apollosv: contact: email: hoganwr@ufl.edu github: hoganwr name: William Hogan orcid: 0000-0002-9881-1017 description: Defines terms and relations necessary for interoperation between epidemic models and public health application software that interface with these models download_owl: http://purl.obolibrary.org/obo/apollo_sv.owl example: '00000443' homepage: https://github.com/ApolloDev/apollo-sv license: CC-BY-4.0 mappings: aberowl: APOLLO_SV bioportal: APOLLO-SV fairsharing: FAIRsharing.ngv2xx obofoundry: apollo_sv ols: apollo_sv ontobee: APOLLO_SV name: Apollo Structured Vocabulary pattern: ^\d{8}$ preferred_prefix: APOLLO_SV 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 repository: https://github.com/ApolloDev/apollo-sv uri_format: http://purl.obolibrary.org/obo/APOLLO_SV_$1 version: 4.1.1 arxiv: description: arXiv is an e-print service in the fields of physics, mathematics, non-linear science, computer science, and quantitative biology. example: 0807.4956v1 homepage: https://arxiv.org/ mappings: biocontext: ARXIV miriam: arxiv n2t: arxiv prefixcommons: arxiv wikidata: P818 name: arXiv ID pattern: ^(\w+(\-\w+)?(\.\w+)?)?\d{4,7}(\.\d+(v\d+)?)?$ preferred_prefix: arxiv providers: - 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 - 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 uri_format: https://arxiv.org/abs/$1 askemo: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A custom ontology to support the epidemiology use case in ASKEM. example: '0000001' homepage: https://indralab.github.io/mira/ontology/ name: ASKEM Ontology pattern: ^\d{7}$ preferred_prefix: askemo uri_format: https://indralab.github.io/mira/ontology/$1 bfo: appears_in: - foodon - pco contact: email: phismith@buffalo.edu github: phismith name: Barry Smith orcid: 0000-0003-1384-116X description: The upper level ontology upon which OBO Foundry ontologies are built. download_obo: http://purl.obolibrary.org/obo/bfo.obo download_owl: http://purl.obolibrary.org/obo/bfo.owl example: '0000001' homepage: http://ifomis.org/bfo/ license: CC-BY-4.0 mappings: aberowl: BFO agroportal: BFO biocontext: BFO bioportal: BFO fairsharing: FAIRsharing.wcpd6f go: BFO obofoundry: bfo ols: bfo ontobee: BFO name: Basic Formal Ontology pattern: ^\d{7}$ preferred_prefix: BFO repository: https://github.com/BFO-ontology/BFO uri_format: http://purl.obolibrary.org/obo/BFO_$1 version: '2019-08-26' bioregistry: contact: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The Bioregistry is integrative meta-registry of biological databases, ontologies, and nomenclatures that is backed by an open database. example: bioregistry homepage: https://bioregistry.io name: Bioregistry preferred_prefix: bioregistry publications: - doi: 10.1101/2022.07.08.499378 pmc: null pubmed: null title: Unifying the Identification of Biomedical Entities with the Bioregistry year: 2022 repository: https://github.com/biopragmatics/bioregistry uri_format: https://bioregistry.io/registry/$1 bioregistry.collection: contact: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Manually curated collections of resources stored in the bioregistry example: '0000001' homepage: https://bioregistry.io/collection name: Bioregistry Collections pattern: ^\d{7}$ preferred_prefix: bioregistry.collection uri_format: https://bioregistry.io/collection/$1 bioregistry.registry: contact: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The Bioregistry's meta-registry example: miriam homepage: https://bioregistry.io/metaregistry/ name: Bioregistry Metaregistry preferred_prefix: bioregistry.registry uri_format: https://bioregistry.io/metaregistry/$1 bioregistry.schema: contact: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Schema for the export of the Bioregistry as RDF example: '0000001' homepage: https://bioregistry.io/schema name: Bioregistry Schema pattern: ^\d{7}$ preferred_prefix: bioregistry.schema uri_format: https://bioregistry.io/schema/#$1 bspo: contact: email: cjmungall@lbl.gov github: cmungall name: Chris Mungall orcid: 0000-0002-6601-2165 description: An ontology for respresenting spatial concepts, anatomical axes, gradients, regions, planes, sides and surfaces. These concepts can be used at multiple biological scales and in a diversity of taxa, including plants, animals and fungi. The BSPO is used to provide a source of anatomical location descriptors for logically defining anatomical entity classes in anatomy ontologies. download_json: http://purl.obolibrary.org/obo/bspo.json download_obo: https://raw.githubusercontent.com/obophenotype/biological-spatial-ontology/master/bspo.obo download_owl: http://purl.obolibrary.org/obo/bspo.owl example: 0000029 homepage: https://github.com/obophenotype/biological-spatial-ontology license: CC-BY-3.0 mappings: aberowl: BSPO biocontext: BSPO bioportal: BSPO fairsharing: FAIRsharing.newa3z obofoundry: bspo ols: bspo ontobee: BSPO name: Biological Spatial Ontology pattern: ^\d{7}$ preferred_prefix: BSPO publications: - doi: 10.1186/2041-1480-5-34 pmc: PMC4137724 pubmed: '25140222' title: 'Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology.' year: 2014 repository: https://github.com/obophenotype/biological-spatial-ontology uri_format: http://purl.obolibrary.org/obo/BSPO_$1 version: '2022-06-28' caro: appears_in: - pco contact: email: haendel@ohsu.edu github: mellybelly name: Melissa Haendel orcid: 0000-0001-9114-8737 description: None download_json: http://purl.obolibrary.org/obo/caro.json download_obo: http://purl.obolibrary.org/obo/caro.obo download_owl: http://purl.obolibrary.org/obo/caro.owl example: '0000000' homepage: https://github.com/obophenotype/caro/ license: CC-BY-4.0 mappings: aberowl: CARO biocontext: CARO bioportal: CARO fairsharing: FAIRsharing.3kcgmr go: CARO obofoundry: caro ols: caro ontobee: CARO name: Common Anatomy Reference Ontology pattern: ^\d{7}$ preferred_prefix: CARO 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 repository: https://github.com/obophenotype/caro uri_format: http://purl.obolibrary.org/obo/CARO_$1 version: '2022-02-18' cemo: contact: email: n.queralt_rosinach@lumc.nl github: NuriaQueralt name: "N\xFAria Queralt Rosinach" orcid: 0000-0003-0169-8159 contributor: email: benjamin_gyori@hms.harvard.edu github: bgyori name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 description: The covid-19 epidemiology and monitoring ontology (cemo) provides a common ontological model to make epidemiological quantitative data for monitoring the covid-19 outbreak machine-readable and interoperable to facilitate its exchange, integration and analysis, to eventually support evidence-based rapid response. download_json: https://raw.githubusercontent.com/cthoyt/covid19-epidemiology-ontology/add-artifacts/owl/cemo.json download_owl: https://raw.githubusercontent.com/NuriaQueralt/covid19-epidemiology-ontology/main/owl/cemo.owl example: secondary_attack_rate github_request_issue: 593 homepage: https://github.com/NuriaQueralt/covid19-epidemiology-ontology license: CC0-1.0 name: The COVID-19 epidemiology and monitoring ontology pattern: ^[0-9a-z_-]+$ preferred_prefix: cemo 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/$1 chebi: appears_in: - cl - envo - foodon - maxo - uberon banana: CHEBI contact: email: amalik@ebi.ac.uk github: amalik01 name: Adnan Malik orcid: 0000-0001-8123-5351 description: Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on 'small' chemical compounds. download_obo: http://purl.obolibrary.org/obo/chebi.obo download_owl: http://purl.obolibrary.org/obo/chebi.owl example: '24867' homepage: http://www.ebi.ac.uk/chebi license: CC-BY-4.0 mappings: aberowl: CHEBI bartoc: '558' biocontext: CHEBI bioportal: CHEBI cellosaurus: ChEBI cheminf: '000407' edam: '1174' fairsharing: FAIRsharing.62qk8w go: CHEBI miriam: chebi n2t: chebi obofoundry: chebi ols: chebi ontobee: CHEBI prefixcommons: chebi re3data: r3d100012626 wikidata: P683 name: Chemical Entities of Biological Interest namespace_in_lui: true pattern: ^\d+$ preferred_prefix: CHEBI 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 repository: https://github.com/ebi-chebi/ChEBI synonyms: - CHEBI - CHEBIID - ChEBI twitter: chebit uri_format: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:$1 version: '211' cido: contact: email: yongqunh@med.umich.edu github: yongqunh name: Yongqun Oliver He orcid: 0000-0001-9189-9661 description: The Ontology of Coronavirus Infectious Disease (CIDO) is a community-driven open-source biomedical ontology in the area of coronavirus infectious disease. The CIDO is developed to provide standardized human- and computer-interpretable annotation and representation of various coronavirus infectious diseases, including their etiology, transmission, pathogenesis, diagnosis, prevention, and treatment. download_owl: https://github.com/CIDO-ontology/cido/raw/master/cido.owl example: '0000005' homepage: https://github.com/cido-ontology/cido license: CC-BY-4.0 mappings: aberowl: CIDO bioportal: CIDO fairsharing: FAIRsharing.aVmpKl obofoundry: cido ols: cido ontobee: CIDO name: Coronavirus Infectious Disease Ontology pattern: ^\d{7}$ preferred_prefix: CIDO publications: - doi: null pmc: null pubmed: '36271389' title: 'A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology' year: null - 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 repository: https://github.com/cido-ontology/cido uri_format: http://purl.obolibrary.org/obo/CIDO_$1 version: 1.0.337 cl: appears_in: - go - uberon banana: CL contact: email: addiehl@buffalo.edu github: addiehl name: Alexander Diehl orcid: 0000-0001-9990-8331 depends_on: - chebi - go - ncbitaxon - pato - pr - ro - uberon description: The Cell Ontology is designed as a structured controlled vocabulary for cell types. The ontology was constructed for use by the model organism and other bioinformatics databases, incorporating cell types from prokaryotes to mammals, and includes plants and fungi. download_obo: https://raw.githubusercontent.com/obophenotype/cell-ontology/master/cl-full.obo download_owl: http://purl.obolibrary.org/obo/cl.owl example: '0000062' homepage: https://obophenotype.github.io/cell-ontology/ license: CC-BY-4.0 mappings: aberowl: CL agroportal: CL biocontext: CL bioportal: CL cellosaurus: CL fairsharing: FAIRsharing.j9y503 go: CL miriam: cl n2t: cl obofoundry: cl ols: cl ontobee: CL prefixcommons: cl wikidata: P7963 name: Cell Ontology namespace_in_lui: true pattern: ^\d{7}$ preferred_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 repository: https://github.com/obophenotype/cell-ontology uri_format: https://www.ebi.ac.uk/ols/ontologies/cl/terms?obo_id=CL:$1 version: '2022-10-28' cmo: contact: email: jrsmith@mcw.edu github: jrsjrs name: Jennifer Smith orcid: 0000-0002-6443-9376 description: Morphological and physiological measurement records generated from clinical and model organism research and health programs. download_obo: http://purl.obolibrary.org/obo/cmo.obo download_owl: http://purl.obolibrary.org/obo/cmo.owl example: '0001350' homepage: http://rgd.mcw.edu/rgdweb/ontology/search.html license: CC0-1.0 mappings: aberowl: CMO biocontext: CMO bioportal: CMO fairsharing: FAIRsharing.dq78pn obofoundry: cmo ols: cmo ontobee: CMO name: Clinical measurement ontology pattern: ^\d{7}$ preferred_prefix: CMO publications: - doi: 10.1186/2041-1480-4-26 pmc: PMC3882879 pubmed: '24103152' title: 'The clinical measurement, measurement method and experimental condition ontologies: expansion, improvements and new applications.' year: 2013 - doi: 10.3389/fgene.2012.00087 pmc: PMC3361058 pubmed: '22654893' title: Three ontologies to define phenotype measurement data. year: 2012 repository: https://github.com/rat-genome-database/CMO-Clinical-Measurement-Ontology twitter: ratgenome uri_format: http://purl.obolibrary.org/obo/CMO_$1 version: '2019-02-19' 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 license: CC-BY-4.0 name: Common Core Ontologies preferred_prefix: commoncoreontology repository: https://github.com/CommonCoreOntology/CommonCoreOntologies uri_format: http://www.ontologyrepository.com/CommonCoreOntologies/$1 covoc: contact: email: zmp@ebi.ac.uk github: zoependlington name: "Zo\xEB May Pendlington" orcid: 0000-0002-4071-8397 description: The COVID-19 Vocabulary (COVoc) is an ontology containing terms related to the research of the COVID-19 pandemic. This includes host organisms, pathogenicity, gene and gene products, barrier gestures, treatments and more. download_json: https://github.com/EBISPOT/covoc/releases/download/current/covoc.json download_obo: https://github.com/EBISPOT/covoc/releases/download/current/covoc.obo download_owl: https://github.com/EBISPOT/covoc/releases/download/current/covoc.owl example: '0010034' homepage: https://github.com/EBISPOT/covoc mappings: ols: covoc name: CoVoc Coronavirus Vocabulary pattern: ^\d{7}$ preferred_prefix: covoc repository: https://github.com/EBISPOT/covoc uri_format: http://purl.obolibrary.org/obo/COVOC_$1 version: '2020-08-28' dbo: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: This ontology is generated from the manually created specifications in the dbpedia mappings wiki. each release of this ontology corresponds to a new release of the dbpedia data set which contains instance data extracted from the different language versions of wikipedia. for information regarding changes in this ontology, please refer to the dbpedia mappings wiki. example: careerPrizeMoney github_request_issue: 515 homepage: https://dbpedia.org/ontology name: DBPedia Ontology preferred_prefix: dbo uri_format: https://dbpedia.org/ontology/$1 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. download_owl: http://aber-owl.net/media/ontologies/DC/3/dc.owl example: contributor homepage: https://www.dublincore.org/specifications/dublin-core/dcmi-terms/ mappings: aberowl: DC biocontext: dc bioportal: DC fairsharing: FAIRsharing.3nx7t name: Dublin Core preferred_prefix: dc synonyms: - dc11 uri_format: http://purl.org/dc/elements/1.1/$1 dcterms: contact: email: futo@stanford.edu github: null name: Michelle Futornick orcid: null contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: This document is an up-to-date specification of all metadata terms maintained by the Dublin Core Metadata Initiative, including properties, vocabulary encoding schemes, syntax encoding schemes, and classes. download_owl: http://aber-owl.net/media/ontologies/dcterms/1/dcterms.owl example: title 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 preferred_prefix: dcterms synonyms: - dc.terms - dct uri_format: http://purl.org/dc/terms/$1 debio: contact: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: A repository for the TSV-based, decentralized, community-curated curation of terms, properties, and relations that get turned into OBO, OWL, and OBO Graph JSON. download_json: https://raw.githubusercontent.com/biopragmatics/debio/main/releases/current/debio.json download_obo: https://raw.githubusercontent.com/biopragmatics/debio/main/releases/current/debio.obo download_owl: https://raw.githubusercontent.com/biopragmatics/debio/main/releases/current/debio.owl example: '0000001' homepage: https://biopragmatics.github.io/debio name: Decentralized Biomedical Ontology pattern: ^\d{7}$ 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/$1 disdriv: contact: email: lynn.schriml@gmail.com github: lschriml name: Lynn Schriml orcid: 0000-0001-8910-9851 description: Drivers of human diseases including environmental, maternal and social exposures. download_owl: http://purl.obolibrary.org/obo/disdriv.owl example: '0000000' homepage: http://www.disease-ontology.org license: CC0-1.0 mappings: aberowl: DISDRIV bioportal: DISDRIV obofoundry: disdriv ols: disdriv ontobee: DISDRIV name: Disease Drivers Ontology pattern: ^\d+$ preferred_prefix: DISDRIV repository: https://github.com/DiseaseOntology/DiseaseDriversOntology twitter: diseaseontology uri_format: http://purl.obolibrary.org/obo/DISDRIV_$1 doi: banana: doi comment: 'The [DOI resolution factsheet](https://www.doi.org/factsheets/DOIProxy.html) specifies that `https://doi.org/DOI` is the preferred format: > Users may resolve DOI names that are structured to use the DOI system Proxy Server (https://doi.org (preferred)). The resolution of the DOI name in this case depends on the use of URL syntax: the example DOI name doi:10.10.123/456 would be resolved from the address: "https://doi.org/10.123/456". Any standard browser encountering a DOI name in this form will be able to resolve it. The proxy service (both doi.org and the **earlier but no longer preferred** dx.doi.org) is accessible over IPv6, and supports DNSSEC. The proxy servers respond to HTTPS (**preferred**) as well as HTTP requests.' contributor_extras: - email: cjmungall@lbl.gov github: cmungall name: Chris Mungall orcid: 0000-0002-6601-2165 - email: null github: dhimmel name: Daniel Himmelstein orcid: 0000-0002-3012-7446 description: The Digital Object Identifier System is for identifying content objects in the digital environment. example: 10.1038/s41597-022-01807-3 example_extras: - 10.21/FQSQT4T3 - 10.1333/s00897980202a - 10.1139/z02-135 - 10.1016/j.foodchem.2008.11.065 - 10.1093/acprof:oso/9780195159561.001.1 homepage: https://www.doi.org/ mappings: biocontext: DOI biolink: doi cellosaurus: DOI edam: '1188' fairsharing: FAIRsharing.hFLKCn go: DOI miriam: doi n2t: doi prefixcommons: doi wikidata: P356 name: Digital Object Identifier pattern: ^10.\d{2,9}/.*$ preferred_prefix: doi providers: - 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 - 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: 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 references: - https://github.com/biopragmatics/bioregistry/issues/287 - https://github.com/biopragmatics/bioregistry/pull/316 uri_format: https://doi.org/$1 doid: banana: DOID contact: email: lynn.schriml@gmail.com github: lschriml name: Lynn Schriml orcid: 0000-0001-8910-9851 description: The Disease Ontology has been developed as a standardized ontology for human disease with the purpose of providing the biomedical community with consistent, reusable and sustainable descriptions of human disease terms, phenotype characteristics and related medical vocabulary disease concepts. download_json: http://purl.obolibrary.org/obo/doid.json download_obo: https://github.com/DiseaseOntology/HumanDiseaseOntology/raw/main/src/ontology/doid.obo download_owl: http://purl.obolibrary.org/obo/doid.owl example: 0110974 homepage: http://www.disease-ontology.org license: CC0-1.0 mappings: aberowl: DOID bartoc: '576' biocontext: DOID bioportal: DOID fairsharing: FAIRsharing.8b6wfq miriam: doid n2t: doid obofoundry: doid ols: doid ontobee: DOID prefixcommons: do wikidata: P699 name: Human Disease Ontology namespace_in_lui: true pattern: ^\d+$ preferred_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 - 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 repository: https://github.com/DiseaseOntology/HumanDiseaseOntology synonyms: - do twitter: diseaseontology uri_format: https://www.ebi.ac.uk/ols/ontologies/doid/terms?obo_id=DOID:$1 version: '2022-09-29' dpo: comment: DPO is a subset of terms from FBcv contact: email: cp390@cam.ac.uk github: Clare72 name: Clare Pilgrim orcid: 0000-0002-1373-1705 description: An ontology for the description of Drosophila melanogaster phenotypes. download_json: http://purl.obolibrary.org/obo/dpo.json download_obo: http://purl.obolibrary.org/obo/dpo.obo download_owl: http://purl.obolibrary.org/obo/dpo.owl homepage: http://purl.obolibrary.org/obo/fbcv license: CC-BY-4.0 mappings: aberowl: DPO bioportal: DPO obofoundry: dpo ols: dpo ontobee: DPO name: Drosophila Phenotype Ontology no_own_terms: true 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 repository: https://github.com/FlyBase/drosophila-phenotype-ontology uri_format: http://purl.obolibrary.org/obo/FBcv_$1 version: '2022-08-11' dron: contact: email: hoganwr@gmail.com github: hoganwr name: William Hogan orcid: 0000-0002-9881-1017 description: We built this ontology primarily to support comparative effectiveness researchers studying claims data. They need to be able to query U.S. National Drug Codes (NDCs) by ingredient, mechanism of action (beta-adrenergic blockade), physiological effect (diuresis), and therapeutic intent (anti-hypertensive). download_json: http://purl.obolibrary.org/obo/dron.json download_obo: http://purl.obolibrary.org/obo/dron.obo download_owl: http://purl.obolibrary.org/obo/dron.owl example: '00023232' homepage: https://github.com/ufbmi/dron license: CC-BY-3.0 mappings: aberowl: DRON biocontext: DRON bioportal: DRON fairsharing: FAIRsharing.w5ntfd obofoundry: dron ols: dron ontobee: DRON name: The Drug Ontology pattern: ^\d{8}$ preferred_prefix: DRON publications: - doi: 10.1186/s13326-017-0121-5 pmc: PMC5335794 pubmed: '28253937' title: 'Therapeutic indications and other