DIP: The Database of Interacting Proteins: 2001 update.' - doi: 10.1093/nar/28.1.289 pubmed_id: 10592249 title: 'DIP: the database of interacting proteins.' - doi: 10.1093/nar/30.1.303 pubmed_id: 11752321 title: 'DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions.' - doi: 10.1093/nar/gkh086 pubmed_id: 14681454 title: 'The Database of Interacting Proteins: 2004 update.' subjects: - Biology mappings: biocontext: DIP edam: '2616' fairsharing: FAIRsharing.qje0v8 miriam: dip n2t: dip prefixcommons: dip re3data: r3d100010670 uniprot: DB-0016 miriam: deprecated: false description: The database of interacting protein (DIP) database stores experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions homepage: https://dip.doe-mbi.ucla.edu/ id: '00000044' name: Database of Interacting Proteins namespaceEmbeddedInLui: false pattern: ^DIP(\:)?\-\d{1,}[ENXS]$ prefix: dip sampleId: DIP-743N uri_format: https://dip.doe-mbi.ucla.edu/dip/DIPview.cgi?ID=$1 n2t: description: The database of interacting protein (DIP) database stores experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions example: DIP-743N homepage: https://dip.doe-mbi.ucla.edu/ name: Database of interacting proteins namespaceEmbeddedInLui: false pattern: ^DIP(\:)?\-\d{1,}[ENXS]$ prefix: dip uri_format: https://dip.doe-mbi.ucla.edu/dip/DIPview.cgi?ID=$1 prefixcommons: description: The database of interacting protein (DIP) database stores experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions example: DIP-743N homepage: http://dip.doe-mbi.ucla.edu keywords: - interaction - protein name: Database of Interacting Proteins pattern: ^DIP[\:\-]\d{3}[EN]$ 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 - doi: 10.1093/nar/30.1.303 pmc: PMC99070 pubmed: '11752321' title: 'DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions.' year: 2002 - doi: 10.1093/nar/29.1.239 pmc: PMC29798 pubmed: '11125102' title: 'DIP: The Database of Interacting Proteins: 2001 update.' year: 2001 - doi: 10.1093/nar/28.1.289 pmc: PMC102387 pubmed: '10592249' title: 'DIP: the database of interacting proteins.' year: 2000 re3data: description: The DIP database catalogs experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions. The data stored within the DIP database were curated, both, manually by expert curators and also automatically using computational approaches that utilize the the knowledge about the protein-protein interaction networks extracted from the most reliable, core subset of the DIP data. Please, check the reference page to find articles describing the DIP database in greater detail. The Database of Ligand-Receptor Partners (DLRP) is a subset of DIP (Database of Interacting Proteins). The DLRP is a database of protein ligand and protein receptor pairs that are known to interact with each other. By interact we mean that the ligand and receptor are members of a ligand-receptor complex and, unless otherwise noted, transduce a signal. In some instances the ligand and/or receptor may form a heterocomplex with other ligands/receptors in order to be functional. We have entered the majority of interactions in DLRP as full DIP entries, with links to references and additional information homepage: https://dip.doe-mbi.ucla.edu/dip/Main.cgi name: Database of Interacting Proteins prefix: r3d100010670 synonyms: - DIP xrefs: fairsharing: FAIRsharing.qje0v8 nif: 0000-00569 omics: 01905 scr: '003167' uniprot: abbreviation: DIP category: Protein-protein interaction databases homepage: https://dip.doe-mbi.ucla.edu/ name: Database of interacting proteins prefix: DB-0016 publications: - doi: 10.1093/nar/gkh086 pubmed: '14681454' uri_format: https://dip.doe-mbi.ucla.edu/dip/Browse.cgi?ID=$1 discoverx: cellosaurus: category: Cell line collections homepage: https://www.discoverx.com/products-applications/cell-lines name: DiscoverX cell line products prefix: DiscoverX uri_format: https://www.discoverx.com/searchproduct?searchtext=$1&searchmode=exact example: 95-0166C6 mappings: cellosaurus: DiscoverX disdriv: aberowl: description: Ontology for drivers and triggers of human diseases, built to classify ExO ontology exposure stressors. An application ontology. Built in collaboration with EnvO, ExO, ECTO and ChEBI. download_owl: http://aber-owl.net/media/ontologies/DISDRIV/1/disdriv.owl homepage: http://www.disease-ontology.org name: Disease Drivers Ontology prefix: DISDRIV bioportal: contact: email: lynn.schriml@gmail.com name: Lynn Schriml description: Ontology for drivers and triggers of human diseases, built to classify ExO ontology exposure stressors. An application ontology. Built in collaboration with EnvO, ExO, ECTO and ChEBI. homepage: https://disease-ontology.org/ name: Disease Drivers Ontology prefix: DISDRIV example: '0000000' mappings: aberowl: DISDRIV bioportal: DISDRIV obofoundry: disdriv ols: disdriv ontobee: DISDRIV obofoundry: contact: lynn.schriml@gmail.com contact.github: lschriml contact.label: Lynn Schriml contact.orcid: 0000-0001-8910-9851 deprecated: false description: Ontology for drivers and triggers of human diseases, built to classify ExO ontology exposure stressors. An application ontology. Built in collaboration with EnvO, ExO, ECTO and ChEBI. domain: health download.owl: http://purl.obolibrary.org/obo/disdriv.owl homepage: http://www.disease-ontology.org license: CC0 1.0 license.url: https://creativecommons.org/publicdomain/zero/1.0/ name: Disease Drivers Ontology preferredPrefix: DISDRIV prefix: disdriv repository: https://github.com/DiseaseOntology/DiseaseDriversOntology twitter: diseaseontology ols: description: Drivers of human diseases including environmental, maternal and social exposures. download: http://purl.obolibrary.org/obo/disdriv.owl homepage: http://www.disease-ontology.org name: Disease Drivers prefix: disdriv ontobee: library: Library name: Disease Drivers Ontology prefix: DISDRIV pattern: ^\d+$ 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$1.htm wikidata: database: Q213103 description: identifier sourced on the Diseases Database example: - '10166' - '8664' homepage: http://www.diseasesdatabase.com name: DiseasesDB pattern: ^\d{2,5}$ prefix: P557 uri_format: http://www.diseasesdatabase.com/ddb$1.htm disprot: biocontext: is_identifiers: true is_obo: false prefix: DISPROT uri_format: http://identifiers.org/disprot/$1 edam: description: Unique identifier for a protein from the DisProt database. name: Protein ID (DisProt) obsolete: false prefix: '2723' fairsharing: abbreviation: DisProt contact: email: silvio.tosatto@unipd.it name: Silvio C.E. Tosatto orcid: 0000-0003-4525-7793 description: The Database of Protein Disorder (DisProt) is a curated database that provides information about intrinsically disordered proteins that lack fixed 3D structure in their putatively native states, either in their entirety or in part. Disordered regions are manually curated from literature. DisProt annotations cover both structural and functional aspects of disorder detected by specific experimental methods. homepage: https://disprot.org/ license: CC-BY-4.0 name: DisProt prefix: FAIRsharing.dt9z89 publications: - doi: 10.1093/nar/gkl893 pubmed_id: 17145717 title: 'DisProt: the Database of Disordered Proteins.' - doi: 10.1093/nar/gkw1056 pubmed_id: 27899601 title: 'DisProt 7.0: a major update of the database of disordered proteins.' - doi: 10.1093/nar/gkz975 pubmed_id: 31713636 title: 'DisProt: intrinsic protein disorder annotation in 2020.' - doi: 10.1093/nar/gkab1082 pubmed_id: null title: 'DisProt in 2022: improved quality and accessibility of protein intrinsic disorder annotation' repository: https://disprot.github.io/ subjects: - Structural Biology - Biomedical Science - Biology twitter: disprot_db mappings: biocontext: DISPROT edam: '2723' fairsharing: FAIRsharing.dt9z89 miriam: disprot n2t: disprot prefixcommons: disprot re3data: r3d100010561 uniprot: DB-0017 miriam: deprecated: false description: DisProt is a database of intrinsically disordered proteins and protein disordered regions, manually curated from literature. homepage: https://disprot.org/ id: 00000199 name: DisProt namespaceEmbeddedInLui: false pattern: ^DP\d{5}$ prefix: disprot sampleId: DP00003 uri_format: https://disprot.org/$1 n2t: description: The Database of Protein Disorder (DisProt) is a curated database that provides information about proteins that lack fixed 