aberowl: availability: alternate_providers: irrelevant contact: missing description: required example: irrelevant fair: true fair_note: null homepage: required license: missing name: required pattern: missing provider: irrelevant search: true synonyms: missing version: present contact: email: ali.syed@kaust.edu.sa github: aliraza995 name: Ali Syed orcid: 0000-0002-5103-9058 description: AberOWL is a framework for ontology-based access to biological data. It consists of a repository of bio-ontologies, a set of webservices which provide access to OWL(-EL) reasoning over the ontologies, and several frontends which utilise the ontology repository and reasoning services to provide access to specific biological datasets. download: http://aber-owl.net/api/ontology/?format=json example: CHEBI governance: accepts_external_contributions: false comments: null curates: false curation: import imports: false public_version_control: false review_team: n/a scope: bio-ontologies status: active homepage: http://aber-owl.net license: See https://github.com/biopragmatics/bioregistry/issues/339 name: AberOWL prefix: aberowl provider_uri_format: http://aber-owl.net/ontology/$1 resolver_type: lookup resolver_uri_format: http://aber-owl.net/ontology/$1/#/Browse/ agroportal: availability: alternate_providers: irrelevant contact: present description: required example: irrelevant fair: false fair_note: The API for AgroPortal requires authentication homepage: required license: present name: required pattern: missing provider: irrelevant search: false synonyms: missing version: present contact: email: clement.jonquet@inrae.fr github: jonquet name: Clement Jonquet orcid: 0000-0002-2404-1582 description: A vocabulary and ontology repository for agronomy and related domains. example: ENVO governance: accepts_external_contributions: true comments: null curates: true curation: opaque-review imports: false public_version_control: false review_team: private scope: agro-ontologies status: active homepage: http://agroportal.lirmm.fr license: See https://github.com/biopragmatics/bioregistry/issues/336 name: AgroPortal prefix: agroportal provider_uri_format: http://agroportal.lirmm.fr/ontologies/$1 biocontext: availability: alternate_providers: missing contact: missing description: missing example: missing fair: true fair_note: null homepage: missing license: missing name: missing pattern: missing provider: present search: false synonyms: missing version: missing contact: email: cjmungall@lbl.gov github: cmungall name: Chris Mungall orcid: 0000-0002-6601-2165 description: BioContext contains modular JSON-LD contexts for bioinformatics data. download: https://raw.githubusercontent.com/prefixcommons/biocontext/master/registry/commons_context.jsonld example: CHEBI governance: accepts_external_contributions: true comments: null curates: true curation: open-review imports: false public_version_control: true review_team: inferrable scope: internal status: active homepage: https://github.com/prefixcommons/biocontext license: missing name: BioContext prefix: biocontext provider_uri_format: https://bioregistry.io/metaregistry/biocontext/$1 biolink: availability: alternate_providers: missing contact: missing description: missing example: missing fair: true fair_note: null homepage: missing license: present name: required pattern: missing provider: required search: false synonyms: missing version: missing bioregistry_prefix: biolink contact: email: deepak.unni3@lbl.gov github: deepakunni3 name: Deepak Unni orcid: 0000-0002-3583-7340 description: A modeling paradigm-specific registry of prefixes and their URL expansions download: https://raw.githubusercontent.com/biolink/biolink-model/master/biolink-model.yaml example: doi governance: accepts_external_contributions: true comments: null curates: true curation: open-review imports: false public_version_control: true review_team: inferrable scope: internal status: active homepage: https://github.com/biolink/biolink-model license: Apache 2.0 name: Biolink Model Registry prefix: biolink short_name: Biolink bioportal: availability: alternate_providers: irrelevant contact: present description: required example: irrelevant fair: false fair_note: The API for BioPortal requires authentication homepage: required license: missing name: required pattern: missing provider: irrelevant search: false synonyms: missing version: required bioregistry_prefix: bioportal contact: email: jgraybeal@stanford.edu github: graybeal name: John Graybeal orcid: 0000-0001-6875-5360 description: The BioPortal is a less stringent registry of biomedical ontologies than the OBO Foundry example: CHEBI governance: accepts_external_contributions: true comments: null curates: true curation: opaque-review imports: false public_version_control: false review_team: private scope: bio-ontologies status: active homepage: https://bioportal.bioontology.org/ license: See https://github.com/biopragmatics/bioregistry/issues/337 name: BioPortal Prefixes prefix: bioportal provider_uri_format: https://bioportal.bioontology.org/ontologies/$1 short_name: BioPortal bioregistry: availability: alternate_providers: present contact: present description: required example: required fair: true fair_note: null homepage: required license: present name: required pattern: present provider: present search: true synonyms: present version: present bioregistry_prefix: bioregistry contact: 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. download: https://bioregistry.io/api/registry/ example: chebi governance: accepts_external_contributions: true comments: null curates: true curation: open-review imports: true public_version_control: true review_team: public scope: life sciences status: active homepage: https://bioregistry.io license: CC0 name: Bioregistry prefix: bioregistry provider_uri_format: https://bioregistry.io/registry/$1 resolver_type: resolver resolver_uri_format: https://bioregistry.io/$1:$2 cellosaurus: availability: alternate_providers: missing contact: missing description: missing example: missing fair: true fair_note: Data is available but requires custom parser homepage: required license: missing name: required pattern: missing provider: required search: false synonyms: missing version: missing bioregistry_prefix: cellosaurus.resource contact: email: Amos.Bairoch@sib.swiss github: AmosBairoch name: Amos Bairoch orcid: 0000-0003-2826-6444 description: The set of prefixes used in the Cellosaurus resource example: 4DN governance: accepts_external_contributions: false comments: null curates: true curation: private imports: false public_version_control: false review_team: n/a scope: internal status: active homepage: https://web.expasy.org/cellosaurus/ license: CC BY 4.0 name: Cellosaurus Registry prefix: cellosaurus short_name: Cellosaurus cheminf: availability: alternate_providers: missing contact: missing description: missing example: missing fair: false fair_note: No additional metadata included besides name in ontology homepage: missing license: missing name: required pattern: missing provider: missing search: false synonyms: missing version: missing bioregistry_prefix: cheminf contact: email: egon.willighagen@gmail.com github: egonw name: Egon Willighagen orcid: 0000-0001-7542-0286 description: Contains entries for various database identifiers example: '000140' governance: accepts_external_contributions: true comments: null curates: true curation: open-review imports: false public_version_control: true review_team: inferrable scope: chemistry status: unresponsive homepage: https://github.com/semanticchemistry/semanticchemistry license: CC BY 3.0 name: Chemical Information Ontology prefix: cheminf provider_uri_format: https://www.ebi.ac.uk/ols/ontologies/cheminf/terms?iri=http%3A%2F%2Fsemanticscience.org%2Fresource%2FCHEMINF_$1 short_name: CHEMINF cropoct: availability: alternate_providers: irrelevant contact: missing description: missing example: irrelevant fair: true fair_note: null homepage: irrelevant* license: missing name: required pattern: missing provider: irrelevant search: true synonyms: missing version: missing contact: email: e.arnaud@cgiar.org github: elizabetharnaud name: Elizabeth Arnaud orcid: 0000-0002-6020-5919 description: The Crop Ontology (CO) current objective is 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 download: https://cropontology.org/metadata example: CO_010 governance: accepts_external_contributions: true comments: null curates: true curation: opaque-review imports: false public_version_control: false review_team: public scope: agro-ontologies status: active homepage: https://www.cropontology.org license: CC BY 4.0 name: Crop Ontology Curation Tool prefix: cropoct provider_uri_format: https://www.cropontology.org/ontology/$1 short_name: CropOCT ecoportal: availability: alternate_providers: irrelevant contact: present description: required example: irrelevant fair: false fair_note: The API for EcoPortal requires authentication homepage: present license: present name: required pattern: missing provider: irrelevant search: false synonyms: missing version: present contact: email: xeni.kechagioglou@lifewatch.eu github: xeniacs name: Xeni Kechagioglou orcid: 0000-0003-4494-839X description: The LifeWatch ERIC repository of semantic resources for the ecological domain. example: ALIENSPECIES governance: accepts_external_contributions: true comments: null curates: true curation: opaque-review imports: false public_version_control: false review_team: private scope: eco-ontologies status: active homepage: http://ecoportal.lifewatch.eu license: See https://github.com/biopragmatics/bioregistry/issues/338 name: EcoPortal prefix: ecoportal provider_uri_format: http://ecoportal.lifewatch.eu/ontologies/$1 edam: availability: alternate_providers: missing contact: missing description: missing example: missing fair: true fair_note: null homepage: missing license: missing name: required pattern: missing provider: missing search: false synonyms: missing version: missing bioregistry_prefix: edam.data contact: email: matus.kalas@uib.no github: matuskalas name: "Mat\xFA\u0161 Kala\u0161" orcid: 0000-0002-1509-4981 description: EDAM is a comprehensive ontology of well-established, familiar concepts that are prevalent within computational biology, bioinformatics, and bioimage informatics. EDAM includes types of data and data identifiers, data formats, operations, and topics related to data analysis 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. download: http://edamontology.org/EDAM.owl example: '1004' governance: accepts_external_contributions: true comments: null curates: true curation: community imports: false public_version_control: true review_team: inferrable scope: Life Sciences status: active homepage: ' http://edamontology.org' license: CC BY 4.0-SA name: EDAM Ontology prefix: edam provider_uri_format: http://edamontology.org/data_$1 short_name: EDAM fairsharing: availability: alternate_providers: missing contact: required description: required example: missing fair: false fair_note: The API for FAIRsharing requires authentication homepage: required license: missing name: required pattern: missing provider: missing search: true synonyms: missing version: missing bioregistry_prefix: fairsharing contact: email: allyson.lister@oerc.ox.ac.uk github: allysonlister name: Allyson Lister orcid: 0000-0002-7702-4495 description: A curated, informative and educational resource on data and metadata standards, inter-related to databases and data policies. example: FAIRsharing.62qk8w governance: accepts_external_contributions: true comments: null curates: true curation: opaque-review imports: false public_version_control: false review_team: private scope: life sciences status: active homepage: https://fairsharing.org/ license: CC BY-SA 4.0 logo_url: https://api.fairsharing.org/img/fairsharing-attribution.svg name: FAIRSharing prefix: fairsharing provider_uri_format: https://fairsharing.org/$1 go: availability: alternate_providers: present contact: missing description: present example: present fair: true fair_note: null homepage: present license: missing name: required pattern: present provider: present search: false synonyms: missing version: missing bioregistry_prefix: go.resource contact: email: cjmungall@lbl.gov github: cmungall name: Chris Mungall orcid: 0000-0002-6601-2165 description: A database-specific registry supporting curation in the Gene Ontology download: https://raw.githubusercontent.com/geneontology/go-site/master/metadata/db-xrefs.yaml example: CHEBI governance: accepts_external_contributions: true comments: null curates: true curation: open-review imports: false public_version_control: true review_team: inferrable scope: internal status: inactive homepage: http://geneontology.org/ license: CC BY 4.0 name: Gene Ontology Registry prefix: go short_name: GO hl7: availability: alternate_providers: irrelevant contact: present description: present example: missing fair: false fair_note: There are no download links nor API endpoints homepage: present license: missing name: required pattern: missing provider: missing search: false synonyms: missing version: missing bioregistry_prefix: oid contact: email: ted@klein.com github: '' name: W. Ted Klein orcid: '' description: HL7 External Code Systems are stored within the greater OID system example: 2.16.840.1.113883.6.88 governance: accepts_external_contributions: true comments: null curates: true curation: opaque-review imports: false public_version_control: false review_team: n/a scope: general status: active homepage: http://www.oid-info.com/get/2.16.840.1.113883.6 license: See https://github.com/biopragmatics/bioregistry/issues/586 name: HL7 External Code Systems prefix: hl7 provider_uri_format: http://www.oid-info.com/get/$1 short_name: HL7 miriam: availability: alternate_providers: present contact: missing description: required example: required fair: true fair_note: null homepage: required license: missing name: required pattern: required provider: required search: true synonyms: missing version: missing bioregistry_prefix: miriam contact: email: hhe@ebi.ac.uk github: hHermjakob name: Henning Hermjakob orcid: 0000-0001-8479-0262 description: The Identifiers.org Resolution Service provides consistent access to life science data using Compact Identifiers. Compact Identifiers consist of an assigned unique prefix and a local provider designated accession number (prefix:accession). download: https://registry.api.identifiers.org/resolutionApi/getResolverDataset example: chebi governance: accepts_external_contributions: true comments: null curates: true curation: opaque-review imports: false public_version_control: false review_team: private scope: life sciences status: unresponsive homepage: https://identifiers.org license: CC BY 4.0 logo_url: https://identifiers.org/identifiers_logo.c7cbd962.png name: Identifiers.org prefix: miriam provider_uri_format: https://registry.identifiers.org/registry/$1 resolver_type: resolver resolver_uri_format: https://identifiers.org/$1:$2 n2t: availability: alternate_providers: present contact: missing description: required example: required fair: true fair_note: null homepage: required license: missing name: required pattern: required provider: required search: false synonyms: present version: missing bioregistry_prefix: n2t contact: email: jak@ucop.edu github: jkunze name: John Kunze orcid: 0000-0001-7604-8041 description: An ARK resolver as well as resolver built with common prefixes as in Identifiers.org download: https://n2t.net/e/n2t_full_prefixes.yaml example: chebi governance: accepts_external_contributions: false comments: null curates: false curation: import imports: true public_version_control: false review_team: n/a scope: life sciences status: active homepage: https://n2t.net license: CC0 logo_url: https://n2t.net/e/images/n2t_net_logo.png name: Name-to-Thing prefix: n2t provider_uri_format: 'https://n2t.net/$1:' resolver_type: resolver resolver_uri_format: https://n2t.net/$1:$2 short_name: N2T ncbi: availability: alternate_providers: missing contact: missing description: missing example: required fair: false fair_note: Requires web scraping homepage: required license: missing name: required pattern: missing provider: missing search: false synonyms: missing version: missing bioregistry_prefix: ncbi.resource contact: email: gb-admin@ncbi.nlm.nih.gov github: null name: GenBank Support orcid: null description: A database-specific registry supporting curation in the NCBI GenBank and related NCBI resources example: ECOCYC governance: accepts_external_contributions: false comments: null curates: true curation: private imports: false public_version_control: false review_team: n/a scope: internal status: inactive homepage: https://www.ncbi.nlm.nih.gov/genbank/collab/db_xref/ license: See https://github.com/biopragmatics/bioregistry/issues/342 name: National Center for Biotechnology Information Registry prefix: ncbi short_name: NCBI obofoundry: availability: alternate_providers: missing contact: required description: required example: missing fair: true fair_note: null homepage: required license: required name: required pattern: missing provider: missing search: false synonyms: missing version: missing contact: email: cjmungall@lbl.gov github: cmungall name: Chris Mungall orcid: 0000-0002-6601-2165 description: The mission of the OBO Foundry is to develop a family of interoperable ontologies that are both logically well-formed and scientifically accurate. download: http://www.obofoundry.org/registry/ontologies.yml example: chebi governance: accepts_external_contributions: true comments: null curates: true curation: open-review imports: false public_version_control: true review_team: public scope: bio-ontologies status: active homepage: http://www.obofoundry.org/ license: CC0 logo_url: https://obofoundry.org/images/foundrylogo.png name: OBO Foundry prefix: obofoundry provider_uri_format: http://www.obofoundry.org/ontology/$1 resolver_type: resolver resolver_uri_format: http://purl.obolibrary.org/obo/$1_$2 ols: availability: alternate_providers: irrelevant contact: present description: required example: irrelevant fair: true fair_note: null homepage: present license: required name: required pattern: missing provider: irrelevant search: true synonyms: missing version: present contact: email: henriette007@ebi.ac.uk github: henrietteharmse name: Henriette Harmse orcid: 0000-0001-7251-9504 description: 'The Ontology Lookup Service (OLS) is a repository for biomedical ontologies that aims to provide a single point of access to the latest ontology versions. ' example: chebi governance: accepts_external_contributions: true comments: Accepts suggestions through the OLS issue tracker at https://github.com/EBISPOT/OLS/issues curates: false curation: import imports: false public_version_control: false review_team: inferrable scope: bio-ontologies status: active homepage: https://www.ebi.ac.uk/ols license: See https://github.com/biopragmatics/bioregistry/issues/340 logo_url: https://www.ebi.ac.uk/ols/img/OLS_logo_2017.png name: Ontology Lookup Service prefix: ols provider_uri_format: https://www.ebi.ac.uk/ols/ontologies/$1 short_name: OLS ontobee: availability: alternate_providers: irrelevant contact: required description: required example: irrelevant fair: false fair_note: No API available, data download requires web scraping homepage: required license: missing name: required pattern: missing provider: irrelevant search: false synonyms: missing version: missing contact: email: yongqunh@med.umich.edu github: yongqunh name: Yongqun Oliver He orcid: 0000-0001-9189-9661 description: Ontobee is aimed to facilitate ontology data sharing, visualization, query, integration, and analysis. example: AGRO governance: accepts_external_contributions: false comments: null curates: false curation: import imports: false public_version_control: false review_team: n/a scope: bio-ontologies status: active homepage: http://www.ontobee.org/ license: See https://github.com/biopragmatics/bioregistry/issues/341 name: OntoBee prefix: ontobee provider_uri_format: http://www.ontobee.org/ontology/$1 resolver_type: lookup resolver_uri_format: http://www.ontobee.org/ontology/$1?iri=http://purl.obolibrary.org/obo/$1_$2 prefixcc: availability: alternate_providers: present contact: missing description: missing example: missing fair: true fair_note: null homepage: missing license: missing name: missing pattern: missing provider: required search: false synonyms: missing version: missing contact: email: richard@cyganiak.de github: cygri name: Richard Cyganiak orcid: 0000-0001-9950-5209 description: A web-developer centric archive of prefixes and URI prefixes download: https://prefix.cc/context.jsonld example: foaf governance: accepts_external_contributions: true comments: null curates: true curation: community imports: false public_version_control: true review_team: n/a scope: general status: active homepage: https://prefix.cc/ license: CC0 name: Prefix.cc prefix: prefixcc provider_uri_format: https://prefix.cc/$1 prefixcommons: availability: alternate_providers: required contact: missing description: present example: present fair: true fair_note: null homepage: present license: missing name: required pattern: present provider: present search: true synonyms: present version: missing bioregistry_prefix: prefixcommons contact: email: michel.dumontier@gmail.com github: micheldumontier name: Michel Dumontier orcid: 0000-0003-4727-9435 description: A registry of commonly used prefixes in the life sciences and linked data download: https://raw.githubusercontent.com/prefixcommons/data-ingest/master/yml/lsregistry.yml example: CHEBI governance: accepts_external_contributions: true comments: null curates: true curation: community imports: false public_version_control: false review_team: public scope: life sciences status: active homepage: https://prefixcommons.org license: missing name: Prefix Commons prefix: prefixcommons provider_uri_format: https://prefixcommons.org/?q=$1 re3data: availability: alternate_providers: missing contact: present description: required example: missing fair: false fair_note: The API for Re3data does not provide a bulk download homepage: required license: present name: required pattern: missing provider: missing search: true synonyms: missing version: missing bioregistry_prefix: re3data contact: email: mwitt@purdue.edu github: mwittin name: Michael Witt orcid: 0000-0003-4221-7956 description: Re3data is a global registry of research data repositories that covers research data repositories from different academic disciplines. example: r3d100010772 governance: accepts_external_contributions: true comments: null curates: true curation: opaque-review imports: false public_version_control: false review_team: private scope: general status: active homepage: https://www.re3data.org license: CC 0 name: Registry of Research Data Repositories prefix: re3data provider_uri_format: https://www.re3data.org/repository/$1 short_name: re3data uniprot: availability: alternate_providers: missing contact: missing description: missing example: missing fair: true fair_note: null homepage: required license: missing name: required pattern: missing provider: required search: true synonyms: missing version: missing bioregistry_prefix: uniprot.resource contact: email: agb@ebi.ac.uk github: bateman-research name: Alex Bateman orcid: 0000-0002-6982-4660 description: The cross-references section of UniProtKB entries displays explicit and implicit links to databases such as nucleotide sequence databases, model organism databases and genomics and proteomics resources. download: https://www.uniprot.org/database/?format=rdf example: '0174' governance: accepts_external_contributions: false comments: null curates: true curation: private imports: false public_version_control: false review_team: n/a scope: internal status: active homepage: https://www.uniprot.org/database/ license: CC BY 4.0 name: UniProt Cross-ref database prefix: uniprot provider_uri_format: https://www.uniprot.org/database/DB-$1 short_name: UniProt wikidata: availability: alternate_providers: present contact: present* description: required example: present fair: true fair_note: null homepage: present license: present* name: required pattern: present provider: present search: true synonyms: missing version: present* bioregistry_prefix: wikidata contact: email: info@wikidata.org github: null name: WikiData Support orcid: null description: An open, community-curated knowledgebase that contains several properties corresponding to resources listed in other biomedical registries. example: P683 governance: accepts_external_contributions: true comments: null curates: true curation: open-review imports: false public_version_control: false review_team: inferrable scope: general status: active homepage: https://www.wikidata.org license: CC0 logo_url: https://upload.wikimedia.org/wikipedia/commons/6/66/Wikidata-logo-en.svg name: Wikidata Property prefix: wikidata provider_uri_format: https://www.wikidata.org/wiki/Property:$1 short_name: Wikidata