use-case-driven updates in the drug ontology: anti-malarials, anti-hypertensives, opioid analgesics, and a large term request.' year: 2017 - doi: 10.1186/s13326-016-0048-2 pmc: PMC4836073 pubmed: '27096073' title: An accurate and precise representation of drug ingredients. year: 2016 - doi: 10.1186/2041-1480-4-44 pmc: PMC3931349 pubmed: '24345026' title: Building a drug ontology based on RxNorm and other sources. year: 2013 repository: https://github.com/ufbmi/dron uri_format: http://purl.obolibrary.org/obo/DRON_$1 version: '2022-04-22' dso: contact: email: evan@epatters.org github: epatters name: Evan Patterson orcid: 0000-0002-8600-949X contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The Data Science Ontology is a research project of IBM Research AI and Stanford University Statistics. Its long-term objective is to improve the efficiency and transparency of collaborative, data-driven science. example: classification-model homepage: https://www.datascienceontology.org/ name: Data Science Ontology preferred_prefix: dso repository: https://github.com/IBM/datascienceontology uri_format: https://www.datascienceontology.org/concept/$1 eco: banana: ECO contact: email: mgiglio@som.umaryland.edu github: mgiglio99 name: Michelle Giglio orcid: 0000-0001-7628-5565 description: Evidence codes can be used to specify the type of supporting evidence for a piece of knowledge. This allows inference of a 'level of support' between an entity and an annotation made to an entity. download_obo: http://purl.obolibrary.org/obo/eco.obo download_owl: http://purl.obolibrary.org/obo/eco.owl example: 0007807 homepage: https://www.evidenceontology.org license: CC0-1.0 mappings: aberowl: ECO bartoc: '1028' biocontext: ECO bioportal: ECO fairsharing: FAIRsharing.wvpgwn go: ECO miriam: eco n2t: eco obofoundry: eco ols: eco ontobee: ECO prefixcommons: eco wikidata: P3811 name: Evidence ontology namespace_in_lui: true pattern: ^\d{7}$ preferred_prefix: ECO publications: - doi: null pmc: null pubmed: '34986598' title: 'ECO: the Evidence and Conclusion Ontology, an update for 2022.' year: null - 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 repository: https://github.com/evidenceontology/evidenceontology uri_format: https://www.ebi.ac.uk/ols/ontologies/eco/terms?obo_id=ECO:$1 version: '2022-08-05' efo: contact: email: plwhetzel@gmail.com github: twhetzel name: Trish Whetzel orcid: 0000-0002-3458-4839 description: The Experimental Factor Ontology (EFO) provides a systematic description of many experimental variables available in EBI databases. It combines parts of several biological ontologies, such as anatomy, disease and chemical compounds. The scope of EFO is to support the annotation, analysis and visualization of data handled by the EBI Functional Genomics Team. download_obo: http://www.ebi.ac.uk/efo/efo.obo download_owl: http://www.ebi.ac.uk/efo/efo.owl example: '0005147' homepage: http://www.ebi.ac.uk/efo mappings: aberowl: EFO agroportal: EFO biocontext: EFO biolink: EFO bioportal: EFO cellosaurus: EFO fairsharing: FAIRsharing.1gr4tz miriam: efo n2t: efo ols: efo ontobee: EFO name: Experimental Factor Ontology pattern: ^\d{7}$ preferred_prefix: EFO providers: - code: ebi description: EFO through Functional Genomics Group (EBI) homepage: https://www.ebi.ac.uk/efo/ name: EFO through Functional Genomics Group (EBI) uri_format: https://www.ebi.ac.uk/efo/EFO_$1 publications: - doi: 10.1093/bioinformatics/btq099 pmc: PMC2853691 pubmed: '20200009' title: Modeling sample variables with an Experimental Factor Ontology. year: 2010 repository: https://github.com/EBISPOT/efo/ uri_format: http://www.ebi.ac.uk/efo/EFO_$1 version: 3.48.0 envo: appears_in: - foodon - pco banana: ENVO contact: email: pier.buttigieg@awi.de github: pbuttigieg name: Pier Luigi Buttigieg orcid: 0000-0002-4366-3088 depends_on: - chebi - foodon - go - ncbitaxon - pco - ro - uberon description: The Environment Ontology is a resource and research target for the semantically controlled description of environmental entities. The ontology's initial aim was the representation of the biomes, environmental features, and environmental materials pertinent to genomic and microbiome-related investigations. download_json: http://purl.obolibrary.org/obo/envo.json download_obo: http://purl.obolibrary.org/obo/envo.obo download_owl: http://purl.obolibrary.org/obo/envo.owl example: 09200010 homepage: http://environmentontology.org/ license: CC0-1.0 mappings: aberowl: ENVO agroportal: ENVO biocontext: ENVO bioportal: ENVO fairsharing: FAIRsharing.azqskx miriam: envo n2t: envo obofoundry: envo ols: envo ontobee: ENVO name: Environment Ontology namespace_in_lui: true pattern: ^\d{7,8}$ preferred_prefix: ENVO publications: - doi: 10.1186/s13326-016-0097-6 pmc: PMC5035502 pubmed: '27664130' title: 'The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation.' year: 2016 - doi: 10.1093/database/baw005 pmc: PMC4761108 pubmed: '26896844' title: 'EXTRACT: interactive extraction of environment metadata and term suggestion for metagenomic sample annotation.' year: 2016 - doi: 10.7717/peerj.1470 pmc: PMC4690371 pubmed: '26713234' title: Emerging semantics to link phenotype and environment. year: 2015 - doi: 10.1186/2041-1480-4-43 pmc: PMC3904460 pubmed: '24330602' title: 'The environment ontology: contextualising biological and biomedical entities.' year: 2013 repository: https://github.com/EnvironmentOntology/envo uri_format: https://www.ebi.ac.uk/ols/ontologies/envo/terms?obo_id=ENVO:$1 version: '2021-05-14' ero: contact: email: Marc_Ciriello@hms.harvard.edu github: null name: Marc Ciriello orcid: null deprecated: true description: An ontology of research resources such as instruments. protocols, reagents, animal models and biospecimens. download_owl: http://purl.obolibrary.org/obo/ero.owl example: '0001655' homepage: https://open.med.harvard.edu/wiki/display/eaglei/Ontology license: CC BY 2.0 mappings: aberowl: ERO biocontext: ERO bioportal: ERO fairsharing: FAIRsharing.nwgynk obofoundry: ero ols: ero ontobee: ERO name: eagle-i resource ontology pattern: ^\d{7}$ preferred_prefix: ERO publications: - doi: 10.1109/jcdl.2017.7991571 pmc: PMC5868434 pubmed: '29599662' title: 'Automating data citation: the eagle-i experience.' year: 2017 - doi: 10.1093/database/bar067 pmc: PMC3308157 pubmed: '22434835' title: 'Research resources: curating the new eagle-i discovery system.' year: 2012 uri_format: http://purl.obolibrary.org/obo/ERO_$1 version: '2016-07-27' exo: contact: email: annethessen@gmail.com github: diatomsRcool name: Anne Thessen orcid: 0000-0002-2908-3327 description: ExO is intended to bridge the gap between exposure science and diverse environmental health disciplines including toxicology, epidemiology, disease surveillance, and epigenetics. download_obo: http://purl.obolibrary.org/obo/exo.obo download_owl: http://purl.obolibrary.org/obo/exo.owl example: 0000078 homepage: https://github.com/CTDbase/exposure-ontology license: CC-BY-4.0 mappings: aberowl: EXO biocontext: EXO biolink: ExO bioportal: EXO fairsharing: FAIRsharing.6hna78 obofoundry: exo ols: exo ontobee: ExO name: Exposure ontology pattern: ^\d{7}$ preferred_prefix: ExO publications: - doi: 10.1021/es2033857 pmc: PMC3314380 pubmed: '22324457' title: 'Providing the missing link: the exposure science ontology ExO.' year: 2012 repository: https://github.com/CTDbase/exposure-ontology synonyms: - ExO uri_format: http://purl.obolibrary.org/obo/EXO_$1 version: '2022-06-29' fbbt: contact: email: cp390@cam.ac.uk github: Clare72 name: Clare Pilgrim orcid: 0000-0002-1373-1705 description: An ontology of Drosophila melanogaster anatomy. download_json: http://purl.obolibrary.org/obo/fbbt.json download_obo: http://purl.obolibrary.org/obo/fbbt.obo download_owl: http://purl.obolibrary.org/obo/fbbt.owl example: 00007294 homepage: http://purl.obolibrary.org/obo/fbbt license: CC-BY-4.0 mappings: aberowl: FBBT biocontext: FBbt bioportal: FB-BT fairsharing: FAIRsharing.y2qkst go: FBbt obofoundry: fbbt ols: fbbt ontobee: FBbt prefixcommons: fbbt name: Drosophila gross anatomy part_of: flybase pattern: ^\d{8}$ preferred_prefix: FBbt publications: - doi: 10.1186/2041-1480-4-32 pmc: PMC4015547 pubmed: '24139062' title: The Drosophila anatomy ontology. year: 2013 - doi: 10.1093/bioinformatics/bts113 pmc: null pubmed: '22402613' title: A strategy for building neuroanatomy ontologies. year: 2012 - doi: 10.1093/bioinformatics/btr677 pmc: null pubmed: '22180411' title: The Virtual Fly Brain browser and query interface. year: 2011 - doi: 10.1093/nar/gkj068 pmc: PMC1347431 pubmed: '16381917' title: 'FlyBase: anatomical data, images and queries.' year: 2006 repository: https://github.com/FlyBase/drosophila-anatomy-developmental-ontology synonyms: - FBbt - FBbt_root uri_format: https://flybase.org/cgi-bin/cvreport.pl?id=FBbt:$1 version: '2022-06-09' fbdv: contact: email: cp390@cam.ac.uk github: Clare72 name: Clare Pilgrim orcid: 0000-0002-1373-1705 description: An ontology of Drosophila melanogaster developmental stages. download_json: http://purl.obolibrary.org/obo/fbdv.json download_obo: http://purl.obolibrary.org/obo/fbdv.obo download_owl: http://purl.obolibrary.org/obo/fbdv.owl example: '00000000' homepage: http://purl.obolibrary.org/obo/fbdv license: CC-BY-4.0 mappings: aberowl: FBDV biocontext: FBdv bioportal: FB-DV fairsharing: FAIRsharing.p52pzj obofoundry: fbdv ols: fbdv ontobee: FBdv prefixcommons: fbdv name: Drosophila development pattern: ^\d{8}$ preferred_prefix: FBdv repository: https://github.com/FlyBase/drosophila-developmental-ontology synonyms: - FBdv uri_format: http://purl.obolibrary.org/obo/FBdv_$1 version: '2022-06-08' fma: banana: FMA contact: email: mejino@u.washington.edu github: null name: Onard Mejino orcid: null deprecated: true description: The Foundational Model of Anatomy Ontology (FMA) is a biomedical informatics ontology. It is concerned with the representation of classes or types and relationships necessary for the symbolic representation of the phenotypic structure of the human body. Specifically, the FMA is a domain ontology that represents a coherent body of explicit declarative knowledge about human anatomy. download_owl: http://purl.obolibrary.org/obo/fma.owl example: '63189' homepage: http://si.washington.edu/projects/fma license: CC-BY-3.0 mappings: aberowl: FMA bartoc: '571' biocontext: FMA bioportal: FMA edam: '1182' fairsharing: FAIRsharing.x56jsy