3D structure in their putatively native states, either in their entirety or in part. example: DP00003 homepage: http://www.disprot.org/ name: DisProt at Indiana University namespaceEmbeddedInLui: false pattern: ^DP\d{5}$ prefix: disprot uri_format: http://www.disprot.org/$1 prefixcommons: description: The Database of Protein Disorder (DisProt) is a curated database that provides information about proteins that lack fixed 3D structure in their putatively native states, either in their entirety or in part. example: DP00001 homepage: http://www.disprot.org/ keywords: - protein - structure name: Database of protein disorder pattern: ^DP\d{5}$ prefix: disprot pubmed_ids: - '17145717' uri_format: http://www.disprot.org/protein.php?id=$1 publications: - doi: 10.1093/nar/gkab1082 pmc: PMC8728214 pubmed: '34850135' title: 'DisProt in 2022: improved quality and accessibility of protein intrinsic disorder annotation.' year: 2022 - doi: 10.1093/nar/gkz975 pmc: PMC7145575 pubmed: '31713636' title: 'DisProt: intrinsic protein disorder annotation in 2020.' year: 2020 - doi: 10.1093/nar/gkw1056 pmc: PMC5210544 pubmed: '27899601' title: 'DisProt 7.0: a major update of the database of disordered proteins.' year: 2016 - doi: 10.1093/nar/gkl893 pmc: PMC1751543 pubmed: '17145717' title: 'DisProt: the Database of Disordered Proteins.' year: 2006 - doi: 10.1093/bioinformatics/bth476 pmc: null pubmed: '15310560' title: 'DisProt: a database of protein disorder.' year: 2004 re3data: description: 'The Database of Protein Disorder (DisProt) is a curated database that provides information about proteins that lack fixed 3D structure in their putatively native states, either in their entirety or in part. DisProt is a community resource annotating protein sequences for intrinsically disorder regions from the literature. It classifies intrinsic disorder based on experimental methods and three ontologies for molecular function, transition and binding partner.' homepage: https://www.disprot.org/ name: DisProt prefix: r3d100010561 synonyms: - Database of Protein Disorder xrefs: fairsharing: FAIRsharing.dt9z89 nif: 0000-02754 scr: 007097 uniprot: abbreviation: DisProt category: Family and domain databases homepage: https://disprot.org name: Database of protein disorder prefix: DB-0017 publications: - doi: 10.1093/bioinformatics/bth476 pubmed: '15310560' uri_format: https://disprot.org/$1 disprot.region: mappings: miriam: disprot.region miriam: deprecated: false description: DisProt is a database of intrisically disordered proteins and protein disordered regions, manually curated from literature. homepage: https://www.disprot.org id: '00000745' name: DisProt region namespaceEmbeddedInLui: false pattern: ^DP\d{5}r\d{3}$ prefix: disprot.region sampleId: DP00086r013 uri_format: https://www.disprot.org/$1 part_of: disprot dlxb: mappings: miriam: dlxb miriam: deprecated: false description: DOULIX lab-tested standard biological parts, in this case linear double stranded DNA sequences. homepage: https://doulix.com id: '00000747' name: Linear double stranded DNA sequences namespaceEmbeddedInLui: false pattern: ^[A-Z0-9]{6,7}$ 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 keywords: - metadata - rdf - semantic web 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 contact: email: silvio.peroni@unibo.it name: Silvio Peroni orcid: 0000-0003-0530-4305 description: The Document Components Ontology (DoCO) is an ontology that provides a structured vocabulary written of document components, both structural (e.g., block, inline, paragraph, section, chapter) and rhetorical (e.g., introduction, discussion, acknowledgements, reference list, figure, appendix). homepage: http://www.sparontologies.net/ontologies/doco license: CC-BY-4.0 name: 'Document Components Ontology ' prefix: FAIRsharing.162003 publications: - doi: 10.3233/SW-150177 pubmed_id: null title: The Document Components Ontology (DoCO) repository: https://github.com/sparontologies/doco subjects: - Subject Agnostic twitter: sparontologies homepage: http://www.sparontologies.net/ontologies/doco mappings: fairsharing: FAIRsharing.162003 name: Document Components Ontology preferred_prefix: DoCO publications: - doi: 10.3233/sw-150177 pmc: null pubmed: null title: "The\_Document\_Components\_Ontology\_(DoCO)" year: 2016 repository: https://github.com/sparontologies/doco uri_format: http://purl.org/spar/doco/$1 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: 10.1038/s41597-022-01807-3 example_extras: - 10.21/FQSQT4T3 - 10.1333/s00897980202a - 10.1139/z02-135 - 10.1016/j.foodchem.2008.11.065 - 10.1093/acprof:oso/9780195159561.001.1 fairsharing: abbreviation: DOI 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." homepage: https://www.doi.org name: Digital Object Identifier prefix: FAIRsharing.hFLKCn publications: [] subjects: - Knowledge and Information Systems go: homepage: http://dx.doi.org/ name: Digital Object Identifier prefix: DOI uri_format: http://dx.doi.org/$1 mappings: biocontext: DOI biolink: doi cellosaurus: DOI edam: '1188' fairsharing: FAIRsharing.hFLKCn go: DOI miriam: doi n2t: doi prefixcommons: doi wikidata: P356 miriam: deprecated: false description: The Digital Object Identifier System is for identifying content objects in the digital environment. homepage: https://www.doi.org/ id: 00000019 name: DOI namespaceEmbeddedInLui: false pattern: ^(doi\:)?10\.\d+/.*$ prefix: doi providers: - code: scholia description: Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata. homepage: https://scholia.toolforge.org/ name: Scholia uri_format: https://scholia.toolforge.org/doi/$1 sampleId: 10.1038/nbt1156 uri_format: https://doi.org/$1 n2t: description: The Digital Object Identifier System is for identifying content objects in the digital environment. example: 10.1038/nbt1156 homepage: https://www.doi.org/ name: Digital Object Identifier namespaceEmbeddedInLui: false pattern: ^(doi\:)?\d{2}\.\d{4}.*$ prefix: doi uri_format: https://doi.org/$1 name: Digital Object Identifier pattern: ^10.\d{2,9}/.*$ 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/$1 wikidata: database: Q25670 description: serial code used to uniquely identify digital objects like academic papers (use upper case letters only) example: - 10.12987/YALE/9780300197051.003.0010 - 10.1371/JOURNAL.PONE.0029797 miriam: doi name: DOI pattern: ^(?i)10.\d{4,9}/[-._;()/:A-Z0-9]+$ prefix: P356 uri_format: https://doi.org/$1 uri_format_rdf: - http://dx.doi.org/$1 doid: aberowl: description: An ontology for describing the classification of human diseases organized by etiology. download_owl: http://aber-owl.net/media/ontologies/DOID/665/doid.owl homepage: http://www.disease-ontology.org name: Human Disease Ontology prefix: DOID bartoc: abbreviation: DO description: "The Disease Ontology has been developed as a standardized ontology\ \ for human disease with the purpose of providing the biomedical community with\ \ consistent, reusable and sustainable descriptions of human disease terms,\ \ phenotype characteristics and related medical vocabulary disease concepts\ \ through collaborative efforts of researchers at Northwestern University, Center\ \ for Genetic Medicine and the University of Maryland School of Medicine, Institute\ \ for Genome Sciences.