go: FMA hl7: 2.16.840.1.113883.6.119 miriam: fma n2t: fma obofoundry: fma ols: fma ontobee: FMA prefixcommons: fma wikidata: P1402 name: Foundational Model of Anatomy namespace_in_lui: true pattern: ^\d+$ preferred_prefix: FMA publications: - doi: 10.1016/j.artmed.2016.04.003 pmc: PMC4915823 pubmed: '27235801' title: 'From frames to OWL2: Converting the Foundational Model of Anatomy.' year: 2016 - doi: 10.1016/j.websem.2007.12.001 pmc: PMC2500209 pubmed: '18688289' title: Translating the Foundational Model of Anatomy into OWL. year: 2008 - doi: 10.1016/j.websem.2006.05.007 pmc: PMC2270940 pubmed: '18360535' title: 'The foundational model of anatomy in OWL: Experience and perspectives.' year: 2006 - doi: 10.1109/iembs.2004.1404513 pmc: null pubmed: '17271570' title: 'The foundational model of anatomy: a template for the symbolic representation of multi-scale physiological functions.' year: null - doi: null pmc: PMC1560487 pubmed: '16779026' title: 'Challenges in converting frame-based ontology into OWL: the Foundational Model of Anatomy case-study.' year: 2005 - doi: 10.1016/j.jbi.2003.11.007 pmc: null pubmed: '14759820' title: 'A reference ontology for biomedical informatics: the Foundational Model of Anatomy.' year: 2003 repository: https://bitbucket.org/uwsig/fma synonyms: - FMAID - FMA_RETIRED uri_format: https://www.ebi.ac.uk/ols/ontologies/fma/terms?obo_id=FMA:$1 version: '2020-04-13' foaf: contact: email: rafael.goncalves@stanford.edu github: null name: "Rafael Gon\xE7alves" orcid: null contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: 'FOAF is a project devoted to linking people and information using the Web. Regardless of whether information is in people''s heads, in physical or digital documents, or in the form of factual data, it can be linked. FOAF integrates three kinds of network: social networks of human collaboration, friendship and association; representational networks that describe a simplified view of a cartoon universe in factual terms, and information networks that use Web-based linking to share independently published descriptions of this inter-connected world.' download_owl: http://aber-owl.net/media/ontologies/foaf/1/foaf.owl example: familyName homepage: http://xmlns.com/foaf/spec/ mappings: aberowl: foaf biocontext: foaf biolink: foaf bioportal: FOAF name: Friend of a Friend preferred_prefix: foaf uri_format: http://xmlns.com/foaf/0.1/$1 foodon: appears_in: - envo - maxo banana: FOODON contact: email: damion_dooley@sfu.ca github: ddooley name: Damion Dooley orcid: 0000-0002-8844-9165 depends_on: - bfo - chebi - envo - ncbitaxon - obi - ro - uberon description: FoodOn is a comprehensive and easily accessible global farm-to-fork ontology about food that accurately and consistently describes foods commonly known in cultures from around the world. It is a consortium-driven project built to interoperate with the The Open Biological and Biomedical Ontology Foundry library of ontologies. download_obo: http://purl.obolibrary.org/obo/foodon.obo download_owl: http://purl.obolibrary.org/obo/foodon.owl example: 03307879 homepage: https://foodon.org/ license: CC-BY-3.0 mappings: aberowl: FOODON agroportal: FOODON biocontext: FOODON bioportal: FOODON fairsharing: FAIRsharing.dzxae miriam: foodon n2t: foodon obofoundry: foodon ols: foodon ontobee: FOODON name: The Food Ontology namespace_in_lui: true pattern: ^[0-9]{8}$ preferred_prefix: FOODON publications: - doi: 10.1038/s41538-018-0032-6 pmc: PMC6550238 pubmed: '31304272' title: 'FoodOn: a harmonized food ontology to increase global food traceability, quality control and data integration.' year: 2018 - doi: 10.3389/fmicb.2017.01068 pmc: PMC5483436 pubmed: '28694792' title: 'Context Is Everything: Harmonization of Critical Food Microbiology Descriptors and Metadata for Improved Food Safety and Surveillance.' year: 2017 repository: https://github.com/FoodOntology/foodon uri_format: https://www.ebi.ac.uk/ols/ontologies/foodon/terms?obo_id=FOODON:$1 version: '2022-02-01' gaz: contact: email: lschriml@som.umaryland.edu github: lschriml name: Lynn Schriml orcid: 0000-0001-8910-9851 deprecated: true description: A gazetteer constructed on ontological principles download_obo: http://purl.obolibrary.org/obo/gaz.obo download_owl: http://purl.obolibrary.org/obo/gaz.owl example: '00620027' homepage: http://environmentontology.github.io/gaz/ license: CC0-1.0 mappings: aberowl: GAZ biocontext: GAZ bioportal: GAZ fairsharing: FAIRsharing.wkdjpb obofoundry: gaz ols: gaz ontobee: GAZ wikidata: P6778 name: Gazetteer pattern: ^\d{8}$ preferred_prefix: GAZ repository: https://github.com/EnvironmentOntology/gaz uri_format: http://purl.obolibrary.org/obo/GAZ_$1 geno: contact: email: mhb120@gmail.com github: mbrush name: Matthew Brush orcid: 0000-0002-1048-5019 description: "GENO is an OWL model of genotypes, their more fundamental sequence\ \ components, and links to related biological and experimental entities. At present\ \ many parts of the model are exploratory and set to undergo refactoring. In\ \ addition, many classes and properties have GENO URIs but are place holders for\ \ classes that will be imported from an external ontology (e.g. SO, ChEBI, OBI,\ \ etc). Furthermore, ongoing work will implement a model of genotype-to-phenotype\ \ associations. This will support description of asserted and inferred relationships\ \ between a genotypes, phenotypes, and environments, and the evidence/provenance\ \ behind these associations. \n\nDocumentation is under development as well, and\ \ for now a slidedeck is available at http://www.slideshare.net/mhb120/brush-icbo-2013" download_json: http://purl.obolibrary.org/obo/geno.json download_obo: https://raw.githubusercontent.com/monarch-initiative/GENO-ontology/develop/geno-full.obo download_owl: http://purl.obolibrary.org/obo/geno.owl example: '0000632' homepage: https://github.com/monarch-initiative/GENO-ontology/ license: CC-BY-4.0 mappings: aberowl: GENO biocontext: GENO bioportal: GENO fairsharing: FAIRsharing.kpbna7 obofoundry: geno ols: geno ontobee: GENO name: Genotype Ontology pattern: ^\d{7}$ preferred_prefix: GENO repository: https://github.com/monarch-initiative/GENO-ontology uri_format: http://purl.obolibrary.org/obo/GENO_$1 version: '2022-03-05' geogeo: banana: GEO banana_peel: _ contact: email: hoganwr@gmail.com github: hoganwr name: Bill Hogan orcid: 0000-0002-9881-1017 description: An ontology and inventory of geopolitical entities such as nations and their components (states, provinces, districts, counties) and the actual physical territories over which they have jurisdiction. We thus distinguish and assign different identifiers to the US in "The US declared war on Germany" vs. the US in "The plane entered US airspace". download_owl: http://purl.obolibrary.org/obo/geo.owl example: '000000021' homepage: https://github.com/ufbmi/geographical-entity-ontology/wiki license: CC-BY-4.0 mappings: biocontext: GEO bioportal: GEO miriam: geogeo obofoundry: geo ols: geo ontobee: GEO name: Geographical Entity Ontology namespace_in_lui: true pattern: ^\d{9}$ preferred_prefix: GEOGEO repository: https://github.com/ufbmi/geographical-entity-ontology uri_format: http://purl.obolibrary.org/obo/GEO_$1 version: '2016-03-26' gfo: contact: email: heinrich.herre@imise.uni-leipzig.de github: null name: Heinrich Herre orcid: null contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: The General Formal Ontology is a top-level ontology for conceptual modeling, which is being constantly further developed by Onto-Med. It includes elaborations of categories like objects, processes, time and space, properties, relations, roles, functions, facts, and situations. Moreover, we are working on an integration with the notion of levels of reality in order to more appropriately capture entities in the material, mental, and social areas. download_owl: http://www.onto-med.de/ontologies/gfo.owl example: projects_to homepage: https://www.onto-med.de/ontologies/gfo mappings: aberowl: GFO bioportal: GFO fairsharing: FAIRsharing.175hsz name: General Formal Ontology preferred_prefix: gfo uri_format: http://www.onto-med.de/ontologies/gfo.owl#$1 go: appears_in: - cl - envo - maxo - pco - uberon banana: GO contact: email: suzia@stanford.edu github: suzialeksander name: Suzi Aleksander orcid: 0000-0001-6787-2901 depends_on: - cl - ncbitaxon - ro - uberon description: The Gene Ontology project provides a controlled vocabulary to describe gene and gene product attributes in any organism. download_json: http://purl.obolibrary.org/obo/go.json download_obo: http://purl.obolibrary.org/obo/go.obo download_owl: http://purl.obolibrary.org/obo/go.owl example: '0032571' homepage: http://geneontology.org/ license: CC-BY-4.0 mappings: aberowl: GO agroportal: GO bartoc: '572' biocontext: GO bioportal: GO edam: '1176' fairsharing: FAIRsharing.6xq0ee go: GO hl7: 2.16.840.1.113883.6.128 miriam: go n2t: go ncbi: GO obofoundry: go ols: go ontobee: GO prefixcommons: go uniprot: DB-0037 wikidata: P686 name: Gene Ontology namespace_in_lui: true pattern: ^\d{7}$ preferred_prefix: GO providers: - code: CURATOR_REVIEW description: GO Browser homepage: http://www.informatics.jax.org/searches/GO_form.shtml name: GO Browser uri_format: http://www.informatics.jax.org/searches/GO.cgi?id=GO:$1 - code: CURATOR_REVIEW description: GO through PANTHER homepage: http://www.pantherdb.org/ name: GO through PANTHER uri_format: http://www.pantherdb.org/panther/category.do?categoryAcc=GO:$1 - code: jax description: The JAX endpoint for exploring GO homepage: http://www.informatics.jax.org name: Jackson Laboratories uri_format: http://www.informatics.jax.org/vocab/gene_ontology/GO:$1 - code: quickgo description: QuickGO (Gene Ontology browser) homepage: https://www.ebi.ac.uk/QuickGO/ name: QuickGO (Gene Ontology browser) uri_format: https://www.ebi.ac.uk/QuickGO/GTerm?id=GO:$1 publications: - doi: 10.1093/nar/gkaa1113 pmc: PMC7779012 pubmed: '33290552' title: 'The Gene Ontology resource: enriching a GOld mine.' year: 2021 - doi: 10.1093/nar/gky1055 pmc: PMC6323945 pubmed: '30395331' title: 'The Gene Ontology Resource: 20 years and still GOing strong.' year: 2019 - doi: 10.1093/nar/gku1179 pmc: PMC4383973 pubmed: '25428369' title: 'Gene Ontology Consortium: going forward.' year: 2014 - doi: 10.1186/1471-2164-14-513 pmc: PMC3733925 pubmed: '23895341' title: 'Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology.' year: 