\n\nThe Disease Ontology semantically integrates disease\ \ and medical vocabularies through extensive cross mapping of DO terms to MeSH,\ \ ICD, NCI\u2019s thesaurus, SNOMED and OMIM." homepage: http://disease-ontology.org/ name: Disease Ontology prefix: '576' wikidata_database: Q5282129 biocontext: is_identifiers: false is_obo: true prefix: DOID uri_format: http://purl.obolibrary.org/obo/DOID_$1 bioportal: 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 contact: email: lynn.schriml@gmail.com name: Lynn Schriml orcid: 0000-0001-8910-9851 description: The Disease Ontology has been developed as a standardized ontology for human disease with the purpose of providing the biomedical community with consistent, reusable and sustainable descriptions of human disease terms, phenotype characteristics, underlying mechanisms and related medical vocabulary disease concepts. homepage: http://www.disease-ontology.org license: CC0-1.0 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 & 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.' repository: https://github.com/DiseaseOntology/HumanDiseaseOntology subjects: - Life Science - Biomedical Science twitter: diseaseontology mappings: aberowl: DOID bartoc: '576' 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:$1 obofoundry: appears_in: - clo - scdo contact: lynn.schriml@gmail.com contact.github: lschriml contact.label: Lynn Schriml contact.orcid: 0000-0001-8910-9851 deprecated: false description: An ontology for describing the classification of human diseases organized by etiology. domain: health download.obo: http://purl.obolibrary.org/obo/doid.obo download.owl: http://purl.obolibrary.org/obo/doid.owl homepage: http://www.disease-ontology.org license: CC0 1.0 license.url: https://creativecommons.org/publicdomain/zero/1.0/ name: Human Disease Ontology preferredPrefix: DOID prefix: doid publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/25348409 title: 'Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data' - id: https://www.ncbi.nlm.nih.gov/pubmed/34755882 title: The Human Disease Ontology 2022 update repository: https://github.com/DiseaseOntology/HumanDiseaseOntology twitter: diseaseontology ols: description: The Disease Ontology has been developed as a standardized ontology for human disease with the purpose of providing the biomedical community with consistent, reusable and sustainable descriptions of human disease terms, phenotype characteristics and related medical vocabulary disease concepts. download: http://purl.obolibrary.org/obo/doid.owl name: Human Disease Ontology prefix: doid version: '2022-09-29' version.iri: http://purl.obolibrary.org/obo/doid/releases/2022-09-29/doid.owl ontobee: library: Foundry name: Human Disease Ontology prefix: DOID pattern: ^\d+$ 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/nar/gkab1063 pmc: PMC8728220 pubmed: '34755882' title: The Human Disease Ontology 2022 update. year: 2022 - doi: 10.1093/bib/bbab191 pmc: PMC8195003 pubmed: '34015823' title: COVID-19 biomarkers and their overlap with comorbidities in a disease biomarker data model. year: 2021 - doi: 10.7554/elife.52614 pmc: PMC7077981 pubmed: '32180547' title: Wikidata as a knowledge graph for the life sciences. year: 2020 - doi: 10.1093/nar/gky1036 pmc: PMC6323956 pubmed: '30407590' title: 'ECO, the Evidence & Conclusion Ontology: community standard for evidence information.' year: 2019 - doi: 10.1093/nar/gky1032 pmc: PMC6323977 pubmed: '30407550' title: 'Human Disease Ontology 2018 update: classification, content and workflow expansion.' year: 2019 - doi: 10.1242/dmm.032839 pmc: PMC5897730 pubmed: '29590633' title: 'Disease Ontology: improving and unifying disease annotations across species.' year: 2018 - doi: 10.1093/database/baw015 pmc: PMC4795929 pubmed: '26989148' title: Wikidata as a semantic framework for the Gene Wiki initiative. year: 2016 - doi: 10.1016/j.ajhg.2015.05.020 pmc: PMC4572507 pubmed: '26119816' title: 'The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease.' year: 2015 - doi: 10.1007/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: 10.1093/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: 10.1093/nar/gku1011 pmc: PMC4383880 pubmed: '25348409' title: 'Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data.' year: 2014 - doi: 10.1093/nar/gkr972 pmc: PMC3245088 pubmed: '22080554' title: 'Disease Ontology: a backbone for disease semantic integration.' year: 2011 - doi: 10.1186/1471-2164-10-s1-s6 pmc: PMC2709267 pubmed: '19594883' title: Annotating the human genome with Disease Ontology. year: 2009 - doi: 10.1093/bioinformatics/btp193 pmc: PMC2687947 pubmed: '19478018' title: 'From disease ontology to disease-ontology lite: statistical methods to adapt a general-purpose ontology for the test of gene-ontology associations.' year: 2009 synonyms: - do wikidata: database: Q5282129 description: identifier in the Disease Ontology database example: - DOID:769 - DOID:8778 homepage: http://disease-ontology.org miriam: doid name: Disease Ontology ID pattern: ^DOID:([0-9]{7}|[1-9][0-9]{0,4})$ prefix: P699 uri_format: http://www.disease-ontology.org/?id=$1 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/$1 mappings: biocontext: DOOR miriam: door n2t: door prefixcommons: door re3data: r3d100014113 miriam: deprecated: false description: DOOR (Database for prOkaryotic OpeRons) contains computationally predicted operons of all the sequenced prokaryotic genomes. It includes operons for RNA genes. homepage: http://csbl.bmb.uga.edu/DOOR/operon.php id: '00000453' name: DOOR namespaceEmbeddedInLui: false pattern: ^\d+$ 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 re3data: description: DOOR is the open institutional repository of the University for Continuing Education Krems, formerly known as Danube University Krems. DOOR runs on the fedora Software and is a partner repository of Phaidra Vienna and other fedora users in Austria. We provide access to OA publications, scientific data and much more for interested users and support our scientists and co-workers in their publication processis. homepage: https://door.donau-uni.ac.at/ name: DOOR prefix: r3d100014113 synonyms: - DOOR University for Continuing Education Krems - "DOOR Universit\xE4t f\xFCr Weiterbildung Krems" - Danube University Open Online Repository 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/24/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: '2022-12-02' comment: DPO is a subset of terms from FBcv mappings: aberowl: DPO bioportal: DPO obofoundry: dpo ols: dpo ontobee: DPO no_own_terms: true obofoundry: contact: cp390@cam.ac.uk contact.github: Clare72 contact.label: Clare Pilgrim contact.orcid: 0000-0002-1373-1705 deprecated: false description: An ontology of commonly encountered and/or high level Drosophila phenotypes. domain: phenotype download.json: http://purl.obolibrary.org/obo/dpo.json download.obo: http://purl.obolibrary.org/obo/dpo.obo download.owl: http://purl.obolibrary.org/obo/dpo.owl homepage: http://purl.obolibrary.org/obo/fbcv license: CC BY 4.0 license.url: http://creativecommons.org/licenses/by/4.0/ name: Drosophila Phenotype Ontology preferredPrefix: FBcv prefix: dpo publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/24138933 title: The Drosophila phenotype ontology. repository: https://github.com/FlyBase/drosophila-phenotype-ontology ols: description: An ontology 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/$1 mappings: biocontext: DPV miriam: dpv n2t: dpv prefixcommons: dpvweb miriam: deprecated: false description: Description of Plant Viruses (DPV) provides information about viruses, viroids and satellites of plants, fungi and protozoa. It provides taxonomic information, including brief descriptions of each family and genus, and classified lists of virus sequences. The database also holds detailed information for all sequences of viruses, viroids and satellites of plants, fungi and protozoa that are complete or that contain at least one complete gene. homepage: http://www.dpvweb.net/ id: 00000280 name: DPV namespaceEmbeddedInLui: false pattern: ^\d+$ prefix: dpv sampleId: '100' uri_format: 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=$1 name: Description of Plant Viruses prefixcommons: description: DPVweb provides a central source of information about viruses, viroids and satellites of plants, fungi and protozoa. Comprehensive taxonomic information, including brief descriptions of each family and genus, and classified lists of virus sequences are provided. The database also holds detailed, curated, information for all sequences of viruses, viroids and satellites of plants, fungi and protozoa that are complete or that contain at least one complete gene (currently, n~9000). example: '100' homepage: http://www.dpvweb.net keywords: - classification - gene name: Description of Plant Viruses pattern: ^\d+$ prefix: dpvweb pubmed_ids: - '16381892' uri_format: http://www.dpvweb.net/dpv/showdpv.php?dpvno=$1 publications: - doi: 10.1093/nar/gkj023 pmc: PMC1347386 pubmed: '16381892' title: 'DPVweb: a comprehensive database of plant and fungal virus genes and genomes.' year: 2006 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=$1&class=Allele n2t: description: DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to allele information. example: cho homepage: http://www.antirrhinum.net/ name: DragonDB Allele at University of British Columbia namespaceEmbeddedInLui: false pattern: ^\w+$ prefix: dragondb.allele uri_format: http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1&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=$1&class=Locus n2t: description: DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to Locus information. example: DEF homepage: http://www.antirrhinum.net/ name: DragonDB Locus at University of British Columbia namespaceEmbeddedInLui: false pattern: ^\w+$ prefix: dragondb.locus uri_format: http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1&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 drduke: mappings: wikidata: P10074 wikidata: database: Q48998259 description: identifier for chemicals linked to information on occurrence in plants example: - '19' - '32' homepage: https://phytochem.nal.usda.gov/phytochem/search/list name: Dr. Duke's Phytochemical and Ethnobotanical Databases chemical ID prefix: P10074 uri_format: https://phytochem.nal.usda.gov/phytochem/chemicals/show/$1 dron: aberowl: description: An ontology to support comparative effectiveness researchers studying claims data. download_owl: http://aber-owl.net/media/ontologies/DRON/18/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: '2022-10-22' download_json: http://purl.obolibrary.org/obo/dron.json download_obo: http://purl.obolibrary.org/obo/dron.obo example: '00023232' fairsharing: abbreviation: DrOn contact: email: hoganwr@gmail.com name: William Hogan orcid: 0000-0002-9881-1017 description: An ontology of drug products and packaged drug products. homepage: https://ontology.atlassian.net/wiki/display/DRON/Drug+Ontology+Home license: CC-BY-3.0 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. domain: health download.owl: http://purl.obolibrary.org/obo/dron.owl homepage: https://github.com/ufbmi/dron license: CC BY 3.0 license.url: http://creativecommons.org/licenses/by/3.0/ name: The Drug Ontology preferredPrefix: DRON prefix: dron publications: - id: https://doi.org/10.1186/s13326-017-0121-5 title: 'Therapeutic indications and other use-case-driven updates in the drug ontology: anti-malarials, anti-hypertensives, opioid analgesics, and a large term request' repository: https://github.com/ufbmi/dron ols: description: 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/s13326-017-0121-5 pmc: PMC5335794 pubmed: '28253937' title: 'Therapeutic indications and other use-case-driven updates in the drug ontology: anti-malarials, anti-hypertensives, opioid analgesics, and a large term request.' year: 2017 - doi: 10.1186/s13326-016-0048-2 pmc: PMC4836073 pubmed: '27096073' title: An accurate and precise representation of drug ingredients. year: 2016 - doi: 10.1186/2041-1480-4-44 pmc: PMC3931349 pubmed: '24345026' title: Building a drug ontology based on RxNorm and other sources. year: 2013 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: bartoc: description: The DrugBank database is a unique bioinformatics and cheminformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. The database contains 8246 drug entries including 2012 FDA-approved small molecule drugs, 229 FDA-approved biotech (protein/peptide) drugs, 94 nutraceuticals and over 6000 experimental drugs. Additionally, 4344 non-redundant protein (i.e. drug target/enzyme/transporter/carrier) sequences are linked to these drug entries. Each DrugCard entry contains more than 200 data fields with half of the information being devoted to drug/chemical data and the other half devoted to drug target or protein data. homepage: http://www.drugbank.ca/ license: CC BY-NC 3.0 name: DrugBank prefix: '18377' wikidata_database: Q1122544 biocontext: 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 contact: email: david.wishart@ualberta.ca name: David Wishart orcid: 0000-0002-3207-2434 description: The DrugBank database is a freely available bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. homepage: http://www.drugbank.ca/ name: DrugBank prefix: FAIRsharing.353yat publications: - doi: 10.1093/nar/gkt1068 pubmed_id: 24203711 title: 'DrugBank 4.0: shedding new light on drug metabolism.' - doi: 10.1093/nar/gkq1126 pubmed_id: 21059682 title: 'DrugBank 3.0: a comprehensive resource for ''omics'' research on drugs.' - doi: 10.1093/nar/gkm958 pubmed_id: 18048412 title: 'DrugBank: a knowledgebase for drugs, drug actions and drug targets.' - doi: 10.1093/nar/gkj067 pubmed_id: 16381955 title: 'DrugBank: a comprehensive resource for in silico drug discovery and exploration.' subjects: - Life Science - Biomedical Science twitter: DrugBankDB homepage: http://www.drugbank.ca mappings: bartoc: '18377' biocontext: DrugBank cellosaurus: DrugBank cheminf: '000406' edam: '2326' fairsharing: FAIRsharing.353yat miriam: drugbank n2t: drugbank prefixcommons: drugbank re3data: r3d100010544 uniprot: DB-0019 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/gkt1068 pmc: PMC3965102 pubmed: '24203711' title: 'DrugBank 4.0: shedding new light on drug metabolism.' year: 2013 - doi: 10.1093/nar/gkq1126 pmc: PMC3013709 pubmed: '21059682' title: 'DrugBank 3.0: a comprehensive resource for ''omics'' research on drugs.' year: 2010 - doi: 10.1093/nar/gkm958 pmc: PMC2238889 pubmed: '18048412' title: 'DrugBank: a knowledgebase for drugs, drug actions and drug targets.' year: 2007 - doi: 10.1093/nar/gkj067 pmc: PMC1347430 pubmed: '16381955' title: 'DrugBank: a comprehensive resource for in silico drug discovery and exploration.' year: 2006 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: abbreviation: DrugBank category: Chemistry databases homepage: https://www.drugbank.ca/ name: Drug and drug target database prefix: DB-0019 publications: - doi: 10.1093/nar/gkj067 pubmed: '16381955' uri_format: https://www.drugbank.ca/drugs/$1 wikidata: database: Q1122544 description: identifier in the bioinformatics and cheminformatics database from the University of Alberta example: - '00126' - CAT005101 homepage: https://www.drugbank.ca name: DrugBank ID pattern: ^(SALT\d{1}|CAT\d{1})?\d{5}$ prefix: P715 uri_format: https://go.drugbank.com/drugs/DB$1 drugbank.category: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Close to 5K Categorizations for drugs, similar to ATCC. example: DBCAT000600 homepage: https://go.drugbank.com/categories keywords: - chemistry - drugs - metascience - topics name: DrugBank Drug Category part_of: drugbank pattern: ^DBCAT\d+$ 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 contact: email: toprea@salud.unm.edu name: Tudor Oprea orcid: 0000-0002-6195-6976 description: DrugCentral is online drug information that provides information on active ingredients, chemical entities, pharmaceutical products, drug mode of action, indications, and pharmacologic mode of action. DrugCentral monitors FDA, EMA, and PMDA for new drug approval on regular basis to ensure currency of the resource. This resource was created and is maintained by the Division of Translational Informatics at the University of New Mexico School of Medicine. homepage: http://drugcentral.org/ license: CC BY-SA 4.0 name: DrugCentral prefix: FAIRsharing.3me82d publications: - doi: 10.1093/nar/gkw993 pubmed_id: 27789690 title: 'DrugCentral: online drug compendium.' subjects: - Drug Discovery - Drug Repositioning - Drug Development - Pharmacy - Pharmacology - Biomedical Science homepage: http://drugcentral.org mappings: biolink: DrugCentral fairsharing: FAIRsharing.3me82d miriam: drugcentral uniprot: DB-0239 wikidata: P11198 miriam: deprecated: false description: DrugCentral (http://drugcentral.org) is an open-access online drug compendium. DrugCentral integrates structure, bioactivity, regulatory, pharmacologic actions and indications for active pharmaceutical ingredients approved by FDA and other regulatory agencies. Monitoring of regulatory agencies for new drugs approvals ensures the resource is up-to-date. DrugCentral integrates content for active ingredients with pharmaceutical formulations, indexing drugs and drug label annotations, complementing similar resources available online. Its complementarity with other online resources is facilitated by cross referencing to external resources. At the molecular level, DrugCentral bridges drug-target interactions with pharmacological action and indications. The integration with FDA drug labels enables text mining applications for drug adverse events and clinical trial information. Chemical structure overlap between DrugCentral and five online drug resources, and the overlap between DrugCentral FDA-approved drugs and their presence in four different chemical collections, are discussed. DrugCentral can be accessed via the web application or downloaded in relational database format. homepage: http://www.unm.edu/ id: 00000966 name: DrugCentral namespaceEmbeddedInLui: false pattern: ^[0-9]+$ prefix: drugcentral sampleId: '257' uri_format: https://drugcentral.org/drugcard/$1 name: Drug Central pattern: ^\d+$ publications: - doi: 10.1093/nar/gky963 pmc: PMC6323925 pubmed: '30371892' title: 'DrugCentral 2018: an update.' year: 2019 - doi: 10.1093/nar/gkw993 pmc: PMC5210665 pubmed: '27789690' title: 'DrugCentral: online drug compendium.' year: 2016 - doi: 10.1093/nar/gkw993 pmc: null pubmed: '27789690' title: 'DrugCentral: online drug compendium.' year: null - doi: 10.1093/nar/gky963 pmc: null pubmed: '30371892' title: null year: null synonyms: - Drug_Central uniprot: abbreviation: DrugCentral category: Chemistry databases homepage: https://drugcentral.org/ name: DrugCentral prefix: DB-0239 publications: - doi: 10.1093/nar/gky963 pubmed: '30371892' uri_format: https://drugcentral.org/target/$1 uri_format: http://drugcentral.org/drugcard/$1 wikidata: database: Q27697289 description: ID of a chemical compound in DrugCentral example: - '158' - '21' - '947' homepage: https://drugcentral.org/ name: DrugCentral ID pattern: ^\d+$ prefix: P11198 uri_format: https://drugcentral.org/drugcard/$1 dsm4: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A terminology published by the American Psychiatric Association (APA) for the classification of mental disorders using a common language and standard criteria. [wikipedia] example: '315.1' example_extras: - '291.89' hl7: description: 'Diagnostic and Statistical Manual of Mental Disorders (DSM-IV). 4th ed. Washington (DC): American Psychiatric Association, 1994.' homepage: http://www.psych.org name: DSM-IV organization: American Psychiatric Association preferred_prefix: dsm4 prefix: 2.16.840.1.113883.6.126 status: Complete homepage: https://en.wikipedia.org/wiki/Diagnostic_and_Statistical_Manual_of_Mental_Disorders#DSM-IV-TR_(2000) mappings: hl7: 2.16.840.1.113883.6.126 wikidata: P663 name: Diagnostic and Statistical Manual of Mental Disorders (4th Edition) pattern: ^\d+\.\d+$ synonyms: - dsm-iv wikidata: database: Q3078495 description: identifier for a mental disorder in the 4th edition of Diagnostic and Statistical Manual of Mental Disorders example: - '291.89' - '315.1' homepage: https://en.wikipedia.org/wiki/DSM-IV_codes name: DSM-IV classification pattern: ^\d+\.\d+$ prefix: P663 dsm5: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A terminology published by the American Psychiatric Association (APA) for the classification of mental disorders using a common language and standard criteria. [wikipedia] example: '312.33' hl7: description: The Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition (DSM-5) is the 2013 update to the Diagnostic and Statistical Manual of Mental Disorders, the taxonomic and diagnostic tool published by the American Psychiatric Association (APA). In the United States, the DSM serves as a universal authority for psychiatric diagnoses. Treatment recommendations, as well as payment by health care providers, are often determined by DSM classifications, so the appearance of a new version has significant practical importance.The DSM-5 was published on May 18, 2013, superseding the DSM-IV-TR, which was published in 2000. homepage: https://www.psychiatry.org name: DSM-5 organization: American Psychiatry Association preferred_prefix: dsm5 prefix: 2.16.840.1.113883.6.344 status: Complete homepage: https://en.wikipedia.org/wiki/DSM-5 mappings: hl7: 2.16.840.1.113883.6.344 wikidata: P1930 name: Diagnostic and Statistical Manual of Mental Disorders (5th Edition) pattern: ^\d{3}\.\d{2}$ references: - https://archive.org/details/diagnosticstatis0005unse synonyms: - dsm-v wikidata: database: Q3064664 description: identifier for a mental disorder in the 5th edition of Diagnostic and Statistical Manual of Mental Disorders example: - '312.33' name: DSM-5 classification pattern: ^\d\d\d\.\d\d$ prefix: P1930 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/ keywords: - data science - ontology 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). homepage: http://drugtargetontology.org/ license: CC-BY-3.0 name: Drug Target Ontology prefix: FAIRsharing.tke3y2 publications: - doi: 10.1186/s13326-017-0161-x pubmed_id: 29122012 title: Drug target ontology to classify and integrate drug discovery data. repository: https://github.com/DrugTargetOntology/DTO 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 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). homepage: https://raw.githubusercontent.com/EBISPOT/DUO/master/duo.owl license: CC-BY-3.0 name: The Data Use Ontology prefix: FAIRsharing.5dnjs2 publications: - doi: 10.1016/j.xgen.2021.100028 pubmed_id: null title: The Data Use Ontology to streamline responsible access to human biomedical datasets repository: https://github.com/EBISPOT/duo/issues subjects: - Subject Agnostic - Biomedical Science 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. domain: information download.owl: http://purl.obolibrary.org/obo/duo.owl homepage: https://github.com/EBISPOT/DUO license: CC BY 4.0 license.url: http://creativecommons.org/licenses/by/4.0/ name: Data Use Ontology preferredPrefix: DUO prefix: duo repository: https://github.com/EBISPOT/DUO ols: 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}$ publications: - doi: 10.1016/j.xgen.2021.100028 pmc: PMC8591903 pubmed: '34820659' title: The Data Use Ontology to streamline responsible access to human biomedical datasets. year: 2021 repository: https://github.com/EBISPOT/DUO 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: '>>>!!!<<< The repository is no longer available. >>>!!!<<< The eagle-i National Network and eagle-i resource search at www.eagle-.net was retired on November 4, 2021.!!! 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://open.catalyst.harvard.edu/products/eagle-i/ 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/ keywords: - conferences - metascience name: EasyChair Call for Paper uri_format: https://easychair.org/cfp/$1 easychair.topic: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Call for paper topics in EasyChair example: '27106865' homepage: https://easychair.org/cfp/ keywords: - metascience - topics name: EasyChair Topic pattern: ^\d+$ 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=$1 ecao: aberowl: description: An ontology for the development and anatomy of the different species of the phylum Echinodermata (NCBITaxon:7586). download_owl: http://aber-owl.net/media/ontologies/ECAO/1/ecao.owl homepage: https://github.com/echinoderm-ontology/ecao_ontology name: The Echinoderm Anatomy and Development Ontology prefix: ECAO bioportal: contact: email: ettensohn@cmu.edu name: Charles Ettensohn description: An ontology for the development and anatomy of the different species of the phylum Echinodermata (NCBITaxon:7586). homepage: https://github.com/echinoderm-ontology/ecao_ontology name: The Echinoderm Anatomy and Development Ontology prefix: ECAO example: 0107180 mappings: aberowl: ECAO bioportal: ECAO obofoundry: ecao ols: ecao ontobee: ECAO obofoundry: contact: ettensohn@cmu.edu contact.github: ettensohn contact.label: Charles Ettensohn contact.orcid: 0000-0002-3625-0955 depends_on: - cl - ro - uberon deprecated: false description: An ontology for the development and anatomy of the different species of the phylum Echinodermata (NCBITaxon:7586). domain: anatomy and development download.obo: http://purl.obolibrary.org/obo/ecao.obo download.owl: http://purl.obolibrary.org/obo/ecao.owl homepage: https://github.com/echinoderm-ontology/ecao_ontology license: CC BY 3.0 license.url: http://creativecommons.org/licenses/by/3.0/ name: The Echinoderm Anatomy and Development Ontology preferredPrefix: ECAO prefix: ecao repository: https://github.com/echinoderm-ontology/ecao_ontology ols: description: None download: http://purl.obolibrary.org/obo/ecao.owl homepage: https://github.com/echinoderm-ontology/ecao_ontology name: Echinoderm Anatomy and Development Ontology prefix: ecao version: '2020-05-22' version.iri: http://purl.obolibrary.org/obo/ecao/releases/2020-05-22/ecao.owl ontobee: library: Library name: The Echinoderm Anatomy and Development Ontology prefix: ECAO pattern: ^\d{7}$ eccode: bartoc: description: By the late 1950's it had become evident that the nomenclature of enzymology, in the absence of any guiding authority, in a period when the number of known enzymes was increasing rapidly, was getting out of hand. The naming of enzymes by individual workers had proved far from satisfactory in practice. In many cases the same enzymes became known by several different names, while conversely the same name was sometimes given to different enzymes. Many of the names conveyed little or no idea of the nature of the reactions catalysed, and similar names were sometimes given to enzymes of quite different types. To meet this situation, various attempts to bring order into the general nomenclature of enzymes, or into that of particular groups of enzymes, were made by individuals or small groups of specialists, but none of the resulting nomenclatures met with general approval. (...) The Enzyme List in the sixth edition (1992) contains 3540 entries, of which 178 record enzymes which are now transferred elsewhere in the list, and 166 have been deleted completely. Thus the number of enzymes actually listed is 3196, an increase of 29% on the 1984 edition. homepage: https://www.abbexa.com/enzyme-commission-number name: Enzyme Nomenclature prefix: '671' wikidata_database: Q741108 biocontext: is_identifiers: true is_obo: false prefix: EC-CODE uri_format: http://identifiers.org/ec-code/$1 contact: email: kristian.axelsen@sib.swiss github: kaxelsen name: Kristian Axelsen orcid: 0000-0003-3889-2879 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: EC Number description: In its report in 1961, the first Enzyme Commission devised a system for enzyme classification that also serves as a basis for assigning code numbers. These code numbers, prefixed by EC, contain four elements separated by points / full stops and are now widely in use. The first number shows to which of the six main divisions (classes) the enzyme belongs and therefore identifies the class of reaction catalysed. The second number indicates the subclass, and generally contains information about the type of compound or group involved. The third figure gives the sub-subclass, which further specifies the type of reaction involved. The fourth figure is the serial number of the enzyme in its sub-subclass. homepage: https://www.qmul.ac.uk/sbcs/iubmb/enzyme/rules.html name: Enzyme Commission Number prefix: FAIRsharing.rfLD2u publications: [] subjects: - Biochemistry - Enzymology go: homepage: http://enzyme.expasy.org/ name: Enzyme Commission prefix: EC uri_format: https://enzyme.expasy.org/EC/$1 homepage: https://www.enzyme-database.org/ mappings: bartoc: '671' biocontext: EC-CODE edam: '1011' fairsharing: FAIRsharing.rfLD2u go: EC miriam: ec-code n2t: ec-code prefixcommons: intenz re3data: r3d100010803 uniprot: DB-0024 wikidata: P591 miriam: deprecated: false description: The Enzyme Classification contains the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the nomenclature and classification of enzyme-catalysed reactions. homepage: https://www.ebi.ac.uk/intenz/ id: '00000004' name: Enzyme Nomenclature namespaceEmbeddedInLui: false pattern: ^\d+\.-\.-\.-|\d+\.\d+\.-\.-|\d+\.\d+\.\d+\.-|\d+\.\d+\.\d+\.(n)?\d+$ 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 publications: - doi: 10.1093/nar/28.1.304 pmc: PMC102465 pubmed: '10592255' title: The ENZYME database in 2000. year: 2000 re3data: description: IntEnz contains the recommendation of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the nomenclature and classification of enzyme-catalyzed reactions. Users can browse by enzyme classification or use advanced search options to search enzymes by class, subclass and sub-subclass information. homepage: https://www.ebi.ac.uk/intenz/ name: Integrated Relational Enzyme database prefix: r3d100010803 synonyms: - IntEnz xrefs: fairsharing: FAIRsharing.q1fdkc nif: 0000-03028 omics: 02684 scr: 002992 references: - https://github.com/biopragmatics/bioregistry/issues/681 synonyms: - EC - EC number - EC-CODE - ECCODE - EC_CODE - ec-code - intenz uniprot: abbreviation: ENZYME category: Enzyme and pathway databases homepage: https://enzyme.expasy.org/ name: Enzyme nomenclature database prefix: DB-0024 publications: - doi: 10.1093/nar/28.1.304 pubmed: '10592255' uri_format: https://enzyme.expasy.org/EC/$1 uri_format: https://www.ebi.ac.uk/intenz/query?cmd=SearchEC&ec=$1 wikidata: database: Q741108 description: classification scheme for enzymes example: - 1.1.1.1 - 2.7.3.2 homepage: http://www.chem.qmul.ac.uk/iubmb/enzyme/ name: EC enzyme number pattern: ^\d\.\d{1,2}\.\d{1,2}\.\d{1,3}$ prefix: P591 uri_format: http://enzyme.expasy.org/EC/$1 ecg: aberowl: description: The Electrocardiography (ECG) Ontology is a Driving Biological Project of the NCBO. The ECG Ontology will contain terms for describing electrocardiograms, their capture method(s) and their waveforms. download_owl: http://aber-owl.net/media/ontologies/ECG/12/ecg.owl homepage: http://www.cvrgrid.org name: Electrocardiography Ontology prefix: ECG version: '1' bioportal: contact: email: rwinslow@jhu.edu name: Raimond L. Winslow, PhD & Stephen Granite description: The Electrocardiography (ECG) Ontology is a Driving Biological Project of the NCBO. The ECG Ontology will contain terms for describing electrocardiograms, their capture method(s) and their waveforms. homepage: http://www.cvrgrid.org name: Electrocardiography Ontology prefix: ECG version: '1' contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The Electrocardiography (ECG) Ontology is a Driving Biological Project of the NCBO. The ECG Ontology will contain terms for describing electrocardiograms, their capture method(s) and their waveforms. example: 000000159 fairsharing: abbreviation: ECG contact: email: rwinslow@jhu.edu name: Raimond Winslow orcid: 0000-0003-1719-1651 description: The Electrocardiography (ECG) Ontology is a Driving Biological Project of the NCBO. The ECG Ontology will contain terms for describing electrocardiograms, their capture method(s) and their waveforms. This ontology was developed and is being maintained by the CardioVascular Research Grid (www.cvrg.org). homepage: http://wiki.cvrgrid.org/index.php/Ontology_Development name: ElectroCardioGraphy Ontology prefix: FAIRsharing.azr389 publications: - doi: 10.1016/j.jbi.2010.08.007 pubmed_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=$1 mappings: biocontext: ECHOBASE go: EchoBASE miriam: echobase n2t: echobase prefixcommons: echobase re3data: r3d100011646 uniprot: DB-0020 miriam: deprecated: false description: EchoBASE is a database designed to contain and manipulate information from post-genomic experiments using the model bacterium Escherichia coli K-12. The database is built on an enhanced annotation of the updated genome sequence of strain MG1655 and the association of experimental data with the E.coli genes and their products. homepage: http://www.york.ac.uk/ id: '00000200' name: EchoBASE namespaceEmbeddedInLui: false pattern: ^EB\d+$ prefix: echobase sampleId: EB0170 uri_format: http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=$1 n2t: description: EchoBASE is a database designed to contain and manipulate information from post-genomic experiments using the model bacterium Escherichia coli K-12. The database is built on an enhanced annotation of the updated genome sequence of strain MG1655 and the association of experimental data with the E.coli genes and their products. example: EB0170 homepage: http://www.york.ac.uk/ name: EchoBASE at the University of York namespaceEmbeddedInLui: false pattern: ^EB\d+$ prefix: echobase uri_format: http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=$1 prefixcommons: description: EchoBase is a database that curates new experimental and bioinformatic information about the genes and gene products of the model bacterium Escherichia coli K-12 strain MG1655. example: EB0170 homepage: http://www.ecoli-york.org/ keywords: - gene - gene expression name: EchoBASE - an integrated post-genomic database for E. coli pattern: ^EB\d+$ 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 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: abbreviation: EchoBASE category: Organism-specific databases homepage: https://www.york.ac.uk/res/thomas/ name: EchoBASE - an integrated post-genomic database for E. coli prefix: DB-0020 publications: - doi: 10.1093/nar/gki028 pubmed: '15608209' uri_format: https://www.york.ac.uk/res/thomas/Gene.cfm?recordID=$1 ecmdb: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: "The ECMDB is an expertly curated database containing extensive metabolomic\ \ data and metabolic pathway diagrams about Escherichia coli (strain K12, MG1655).