2013 - doi: 10.1093/nar/gks1050 pmc: PMC3531070 pubmed: '23161678' title: Gene Ontology annotations and resources. year: 2012 - doi: 10.1093/nar/gkr1028 pmc: PMC3245151 pubmed: '22102568' title: 'The Gene Ontology: enhancements for 2011.' year: 2011 - doi: 10.1093/nar/gkp1018 pmc: PMC2808930 pubmed: '19920128' title: 'The Gene Ontology in 2010: extensions and refinements.' year: 2009 - doi: 10.1093/nar/gkh036 pmc: PMC308770 pubmed: '14681407' title: The Gene Ontology (GO) database and informatics resource. year: 2004 - doi: 10.1038/75556 pmc: PMC3037419 pubmed: '10802651' title: 'Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.' year: 2000 repository: https://github.com/geneontology/go-ontology synonyms: - gobp - gobpid - gocc - goccid - gomf - gomfid twitter: news4go uri_format: http://amigo.geneontology.org/amigo/term/GO:$1 version: '2022-07-01' gsso: banana: GSSO contact: email: kronkcj@mail.uc.edu github: Superraptor name: Clair Kronk orcid: 0000-0001-8397-8810 description: The Gender, Sex, and Sexual Orientation (GSSO) ontology is an interdisciplinary ontology connecting terms from biology, medicine, psychology, sociology, and gender studies, aiming to bridge gaps between linguistic variations inside and outside of the health care environment. A large focus of the ontology is its consideration of LGBTQIA+ terminology. download_json: http://purl.obolibrary.org/obo/gsso.json download_obo: http://purl.obolibrary.org/obo/gsso.obo download_owl: http://purl.obolibrary.org/obo/gsso.owl example: 002368 homepage: https://gsso.research.cchmc.org/ license: Apache 2.0 License mappings: aberowl: GSSO bioportal: GSSO miriam: gsso obofoundry: gsso ols: gsso ontobee: GSSO name: Gender, Sex, and Sexual Orientation Ontology namespace_in_lui: true pattern: ^\d{6}$ preferred_prefix: GSSO repository: https://github.com/Superraptor/GSSO uri_format: http://purl.obolibrary.org/obo/GSSO_$1 version: 2.0.5 hgnc: contact: email: hgnc@genenames.org github: null name: Dr. Elspeth Bruford orcid: null description: The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. HGNC identifiers refer to records in the HGNC symbol database. download_owl: http://aber-owl.net/media/ontologies/HGNC/1/hgnc.owl example: '16793' homepage: http://www.genenames.org mappings: aberowl: HGNC biocontext: HGNC bioportal: HGNC cellosaurus: HGNC edam: '2298' fairsharing: FAIRsharing.amcv1e go: HGNC hl7: 2.16.840.1.113883.6.281 miriam: hgnc n2t: hgnc ncbi: HGNC prefixcommons: hgnc uniprot: DB-0042 wikidata: P354 name: HUGO Gene Nomenclature Committee pattern: ^\d{1,5}$ preferred_prefix: hgnc providers: - code: gencc description: "The GenCC DB provides information pertaining to the validity of\ \ gene-disease relationships, with a current focus on Mendelian diseases. Curated\ \ gene-disease relationships are submitted by GenCC member organizations. The\ \ GenCC comprises organizations that currently provide online resources (e.g.\ \ ClinGen, DECIPHER, Genomics England PanelApp, OMIM, Orphanet, PanelApp Australia,\ \ TGMI\u2019s G2P), as well as diagnostic laboratories that have committed to\ \ sharing their internal curated gene-level knowledge (e.g. Ambry, Illumina,\ \ Invitae, Myriad Women\u2019s Health, Mass General Brigham Laboratory for Molecular\ \ Medicine)." homepage: https://thegencc.org name: The Gene Curation Coalition uri_format: https://search.thegencc.org/genes/HGNC:$1 - code: indra description: A large scale database of biomedical statements. homepage: https://db.indra.bio name: INDRA Database uri_format: https://db.indra.bio/statements/from_agents?&format=html&agent0=$1@HGNC publications: - doi: 10.1093/nar/gkaa980 pmc: PMC7779007 pubmed: '33152070' title: 'Genenames.org: the HGNC and VGNC resources in 2021.' year: 2021 - doi: 10.1093/nar/gky930 pmc: PMC6324057 pubmed: '30304474' title: 'Genenames.org: the HGNC and VGNC resources in 2019.' year: 2019 - doi: 10.1159/000131404 pmc: null pubmed: '295268' title: International system for human gene nomenclature (1979) ISGN (1979). year: 1979 uri_format: https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/$1 hp: banana: HP contact: email: dr.sebastian.koehler@gmail.com github: drseb name: Sebastian Koehler orcid: 0000-0002-5316-1399 description: The Human Phenotype Ontology (HPO) aims to provide a standardized vocabulary of phenotypic abnormalities encountered in human disease. Each term in the HPO describes a phenotypic abnormality, such as atrial septal defect. The HPO is currently being developed using the medical literature, Orphanet, DECIPHER, and OMIM. download_json: http://purl.obolibrary.org/obo/hp.json download_obo: http://purl.obolibrary.org/obo/hp.obo download_owl: http://purl.obolibrary.org/obo/hp.owl example: '0011140' homepage: http://www.human-phenotype-ontology.org/ license: hpo mappings: aberowl: HP_O bartoc: '1937' biocontext: HPO bioportal: HP_O fairsharing: FAIRsharing.kbtt7f hl7: 2.16.840.1.113883.6.339 miriam: hp n2t: hp obofoundry: hp ols: hp ontobee: HP wikidata: P3841 name: Human Phenotype Ontology namespace_in_lui: true pattern: ^\d{7}$ preferred_prefix: HP publications: - doi: 10.1093/nar/gky1105 pmc: PMC6324074 pubmed: '30476213' title: Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources. year: 2019 - doi: 10.1093/nar/gkw1039 pmc: PMC5210535 pubmed: '27899602' title: The Human Phenotype Ontology in 2017. year: 2016 - doi: 10.1016/j.ajhg.2015.05.020 pmc: PMC4572507 pubmed: '26119816' title: 'The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease.' year: 2015 - doi: 10.1093/nar/gkt1026 pmc: PMC3965098 pubmed: '24217912' title: 'The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data.' year: 2013 - doi: 10.1111/j.1399-0004.2010.01436.x pmc: null pubmed: '20412080' title: The human phenotype ontology. year: 2010 - doi: 10.1016/j.ajhg.2008.09.017 pmc: PMC2668030 pubmed: '18950739' title: 'The Human Phenotype Ontology: a tool for annotating and analyzing human hereditary disease.' year: 2008 repository: https://github.com/obophenotype/human-phenotype-ontology synonyms: - hpo twitter: hp_ontology uri_format: https://hpo.jax.org/app/browse/term/HP:$1 version: '2022-06-11' hsapdv: contact: email: frederic.bastian@unil.ch github: fbastian name: "Fr\xE9d\xE9ric Bastian" orcid: 0000-0002-9415-5104 description: Life cycle stages for Human download_obo: http://purl.obolibrary.org/obo/hsapdv.obo download_owl: http://purl.obolibrary.org/obo/hsapdv.owl example: 0000194 homepage: https://github.com/obophenotype/developmental-stage-ontologies/wiki/HsapDv license: CC-BY-3.0 mappings: aberowl: HSAPDV biocontext: HSAPDV biolink: HsapDv bioportal: HSAPDV fairsharing: FAIRsharing.c6vhm3 obofoundry: hsapdv ols: hsapdv ontobee: HsapDv name: Human Developmental Stages pattern: ^\d{7}$ preferred_prefix: HsapDv repository: https://github.com/obophenotype/developmental-stage-ontologies synonyms: - HsapDv uri_format: http://purl.obolibrary.org/obo/HSAPDV_$1 version: '2020-03-10' iao: appears_in: - maxo - pco contact: email: jiezheng@pennmedicine.upenn.edu github: zhengj2007 name: Jie Zheng orcid: 0000-0002-2999-0103 description: An ontology of information entities, originally driven by work by the Ontology of Biomedical Investigation (OBI) digital entity and realizable information entity branch. download_obo: http://purl.obolibrary.org/obo/iao.obo download_owl: http://purl.obolibrary.org/obo/iao.owl example: '0000030' homepage: https://github.com/information-artifact-ontology/IAO/ license: CC-BY-4.0 mappings: aberowl: IAO biocontext: IAO bioportal: IAO fairsharing: FAIRsharing.gq1xtx go: IAO miriam: iao n2t: iao obofoundry: iao ols: iao ontobee: IAO name: Information Artifact Ontology pattern: ^\d{7}$ preferred_prefix: IAO providers: - code: legacy description: A URI from the semanticweb.og homepage: http://www.semanticweb.org name: Legacy URI uri_format: http://www.semanticweb.org/ontologies/2011/9/Ontology1317751904226.owl#IAO_$1 publications: - doi: 10.3233/978-1-61499-101-4-68 pmc: null pubmed: '22874154' title: An information artifact ontology perspective on data collections and associated representational artifacts. year: 2012 repository: https://github.com/information-artifact-ontology/IAO uri_format: http://purl.obolibrary.org/obo/IAO_$1 version: '2020-12-09' ico: contact: email: yongqunh@med.umich.edu github: yongqunh name: Yongqun Oliver He orcid: 0000-0001-9189-9661 description: The Informed Consent Ontology (ICO) is an ontology for the informed consent and informed consent process in the medical field. download_owl: http://purl.obolibrary.org/obo/ico.owl example: '0000066' homepage: https://github.com/ICO-ontology/ICO license: CC-BY-3.0 mappings: aberowl: ICO biocontext: ICO bioportal: ICO fairsharing: FAIRsharing.b9znd5 obofoundry: ico ols: ico ontobee: ICO name: Informed Consent Ontology pattern: ^\d{7}$ preferred_prefix: ICO repository: https://github.com/ICO-ontology/ICO uri_format: http://purl.obolibrary.org/obo/ICO_$1 version: 1.0.187 ido: contact: email: Lindsay.Cowell@utsouthwestern.edu github: lgcowell name: Lindsay Cowell orcid: 0000-0003-1617-8244 description: Infectious Disease Ontology holds entities relevant to both biomedical and clinical aspects of most infectious diseases. download_owl: http://purl.obolibrary.org/obo/ido.owl example: '0000504' homepage: http://www.bioontology.org/wiki/index.php/Infectious_Disease_Ontology license: CC-BY-3.0 mappings: aberowl: IDO biocontext: IDO bioportal: IDO fairsharing: FAIRsharing.aae3v6 miriam: ido n2t: ido obofoundry: ido ols: ido ontobee: IDO name: Infectious Disease Ontology pattern: ^[0-9]+$ preferred_prefix: IDO 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/IDO_$1 publications: - doi: null pmc: null pubmed: '34275487' title: The Infectious Disease Ontology in the age of COVID-19 year: null repository: https://github.com/infectious-disease-ontology/infectious-disease-ontology uri_format: https://www.ebi.ac.uk/ols/ontologies/ido/terms?obo_id=IDO:$1 version: '2017-11-03' idocovid19: contact: email: johnbeverley2021@u.northwestern.edu github: johnbeve name: John Beverly orcid: 0000-0002-1118-1738 description: The COVID-19 Infectious Disease Ontology (IDO-COVID-19) is an extension of the Infectious Disease Ontology (IDO) and the Virus Infectious Disease Ontology (VIDO). IDO-COVID-19 follows OBO Foundry guidelines, employs the Basic Formal Ontology as its starting point, and covers epidemiology, classification, pathogenesis, and treatment of terms used to represent infection by the SARS-CoV-2 virus strain, and the associated COVID-19 disease. download_owl: https://raw.githubusercontent.com/infectious-disease-ontology-extensions/ido-covid-19/master/ontology/ido%20covid-19 example: 0001191 homepage: https://github.com/infectious-disease-ontology-extensions/ido-covid-19 mappings: aberowl: IDO-COVID-19 bioportal: IDO-COVID-19 ols: idocovid19 name: The COVID-19 Infectious Disease Ontology pattern: ^\d{7}$ preferred_prefix: idocovid19 providers: - code: obo1 description: This variation uses incorrect usage of dashes instead of underscores homepage: http://purl.obolibrary.org name: Incorrect OBO PURL variation 1 uri_format: http://purl.obolibrary.org/obo/IDO-COVID-19_$1 repository: https://github.com/infectious-disease-ontology-extensions/ido-covid-19 uri_format: http://purl.obolibrary.org/obo/COVIDO_$1 version: '2020-07-21' idomal: contact: email: topalis@imbb.forth.gr github: null name: Pantelis Topalis orcid: null deprecated: true description: An application ontology to cover all aspects of malaria as well as the intervention attempts to control it. download_obo: http://purl.obolibrary.org/obo/idomal.obo download_owl: http://purl.obolibrary.org/obo/idomal.owl example: '0002350' example_extras: - '50000015' homepage: https://www.vectorbase.org/ontology-browser license: CC0-1.0 mappings: aberowl: IDOMAL biocontext: IDOMAL bioportal: IDOMAL fairsharing: FAIRsharing.2q8c28 obofoundry: idomal ols: idomal ontobee: IDOMAL name: Malaria Ontology pattern: ^(5?)