\ \ This database includes significant quantities of \u201Coriginal\u201D data compiled\ \ by members of the Wishart laboratory as well as additional material derived\ \ from hundreds of textbooks, scientific journals, metabolic reconstructions and\ \ other electronic databases. Each metabolite is linked to more than 100 data\ \ fields describing the compound, its ontology, physical properties, reactions,\ \ pathways, references, external links and associated proteins or enzymes." example: ECMDB00005 homepage: https://ecmdb.ca name: E. coli Metabolite Database pattern: ^ECMDB\d+$ synonyms: - ECMDB uri_format: http://ecmdb.ca/compounds/$1 wikidata: database: Q17052437 ecn: cheminf: description: A seven-digit identifier for chemical substances for regulatory purposes within the European Union. name: European Community number obsolete: false prefix: '000447' contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 example: 200-003-9 homepage: https://echa.europa.eu/information-on-chemicals mappings: cheminf: '000447' wikidata: P232 pattern: ^\d{3}-\d{3}-\d$ references: - https://github.com/biopragmatics/bioregistry/issues/257 - https://en.wikipedia.org/wiki/European_Community_number wikidata: database: Q201132 description: identifier for a chemical compound per EINECS or ELINCS example: - 200-001-8 - 200-578-6 name: EC number pattern: ^(\d{3}-){2}\d$ prefix: P232 eco: aberowl: description: An ontology for experimental and other evidence statements. download_owl: http://aber-owl.net/media/ontologies/ECO/107/eco.owl homepage: https://www.evidenceontology.org name: Evidence ontology prefix: ECO bartoc: description: "The Evidence Ontology (ECO) describes types of scientific evidence\ \ within the realm of biological research that can arise from laboratory experiments,\ \ computational methods, manual literature curation, and other means. Researchers\ \ can use these types of evidence to support assertions about things (such as\ \ scientific conclusions, gene annotations, or other statements of fact) that\ \ result from scientific research. ECO comprises two high-level classes, evidence\ \ and assertion method, where evidence is defined as \u201Ca type of information\ \ that is used to support an assertion,\u201D and assertion method is defined\ \ as \u201Ca means by which a statement is made about an entity.\u201D Together\ \ evidence and assertion method can be combined to describe both the support\ \ for an assertion and whether that assertion was made by a human being or a\ \ computer. However, ECO can not be used to make the assertion itself; for that,\ \ one would use another ontology, free text description, or other means. ECO\ \ was originally created around the year 2000 to support gene product annotation\ \ by the Gene Ontology." homepage: http://code.google.com/p/evidenceontology/ name: Evidence Codes Ontology prefix: '1028' biocontext: 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/2022-12-04 example: 0007807 fairsharing: abbreviation: ECO contact: email: mchibucos@som.umaryland.edu name: Marcos Chibucos orcid: 0000-0001-9586-0780 description: The Evidence and Conclusion Ontology (ECO) contains terms that describe types of evidence and assertion methods. ECO terms are used in the process of biocuration to capture the evidence that supports biological assertions (e.g. gene product X has function Y as supported by evidence Z). Capture of this information allows tracking of annotation provenance, establishment of quality control measures, and query of eviden homepage: https://evidenceontology.org/ license: CC0-1.0 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.' repository: https://github.com/evidenceontology/evidenceontology 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_$1 mappings: aberowl: ECO bartoc: '1028' biocontext: ECO bioportal: ECO fairsharing: FAIRsharing.wvpgwn go: ECO miriam: eco n2t: eco obofoundry: eco ols: eco ontobee: ECO prefixcommons: eco wikidata: P3811 miriam: deprecated: false description: Evidence codes can be used to specify the type of supporting evidence for a piece of knowledge. This allows inference of a 'level of support' between an entity and an annotation made to an entity. homepage: https://www.ebi.ac.uk/ols/ontologies/eco id: '00000055' name: Evidence Code Ontology namespaceEmbeddedInLui: true pattern: ECO:\d{7}$ 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:$1 obofoundry: contact: mgiglio@som.umaryland.edu contact.github: mgiglio99 contact.label: Michelle Giglio contact.orcid: 0000-0001-7628-5565 deprecated: false description: An ontology for experimental and other evidence statements. domain: investigations download.obo: http://purl.obolibrary.org/obo/eco.obo download.owl: http://purl.obolibrary.org/obo/eco.owl homepage: https://www.evidenceontology.org license: CC0 1.0 license.url: https://creativecommons.org/publicdomain/zero/1.0/ name: Evidence ontology preferredPrefix: ECO prefix: eco publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/34986598 preferred: true title: 'ECO: the Evidence and Conclusion Ontology, an update for 2022.' - id: https://www.ncbi.nlm.nih.gov/pubmed/30407590 title: 'ECO, the Evidence & Conclusion Ontology: community standard for evidence information.' - id: https://www.ncbi.nlm.nih.gov/pubmed/25052702 title: Standardized description of scientific evidence using the Evidence Ontology (ECO) repository: https://github.com/evidenceontology/evidenceontology ols: description: The Evidence & Conclusion Ontology (ECO) describes types of scientific evidence within the biological research domain that arise from laboratory experiments, computational methods, literature curation, or other means. download: http://purl.obolibrary.org/obo/eco.owl homepage: https://www.evidenceontology.org name: Evidence & Conclusion Ontology (ECO) prefix: eco version: '2022-08-05' version.iri: http://purl.obolibrary.org/obo/eco/releases/2022-08-05/eco.owl ontobee: library: Library name: Evidence ontology prefix: ECO pattern: ^\d{7}$ 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=$1 publications: - doi: 10.1093/nar/gkab1025 pmc: PMC8728134 pubmed: '34986598' title: 'ECO: the Evidence and Conclusion Ontology, an update for 2022.' year: 2022 - doi: 10.1093/nar/gky1036 pmc: PMC6323956 pubmed: '30407590' title: 'ECO, the Evidence & Conclusion Ontology: community standard for evidence information.' year: 2019 - doi: 10.1007/978-1-4939-3743-1_18 pmc: PMC6377151 pubmed: '27812948' title: 'The Evidence and Conclusion Ontology (ECO): Supporting GO Annotations.' year: 2017 - doi: 10.1093/database/bau075 pmc: PMC4105709 pubmed: '25052702' title: Standardized description of scientific evidence using the Evidence Ontology (ECO). year: 2014 - doi: 10.1142/9789812704856_0019 pmc: null pubmed: '14992503' title: An evidence ontology for use in pathway/genome databases. year: 2004 wikidata: database: Q28445410 description: identifier in the Evidence & Conclusion Ontology for capturing evidence in biological research homepage: http://evidenceontology.org/ name: Evidence & Conclusion Ontology ID pattern: ^ECO:[0-9]{7}$ prefix: P3811 ecocore: aberowl: description: Ecocore is a community ontology for the concise and controlled description of ecological traits of organisms. download_owl: http://aber-owl.net/media/ontologies/ECOCORE/8/ecocore.owl homepage: https://github.com/EcologicalSemantics/ecocore name: An ontology of core ecological entities prefix: ECOCORE biocontext: is_identifiers: false is_obo: true prefix: ECOCORE uri_format: http://purl.obolibrary.org/obo/ECOCORE_$1 bioportal: homepage: https://github.com/EcologicalSemantics/ecocore name: An ontology of core ecological entities prefix: ECOCORE version: '2022-03-09' example: '00000001' mappings: aberowl: ECOCORE biocontext: ECOCORE bioportal: ECOCORE obofoundry: ecocore ols: ecocore ontobee: ECOCORE obofoundry: contact: p.buttigieg@gmail.com contact.github: pbuttigieg contact.label: Pier Luigi Buttigieg contact.orcid: 0000-0002-4366-3088 depends_on: - bfo - chebi - envo - go - iao - pato - pco - po - ro - uberon deprecated: false description: Ecocore is a community ontology for the concise and controlled description of ecological traits of organisms. domain: environment download.obo: http://purl.obolibrary.org/obo/ecocore.obo download.owl: http://purl.obolibrary.org/obo/ecocore.owl homepage: https://github.com/EcologicalSemantics/ecocore license: CC BY 3.0 license.url: http://creativecommons.org/licenses/by/3.0/ name: An ontology of core ecological entities preferredPrefix: ECOCORE prefix: ecocore repository: https://github.com/EcologicalSemantics/ecocore ols: description: Ecocore is a community ontology for the concise and controlled description of ecological traits of organisms. download: http://purl.obolibrary.org/obo/ecocore.owl homepage: https://github.com/EcologicalSemantics/ecocore name: An ontology of core ecological entities prefix: ecocore version: '2022-03-09' version.iri: http://purl.obolibrary.org/obo/ecocore/releases/2022-03-09/ecocore.owl ontobee: library: Library name: An ontology of core ecological entities prefix: ECOCORE pattern: ^\d+$ 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 42,000 publications as of 2022. Updates to EcoCyc content continue to improve its comprehensive picture of E. coli biology. The utility of EcoCyc is enhanced by new tools available on the EcoCyc web site, and the development of EcoCyc as a teaching tool is increasing the impact of the knowledge collected in EcoCyc. homepage: https://ecocyc.org/ name: EcoCyc E. coli Database prefix: FAIRsharing.65dmtr publications: - doi: 10.1093/nar/gks1027 pubmed_id: 23143106 title: 'EcoCyc: fusing model organism databases with systems biology.' - doi: 10.1093/nar/gkw1003 pubmed_id: 27899573 title: 'The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.' - doi: 10.1128/ecosalplus.ESP-0009-2013 pubmed_id: 26442933 title: The EcoCyc Database. - doi: 10.3389/fmicb.2021.711077 pubmed_id: 34394059 title: The EcoCyc Database in 2021. subjects: - Biology go: homepage: 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 re3data: r3d100011277 name: EcoCyc ncbi: example: sroC homepage: https://ecocyc.org/ name: E. coli database prefix: ECOCYC publications: - doi: 10.3389/fmicb.2021.711077 pmc: PMC8357350 pubmed: '34394059' title: The EcoCyc Database in 2021. year: 2021 - doi: 10.1093/nar/gkw1003 pmc: PMC5210515 pubmed: '27899573' title: 'The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.' year: 2016 - doi: 10.1128/ecosalplus.esp-0009-2013 pmc: PMC4243172 pubmed: '26442933' title: The EcoCyc Database. year: 2014 - doi: 10.1093/nar/gks1027 pmc: PMC3531154 pubmed: '23143106' title: 'EcoCyc: fusing model organism databases with systems biology.' year: 2012 re3data: description: EcoCyc is a scientific database for the bacterium Escherichia coli K-12 MG1655. The EcoCyc project performs literature-based curation of the entire genome, and of transcriptional regulation, transporters, and metabolic pathways. homepage: https://ecocyc.org/ name: EcoCyc Database prefix: r3d100011277 synonyms: - EcoCyc E. coli Database - Encyclopedia of E. coli Genes and Metabolism xrefs: fairsharing: FAIRsharing.65dmtr nif: 0000-02783 omics: '01645' scr: '002433' uri_format: https://biocyc.org/gene?id=$1 ecogene: biocontext: is_identifiers: false is_obo: false prefix: EcoGene uri_format: http://ecogene.org/gene/$1 fairsharing: abbreviation: EcoGene description: The EcoGene database contains updated information about the E. coli K-12 genome and proteome sequences, including extensive gene bibliographies. A major EcoGene focus has been the re-evaluation of translation start sites. homepage: http://ecogene.org/ name: Escherichia coli strain K12 genome database prefix: FAIRsharing.3q3kvn publications: - doi: 10.1093/nar/28.1.60 pubmed_id: 10592181 title: 'EcoGene: a genome sequence database for Escherichia coli K-12.' subjects: [] mappings: biocontext: EcoGene fairsharing: FAIRsharing.3q3kvn miriam: ecogene n2t: ecogene ncbi: EcoGene prefixcommons: ecogene re3data: r3d100010546 miriam: deprecated: false description: The EcoGene database contains updated information about the E. coli K-12 genome and proteome sequences, including extensive gene bibliographies. A major EcoGene focus has been the re-evaluation of translation start sites. homepage: http://ecogene.org/ id: '00000163' name: EcoGene namespaceEmbeddedInLui: false pattern: ^EG\d+$ 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 keywords: - ecology - environmental science name: EcoLexicon ecoliwiki: biocontext: is_identifiers: true is_obo: false prefix: ECOLIWIKI uri_format: http://identifiers.org/ecoliwiki/$1 fairsharing: abbreviation: EcoliWiki description: EcoliWiki is a community-based resource for the annotation of all non-pathogenic E. coli, its phages, plasmids, and mobile genetic elements. homepage: https://ecoliwiki.org/colipedia/index.php/Welcome_to_EcoliWiki name: EcoliWiki prefix: FAIRsharing.tx95wa publications: - doi: 10.1016/j.tim.2009.04.004 pubmed_id: 19576778 title: What we can learn about Escherichia coli through application of Gene Ontology. subjects: - Genomics - Bioinformatics - Life Science - Ontology and Terminology go: description: EcoliHub\'s subsystem for community annotation of E. coli K-12 homepage: http://ecoliwiki.net/ name: EcoliWiki from EcoliHub prefix: EcoliWiki mappings: biocontext: ECOLIWIKI fairsharing: FAIRsharing.tx95wa go: EcoliWiki miriam: ecoliwiki n2t: ecoliwiki miriam: deprecated: false description: EcoliWiki is a wiki-based resource to store information related to non-pathogenic E. coli, its phages, plasmids, and mobile genetic elements. This collection references genes. homepage: http://ecoliwiki.net/colipedia/ id: '00000442' name: EcoliWiki namespaceEmbeddedInLui: false pattern: ^[A-Za-z0-9-]+$ 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 publications: - doi: 10.1016/j.tim.2009.04.004 pmc: PMC3575750 pubmed: '19576778' title: What we can learn about Escherichia coli through application of Gene Ontology. year: 2009 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/11/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: homepage: https://github.com/EnvironmentOntology/environmental-exposure-ontology name: Environmental conditions, treatments and exposures ontology prefix: ECTO version: '2022-12-12' 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). domain: environment download.json: http://purl.obolibrary.org/obo/ecto.json download.obo: http://purl.obolibrary.org/obo/ecto.obo download.owl: http://purl.obolibrary.org/obo/ecto.owl homepage: https://github.com/EnvironmentOntology/environmental-exposure-ontology license: CC0 1.0 license.url: https://creativecommons.org/publicdomain/zero/1.0/ 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: '2022-12-12' version.iri: http://purl.obolibrary.org/obo/ecto/releases/2022-12-12/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/$1/ n2t: description: E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references entities. example: '23' homepage: http://www.e-cyanobacterium.org/bcs/entity/ name: e-cyanobacterium entity at Masaryk University Brno namespaceEmbeddedInLui: false pattern: ^\d+$ 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/$1/ n2t: description: E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references models. example: '26' homepage: http://e-cyanobacterium.org/models/ name: e-cyanobacterium entity at Masaryk University Brno namespaceEmbeddedInLui: false pattern: ^\d+$ 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/$1/ n2t: description: E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references rules. example: '56' homepage: http://www.e-cyanobacterium.org/bcs/rule/ name: e-cyanobacterium entity at Masaryk University Brno namespaceEmbeddedInLui: false pattern: ^\d+$ 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." homepage: http://edamontology.org license: CC BY-SA 4.0 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.' repository: https://github.com/edamontology/edamontology subjects: - Bioinformatics - Life Science twitter: edamontology 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-FORM