\d{7}$ preferred_prefix: IDOMAL publications: - doi: 10.1186/2041-1480-4-16 pmc: PMC3848731 pubmed: '24034841' title: 'IDOMAL: the malaria ontology revisited.' year: 2013 - doi: 10.1186/1475-2875-9-230 pmc: PMC2925367 pubmed: '20698959' title: 'IDOMAL: an ontology for malaria.' year: 2010 repository: https://github.com/VEuPathDB-ontology/IDOMAL uri_format: http://purl.obolibrary.org/obo/IDOMAL_$1 version: '2015-03-16' maxo: contact: email: Leigh.Carmody@jax.org github: LCCarmody name: Leigh Carmody orcid: 0000-0001-7941-2961 depends_on: - chebi - foodon - go - iao - ro - uberon description: An ontology to represent medically relevant actions, procedures, therapies, interventions, and recommendations. download_json: http://purl.obolibrary.org/obo/maxo.json download_obo: http://purl.obolibrary.org/obo/maxo.obo download_owl: http://purl.obolibrary.org/obo/maxo.owl example: 0000008 homepage: https://github.com/monarch-initiative/MAxO license: CC-BY-3.0 mappings: aberowl: MAXO biolink: MAXO bioportal: MAXO obofoundry: maxo ols: maxo ontobee: MAXO name: Medical Action Ontology pattern: ^\d{7}$ preferred_prefix: MAXO repository: https://github.com/monarch-initiative/MAxO twitter: MonarchInit uri_format: http://purl.obolibrary.org/obo/MAXO_$1 version: '2022-06-23' miro: contact: email: louis@imbb.forth.gr github: null name: Christos (Kitsos) Louis orcid: null deprecated: true description: Application ontology for entities related to insecticide resistance in mosquitos download_obo: http://purl.obolibrary.org/obo/miro.obo download_owl: http://purl.obolibrary.org/obo/miro.owl example: '40000617' homepage: https://github.com/VEuPathDB-ontology/MIRO mappings: aberowl: MIRO biocontext: MIRO bioportal: MIRO fairsharing: FAIRsharing.sjf113 obofoundry: miro ols: miro ontobee: MIRO name: Mosquito insecticide resistance pattern: ^\d{8}$ preferred_prefix: MIRO publications: - doi: 10.1371/journal.pntd.0000465 pmc: PMC2694272 pubmed: '19547750' title: 'MIRO and IRbase: IT tools for the epidemiological monitoring of insecticide resistance in mosquito disease vectors.' year: 2009 repository: https://github.com/VEuPathDB-ontology/MIRO uri_format: http://purl.obolibrary.org/obo/MIRO_$1 version: '2014-05-14' mpath: contact: email: pns12@hermes.cam.ac.uk github: PaulNSchofield name: Paul Schofield orcid: 0000-0002-5111-7263 description: A structured controlled vocabulary of mutant and transgenic mouse pathology phenotypes download_obo: https://raw.githubusercontent.com/PaulNSchofield/mpath/master/mpath.obo download_owl: http://purl.obolibrary.org/obo/mpath.owl example: '728' homepage: http://www.pathbase.net license: CC-BY-3.0 mappings: aberowl: MPATH biocontext: MPATH bioportal: MPATH fairsharing: FAIRsharing.3wbgm0 obofoundry: mpath ols: mpath ontobee: MPATH prefixcommons: mpath name: Mouse pathology ontology pattern: ^\d+$ preferred_prefix: MPATH publications: - doi: 10.1177/0300985810374845 pmc: PMC3038412 pubmed: '20587689' title: Pathbase and the MPATH ontology. Community resources for mouse histopathology. year: 2010 repository: https://github.com/PaulNSchofield/mpath synonyms: - MPATH uri_format: http://purl.obolibrary.org/obo/MPATH_$1 version: '2020-05-19' nbo: contact: email: g.gkoutos@bham.ac.uk github: gkoutos name: George Gkoutos orcid: 0000-0002-2061-091X description: An ontology of human and animal behaviours and behavioural phenotypes download_obo: https://github.com/obo-behavior/behavior-ontology/raw/master/nbo.obo download_owl: http://purl.obolibrary.org/obo/nbo.owl example: '0000564' homepage: https://github.com/obo-behavior/behavior-ontology/ license: CC-BY-3.0 mappings: aberowl: NBO biocontext: NBO bioportal: NBO fairsharing: FAIRsharing.pktgc6 obofoundry: nbo ols: nbo ontobee: NBO name: Neuro Behavior Ontology pattern: ^\d{7}$ preferred_prefix: NBO publications: - doi: 10.1007/s00335-013-9481-z pmc: null pubmed: '24177753' title: Analyzing gene expression data in mice with the Neuro Behavior Ontology. year: 2013 - doi: 10.1016/b978-0-12-388408-4.00004-6 pmc: null pubmed: '23195121' title: 'The neurobehavior ontology: an ontology for annotation and integration of behavior and behavioral phenotypes.' year: 2012 repository: https://github.com/obo-behavior/behavior-ontology uri_format: http://purl.obolibrary.org/obo/NBO_$1 version: '2021-02-15' ncbitaxon: appears_in: - cl - envo - foodon - go - pco contact: email: frederic.bastian@unil.ch github: fbastian name: Frederic Bastian orcid: 0000-0002-9415-5104 description: The taxonomy contains the relationships between all living forms for which nucleic acid or protein sequence have been determined. download_json: http://purl.obolibrary.org/obo/ncbitaxon.json download_obo: http://purl.obolibrary.org/obo/ncbitaxon.obo download_owl: http://purl.obolibrary.org/obo/ncbitaxon.owl example: '2170610' homepage: https://github.com/obophenotype/ncbitaxon license: CC0-1.0 mappings: aberowl: NCBITAXON agroportal: NCBITAXON bartoc: '509' biocontext: TAXONOMY bioportal: NCBITAXON cellosaurus: NCBI_TaxID edam: '1179' fairsharing: FAIRsharing.fj07xj go: taxon hl7: 2.16.840.1.113883.6.205 miriam: taxonomy n2t: taxonomy ncbi: taxon obofoundry: ncbitaxon ols: ncbitaxon ontobee: NCBITaxon prefixcommons: taxonomy re3data: r3d100010415 wikidata: P685 name: NCBI Taxonomy pattern: ^\d+$ preferred_prefix: NCBITaxon providers: - code: CURATOR_REVIEW description: Taxonomy through UniProt PURL homepage: https://www.uniprot.org/taxonomy/ name: Taxonomy through UniProt PURL uri_format: https://purl.uniprot.org/taxonomy/$1 - code: CURATOR_REVIEW description: Bio2RDF homepage: https://bio2rdf.org/ name: Bio2RDF uri_format: https://bio2rdf.org/taxonomy:$1 - code: ebi description: European Nucleotide Archive (ENA) homepage: https://www.ebi.ac.uk/ena/ name: European Nucleotide Archive (ENA) uri_format: https://www.ebi.ac.uk/ena/data/view/Taxon:$1 - code: 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/ncbi-taxon/$1 publications: - doi: 10.1093/database/baaa062 pmc: PMC7408187 pubmed: '32761142' title: 'NCBI Taxonomy: a comprehensive update on curation, resources and tools.' year: 2020 - doi: 10.1093/nar/gkx1094 pmc: PMC5753231 pubmed: '29140468' title: GenBank. year: 2018 - doi: 10.1093/nar/gkr1178 pmc: PMC3245000 pubmed: '22139910' title: The NCBI Taxonomy database. year: 2011 repository: https://github.com/obophenotype/ncbitaxon synonyms: - NCBI Taxonomy - NCBITaxon - NCBI_Taxon_ID - NCBI_taxid - TAX - TaxonomyID - taxid - taxon - taxonomy - uniprot.taxonomy uri_format: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=$1 version: '2022-08-18' ncit: contact: email: haendel@ohsu.edu github: mellybelly name: Melissa Haendel orcid: 0000-0001-9114-8737 description: NCI Thesaurus (NCIt) provides reference terminology covering vocabulary for clinical care, translational and basic research, and public information and administrative activities, providing a stable and unique identification code. download_obo: http://purl.obolibrary.org/obo/ncit.obo download_owl: http://purl.obolibrary.org/obo/ncit.owl example: C138986 homepage: https://github.com/NCI-Thesaurus/thesaurus-obo-edition license: CC-BY-4.0 mappings: aberowl: NCIT biocontext: NCIT bioportal: NCIT cellosaurus: NCIt fairsharing: FAIRsharing.4cvwxa hl7: 2.16.840.1.113883.6.206 miriam: ncit n2t: ncit obofoundry: ncit ols: ncit ontobee: NCIT prefixcommons: ncit wikidata: P1748 name: NCI Thesaurus pattern: ^C\d+$ preferred_prefix: NCIT providers: - code: evs description: Links to a no-longer existing OWL file homepage: https://ncit.nci.nih.gov/ncitbrowser/ name: Legacy NCBI OWL uri_format: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#$1 publications: - doi: 10.3233/ao-2008-0051 pmc: PMC2753293 pubmed: '19789731' title: 'Representing the NCI Thesaurus in OWL DL: Modeling tools help modeling languages.' year: 2008 - doi: 10.3233/978-1-60750-949-3-33 pmc: null pubmed: '15360769' title: 'NCI Thesaurus: using science-based terminology to integrate cancer research results.' year: 2004 repository: https://github.com/NCI-Thesaurus/thesaurus-obo-edition synonyms: - NCI - NCI2004_11_17 - NCIT - NCIT_Thesaurus - NCITm - NCITt - NCI_Thesaurus - NCIt - NCit - ncithesaurus uri_format: http://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI%20Thesaurus&code=$1 version: 22.07d ndfrt: contact: email: michael.lincoln@va.gov github: null name: Michael J. Lincoln MD orcid: null contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: 'NDF-RT combines the NDF hierarchical drug classification with a multi-category reference model. The categories are: Cellular or Molecular Interactions [MoA]; Chemical Ingredients [Chemical/Ingredient]; Clinical Kinetics [PK]; Diseases, Manifestations or Physiologic States [Disease/Finding]Dose Forms [Dose Form]; Pharmaceutical Preparations; Physiological Effects [PE]; Therapeutic Categories [TC]; and VA Drug Interactions [VA Drug Interaction].' example: N0000001662 homepage: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/NDFRT mappings: aberowl: NDFRT bioportal: NDFRT fairsharing: FAIRsharing.901nkj hl7: 2.16.840.1.113883.6.209 ontobee: NDF-RT prefixcommons: ndfrt wikidata: P2115 name: National Drug File - Reference Terminology pattern: ^N[0-9]{10}$ preferred_prefix: ndfrt publications: - doi: null pmc: PMC1480331 pubmed: '14728237' title: Adequacy of representation of the National Drug File Reference Terminology Physiologic Effects reference hierarchy for commonly prescribed medications. year: 2003 synonyms: - NUI - ndf-rt uri_format: https://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#$1 neuronames: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: BrainInfo is designed to help you identify structures in the brain. If you provide the name of a structure, BrainInfo will show it and tell you about it. example: '268' homepage: http://braininfo.rprc.washington.edu/ mappings: wikidata: P4394 name: NeuroNames pattern: ^\d+$ preferred_prefix: neuronames references: - https://en.wikipedia.org/wiki/NeuroNames synonyms: - neuroname uri_format: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=$1 nif.ext: contact: email: tgbugs@gmail.com github: tgbugs name: Tom Gillespie orcid: 0000-0002-7509-4801 contributor: email: tgbugs@gmail.com github: tgbugs name: Tom Gillespie orcid: 0000-0002-7509-4801 description: NIFEXT covers IRIs that were "external" identifiers that were brought into the ontology at some point in time. This was done before most of the current standard ontology and identifier management practices had been developed. example: '7123' homepage: https://github.com/SciCrunch/NIF-Ontology license: CC BY-4.0 name: 'NIF Standard Ontology: External' part_of: nif pattern: ^\d+$ preferred_prefix: nif.ext repository: https://github.com/SciCrunch/NIF-Ontology reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 synonyms: - NIFEXT twitter: SciCrunch uri_format: http://uri.neuinfo.org/nif/nifstd/nifext_$1 nif.std: contact: email: tgbugs@gmail.com github: tgbugs name: Tom Gillespie orcid: 0000-0002-7509-4801 contributor: email: tgbugs@gmail.com github: tgbugs name: Tom Gillespie orcid: 0000-0002-7509-4801 description: NIFSTD is a base namespace (like obo:) which houses many other prefixes. Sometimes NIFSTD prefixed identifiers appear undifferentiated, but usually if it shows up it means that another prefix definition is missing when serializing. download_owl: http://aber-owl.net/media/ontologies/NIFSTD/23/nifstd.owl example: BAMSC981 homepage: https://github.com/SciCrunch/NIF-Ontology license: CC BY-4.0 mappings: aberowl: NIFSTD bioportal: NIFSTD fairsharing: FAIRsharing.vgw1m6 name: NIF Standard Ontology part_of: nif pattern: ^BAMSC\d+$ preferred_prefix: nif.std publications: - doi: 10.1007/s12021-008-9032-z pmc: PMC2743139 pubmed: '18975148' title: 'The NIFSTD and BIRNLex vocabularies: building comprehensive ontologies for neuroscience.' year: 2008 repository: https://github.com/SciCrunch/NIF-Ontology reviewer: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 synonyms: - NIFSTD twitter: SciCrunch uri_format: http://uri.neuinfo.org/nif/nifstd/$1 oae: contact: email: yongqunh@med.umich.edu github: yongqunh name: Yongqunh He orcid: 0000-0001-9189-9661 description: The Ontology of Adverse Eventsy (OAE) is a biomedical ontology in the domain of adverse events. OAE aims to standardize adverse event annotation, integrate various adverse event data, and support computer-assisted reasoning. OAE is a community-based ontology. Its development follows the OBO Foundry principles. Vaccine adverse events have been used as an initial testing use case. OAE also studies adverse events associated with the administration of drug and nutritional products, the operation of surgeries, and the usage of medical devices, etc. download_owl: http://purl.obolibrary.org/obo/oae.owl example: 0002959 homepage: https://github.com/OAE-ontology/OAE/ license: CC-BY-3.0 mappings: aberowl: OAE biocontext: OAE bioportal: OAE fairsharing: FAIRsharing.tw4q8x obofoundry: oae ols: oae ontobee: OAE name: Ontology of Adverse Events pattern: ^\d{7}$ preferred_prefix: OAE publications: - doi: 10.1186/2041-1480-5-29 pmc: PMC4120740 pubmed: '25093068' title: 'OAE: The Ontology of Adverse Events.' year: 2014 repository: https://github.com/OAE-ontology/OAE uri_format: http://purl.obolibrary.org/obo/OAE_$1 version: 1.2.44 obcs: contact: email: jiezheng@pennmedicine.upenn.edu github: zhengj2007 name: Jie Zheng orcid: 0000-0002-2999-0103 description: 'OBCS stands for the Ontology of Biological and Clinical Statistics. OBCS is an ontology in the domain of biological and clinical statistics. It is aligned with the Basic Formal Ontology (BFO) and the Ontology for Biomedical Investigations (OBI). OBCS imports all possible biostatistics terms in OBI and includes many additional biostatistics terms, some of which were proposed and discussed in the OBI face-to-face workshop in Ann Arbor in 2012. ' download_owl: http://purl.obolibrary.org/obo/obcs.owl example: '0000121' homepage: https://github.com/obcs/obcs license: CC-BY-3.0 mappings: aberowl: OBCS biocontext: OBCS bioportal: OBCS fairsharing: FAIRsharing.5p12xh obofoundry: obcs ols: obcs ontobee: OBCS name: Ontology of Biological and Clinical Statistics pattern: ^\d{7}$ preferred_prefix: OBCS publications: - doi: 10.1186/s13326-016-0100-2 pmc: PMC5024438 pubmed: '27627881' title: The Ontology of Biological and Clinical Statistics (OBCS) for standardized and reproducible statistical analysis. year: 2016 repository: https://github.com/obcs/obcs uri_format: http://purl.obolibrary.org/obo/OBCS_$1 version: '101' obi: appears_in: - foodon banana: OBI banana_peel: ':' contact: email: bpeters@lji.org github: bpeters42 name: Bjoern Peters orcid: 0000-0002-8457-6693 description: The Ontology for Biomedical Investigations (OBI) project is developing an integrated ontology for the description of biological and clinical investigations. The ontology will represent the design of an investigation, the protocols and instrumentation used, the material used, the data generated and the type analysis performed on it. Currently OBI is being built under the Basic Formal Ontology (BFO). download_obo: https://github.com/obi-ontology/obi/raw/master/views/obi.obo download_owl: http://purl.obolibrary.org/obo/obi.owl example: 0400109 homepage: http://obi-ontology.org license: CC-BY-4.0 mappings: aberowl: OBI biocontext: OBI bioportal: OBI fairsharing: FAIRsharing.284e1z go: OBI miriam: obi n2t: obi obofoundry: obi ols: obi ontobee: OBI prefixcommons: obi name: Ontology for Biomedical Investigations namespace_in_lui: true pattern: ^\d{7}$ preferred_prefix: OBI publications: - doi: 10.1371/journal.pone.0154556 pmc: PMC4851331 pubmed: '27128319' title: The Ontology for Biomedical Investigations. year: 2016 - doi: 10.1093/database/bau132 pmc: PMC4309925 pubmed: '25632945' title: 'Modeling a microbial community and biodiversity assay with OBO Foundry ontologies: the interoperability gains of a modular approach.' year: 2015 - doi: 10.1186/2041-1480-4-s1-s6 pmc: PMC3633001 pubmed: '23734660' title: 'Query enhancement through the practical application of ontology: the IEDB and OBI.' year: 2013 - doi: 10.4056/sigs.1994602 pmc: PMC3235517 pubmed: '22180825' title: Minimum Information about a Genotyping Experiment (MIGEN). year: 2011 - doi: 10.1186/2041-1480-1-s1-s7 pmc: PMC2903726 pubmed: '20626927' title: Modeling biomedical experimental processes with OBI. year: 2010 repository: https://github.com/obi-ontology/obi uri_format: http://purl.obolibrary.org/obo/OBI_$1 version: '2022-07-11' obib: contact: email: jiezheng@pennmedicine.upenn.edu github: zhengj2007 name: Jie Zheng orcid: 0000-0002-2999-0103 description: The Ontology for Biobanking (OBIB) is an ontology for the annotation and modeling of the activities, contents, and administration of a biobank. Biobanks are facilities that store specimens, such as bodily fluids and tissues, typically along with specimen annotation and clinical data. OBIB is based on a subset of the Ontology for Biomedical Investigation (OBI), has the Basic Formal Ontology (BFO) as its upper ontology, and is developed following OBO Foundry principles. The first version of OBIB resulted from the merging of two existing biobank-related ontologies, OMIABIS and biobank ontology. download_owl: http://purl.obolibrary.org/obo/obib.owl example: 0000389 homepage: https://github.com/biobanking/biobanking license: CC-BY-4.0 mappings: aberowl: OBIB biocontext: OBIB bioportal: OBIB fairsharing: FAIRsharing.bxc508 obofoundry: obib ols: obib ontobee: OBIB name: Ontology for Biobanking pattern: ^\d{7}$ preferred_prefix: OBIB publications: - doi: 10.1186/s13326-016-0068-y pmc: PMC4855778 pubmed: '27148435' title: OBIB-a novel ontology for biobanking. year: 2016 repository: https://github.com/biobanking/biobanking uri_format: http://purl.obolibrary.org/obo/OBIB_$1 version: '2021-11-12' obo: description: The OBO namespace is the top-level namespace used by Open Biological and Biomedical Ontology (OBO) Foundry ontologies. homepage: http://www.obofoundry.org/ mappings: biocontext: OBO fairsharing: FAIRsharing.847069 name: Open Biological and Biomedical Ontologies preferred_prefix: obo uri_format: http://purl.obolibrary.org/obo/$1 oboinowl: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: This meta-ontology is self-describing. OBO metamodel properties are described using OBO metamodel properties download_obo: https://github.com/geneontology/go-ontology/raw/master/contrib/oboInOwl.obo download_owl: https://github.com/geneontology/go-ontology/raw/master/contrib/oboInOwl.owl example: hasDbXref homepage: https://github.com/geneontology/go-ontology/tree/master/contrib mappings: biocontext: oboInOwl biolink: oboformat name: OBO in OWL preferred_prefix: oboInOwl repository: https://github.com/geneontology/go-ontology synonyms: - oboformat - oio uri_format: http://www.geneontology.org/formats/oboInOwl#$1 ogg: contact: email: yongqunh@med.umich.edu github: yongqunh name: Yongqun Oliver He orcid: 0000-0001-9189-9661 description: 'OGG is a biological ontology in the area of genes and genomes. OGG uses the Basic Formal Ontology (BFO) as its upper level ontology. This OGG document contains the genes and genomes of a list of selected organisms, including human, two viruses (HIV and influenza virus), and bacteria (B. melitensis strain 16M, E. coli strain K-12 substrain MG1655, M. tuberculosis strain H37Rv, and P. aeruginosa strain PAO1). More OGG information for other organisms (e.g., mouse, zebrafish, fruit fly, yeast, etc.) may be found in other OGG subsets. ' download_owl: http://purl.obolibrary.org/obo/ogg.owl example: '3000887619' homepage: https://bitbucket.org/hegroup/ogg license: CC-BY-3.0 mappings: aberowl: OGG biocontext: OGG bioportal: OGG fairsharing: FAIRsharing.zmx7nn obofoundry: ogg ols: ogg ontobee: OGG name: The Ontology of Genes and Genomes pattern: ^\d+$ preferred_prefix: OGG repository: https://bitbucket.org/hegroup/ogg uri_format: http://purl.obolibrary.org/obo/OGG_$1 version: 1.0.59 ogms: contact: email: baeverma@jcvi.org github: BAevermann name: Brian Aevermann orcid: 0000-0003-1346-1327 description: 'The Ontology for General Medical Science (OGMS) is an ontology of entities involved in a clinical encounter. OGMS includes very general terms that are used across medical disciplines, including: ''disease'', ''disorder'', ''disease course'', ''diagnosis'', ''patient'', and ''healthcare provider''. OGMS uses the Basic Formal Ontology (BFO) as an upper-level ontology. The scope of OGMS is restricted to humans, but many terms can be applied to a variety of organisms. OGMS provides a formal theory of disease that can be further elaborated by specific disease ontologies. This theory is implemented using OWL-DL and OBO Relation Ontology relations and is available in OWL and OBO formats. OGMS is based on the papers Toward an Ontological Treatment of Disease and Diagnosis and On Carcinomas and Other Pathological Entities. The ontology attempts to address some of the issues raised at the Workshop on Ontology of Diseases (Dallas, TX) and the Signs, Symptoms, and Findings Workshop(Milan, Italy). OGMS was formerly called the clinical phenotype ontology. Terms from OGMS hang from the Basic Formal Ontology.' download_obo: http://purl.obolibrary.org/obo/ogms.obo download_owl: http://purl.obolibrary.org/obo/ogms.owl example: '0000031' homepage: https://github.com/OGMS/ogms license: CC-BY-4.0 mappings: aberowl: OGMS bartoc: '216' biocontext: OGMS bioportal: OGMS fairsharing: FAIRsharing.rvz0m9 obofoundry: ogms ols: ogms ontobee: OGMS name: Ontology for General Medical Science pattern: ^\d{7}$ preferred_prefix: OGMS publications: - doi: null pmc: null pubmed: '25991121' title: Biomarkers in the Ontology for General Medical Science year: null - doi: 10.1186/2041-1480-4-42 pmc: PMC4028878 pubmed: '24314207' title: The neurological disease ontology. year: 2013 repository: https://github.com/OGMS/ogms synonyms: - ogms/OMRE uri_format: http://purl.obolibrary.org/obo/OGMS_$1 version: '2021-08-19' omiabis: contact: email: mbrochhausen@gmail.com github: null name: Mathias Brochhausen orcid: 0000-0003-1834-3856 deprecated: true description: An ontological version of MIABIS (Minimum Information About BIobank data Sharing) download_owl: http://purl.obolibrary.org/obo/omiabis.owl example: 0001079 homepage: https://github.com/OMIABIS/omiabis-dev license: CC-BY-3.0 mappings: aberowl: OMIABIS biocontext: OMIABIS bioportal: OMIABIS obofoundry: omiabis ols: omiabis ontobee: OMIABIS name: Ontologized MIABIS pattern: ^\d{7}$ preferred_prefix: OMIABIS repository: https://github.com/OMIABIS/omiabis-dev uri_format: http://purl.obolibrary.org/obo/OMIABIS_$1 version: '2014-05-28' omim: contact: email: ahamosh@jhmi.edu github: ahamosh name: Ada Hamosh orcid: 0000-0002-1780-5230 description: Online Mendelian Inheritance in Man is a catalog of human genes and genetic disorders. example: '603903' homepage: https://omim.org/ mappings: aberowl: OMIM biocontext: OMIM bioportal: OMIM edam: '1153' fairsharing: FAIRsharing.b084yh go: OMIM hl7: 2.16.840.1.113883.6.174 miriam: mim n2t: mim ncbi: MIM prefixcommons: omim uniprot: DB-0062 wikidata: P492 name: Online Mendelian Inheritance in Man pattern: ^\d+$ preferred_prefix: omim providers: - code: CURATOR_REVIEW description: OMIM mirror at John Hopkins homepage: http://mirror.omim.org/ name: OMIM mirror at John Hopkins uri_format: http://mirror.omim.org/entry/$1 - code: legacy description: This is the actual endpoint for OMIM entries homepage: https://www.omim.org name: OMIM uri_format: https://www.omim.org/entry/$1 - code: ncbi.omim description: An NCBI endpoint for OMIM entries homepage: http://www.ncbi.nlm.nih.gov/omim name: NCBI uri_format: http://www.ncbi.nlm.nih.gov/omim/$1 - code: purl description: An extra purl that was registred, but probably won't be used. homepage: https://www.omim.org name: OMIM PURL (not in use) uri_format: https://purl.org/mim/MIM:$1 - code: purl2 description: An extra purl that was registred, but probably won't be used. homepage: https://www.omim.org name: OMIM PURL (not in use) uri_format: https://omim.org/OMIM:$1 publications: - doi: 10.1093/nar/gku1205 pmc: PMC4383985 pubmed: '25428349' title: "OMIM.org: Online Mendelian Inheritance in Man (OMIM\xAE), an online catalog\ \ of human genes and genetic disorders." year: 2014 - doi: 10.1093/nar/gki033 pmc: PMC539987 pubmed: '15608251' title: Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. year: 2005 references: - https://github.com/biopragmatics/bioregistry/issues/497 synonyms: - OMIM - mim uri_format: https://omim.org/MIM:$1 omrse: contact: email: hoganwr@gmail.com github: hoganwr name: Bill Hogan orcid: 0000-0002-9881-1017 description: This ontology covers the domain of social entities that are related to health care, such as demographic information and the roles of various individuals and organizations. download_json: http://purl.obolibrary.org/obo/omrse.json download_obo: https://github.com/ufbmi/OMRSE/raw/master/omrse-full.obo download_owl: http://purl.obolibrary.org/obo/omrse.owl example: '00000022' homepage: https://github.com/ufbmi/OMRSE/wiki/OMRSE-Overview license: CC-BY-4.0 mappings: aberowl: OMRSE biocontext: OMRSE bioportal: OMRSE fairsharing: FAIRsharing.z0p37e obofoundry: omrse ols: omrse ontobee: OMRSE name: Ontology of Medically Related Social Entities pattern: ^\d{8}$ preferred_prefix: OMRSE publications: - doi: 10.1186/s13326-016-0087-8 pmc: PMC4942889 pubmed: '27406187' title: 'The ontology of medically related social entities: recent developments.' year: 2016 repository: https://github.com/ufbmi/OMRSE uri_format: http://purl.obolibrary.org/obo/OMRSE_$1 version: '2022-04-06' opmi: contact: email: yongqunh@med.umich.edu github: yongqunh name: Yongqun Oliver He orcid: 0000-0001-9189-9661 description: OPMI is a biomedical ontology in the area of precision medicine and its related investigations. It is community-driven and developed by following the OBO Foundry ontology development principles. download_owl: http://purl.obolibrary.org/obo/opmi.owl example: '0000101' homepage: https://github.com/OPMI/opmi license: CC-BY-4.0 mappings: aberowl: OPMI bioportal: OPMI obofoundry: opmi ols: opmi ontobee: OPMI name: Ontology of Precision Medicine and Investigation pattern: ^\d{7}$ preferred_prefix: OPMI repository: https://github.com/OPMI/opmi uri_format: http://purl.obolibrary.org/obo/OPMI_$1 version: 1.0.158 orphanet.ordo: banana: Orphanet banana_peel: _ contact: email: ordo.orphanet@inserm.fr github: null name: Ana Rath orcid: null description: "The Orphanet Rare Disease ontology (ORDO) is a structured vocabulary\ \ for rare diseases, capturing relationships between diseases, genes and other\ \ relevant features which will form a useful resource for the computational analysis\ \ of rare diseases.\r\nIt integrates a nosology (classification of rare diseases),\ \ relationships (gene-disease relations, epiemological data) and connections with\ \ other terminologies (MeSH, UMLS, MedDRA), databases (OMIM, UniProtKB, HGNC,\ \ ensembl, Reactome, IUPHAR, Geantlas) and classifications (ICD10)." download_owl: http://www.orphadata.org/data/ORDO/ordo_orphanet.owl example: C023 example_extras: - '478' homepage: https://www.ebi.ac.uk/ols/ontologies/ordo mappings: aberowl: ordo biocontext: ORPHANET.ORDO biolink: ORPHA bioportal: ORDO cellosaurus: ORDO fairsharing: FAIRsharing.pbbnwa miriam: orphanet.ordo n2t: orphanet.ordo ols: ordo name: Orphanet Rare Disease Ontology pattern: ^C?\d+$ preferred_prefix: orphanet.ordo publications: - doi: null pmc: null pubmed: '22874158' title: 'Rare diseases knowledge management: the contribution of proximity measurements in OntoOrpha and OMIM.' year: 2012 synonyms: - ordo uri_format: http://www.orpha.net/ORDO/Orphanet_$1 version: '4.1' ovae: contact: email: yongqunh@med.umich.edu github: yongqunh name: Yongqunh He orcid: 0000-0001-9189-9661 description: 'OVAE is a biomedical ontology in the area of vaccine adverse events. OVAE is an extension of the community-based Ontology of Adverse Events (OAE). ' download_owl: http://purl.obolibrary.org/obo/ovae.owl example: 0000609 homepage: http://www.violinet.org/ovae/ license: CC-BY-3.0 mappings: aberowl: OVAE biocontext: OVAE bioportal: OVAE fairsharing: FAIRsharing.w4x6n4 obofoundry: ovae ols: ovae ontobee: OVAE name: Ontology of Vaccine Adverse Events pattern: ^\d{7}$ preferred_prefix: OVAE publications: - doi: 10.1186/2041-1480-4-40 pmc: PMC4177204 pubmed: '24279920' title: The Ontology of Vaccine Adverse Events (OVAE) and its usage in representing and analyzing adverse events associated with US-licensed human vaccines. year: 2013 repository: https://github.com/OVAE-Ontology/ovae uri_format: http://purl.obolibrary.org/obo/OVAE_$1 version: 1.0.34 owl: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: 'Overview of the Web Ontology Language (OWL) which provides an introduction to OWL by informally describing the features of each of the sublanguages. ' download_owl: https://triplydb.com/w3c/owl/download.trig.gz example: Ontology homepage: https://www.w3.org/TR/owl-features/ mappings: biocontext: owl fairsharing: FAIRsharing.atygwy name: Web Ontology Language preferred_prefix: owl uri_format: http://www.w3.org/2002/07/owl#$1 pato: appears_in: - cl - pco banana: PATO contact: email: g.gkoutos@gmail.com github: gkoutos name: George Gkoutos orcid: 0000-0002-2061-091X description: PATO is an ontology of phenotypic qualities, intended for use in a number of applications, primarily defining composite phenotypes and phenotype annotation. download_json: http://purl.obolibrary.org/obo/pato.json download_obo: http://purl.obolibrary.org/obo/pato.obo download_owl: http://purl.obolibrary.org/obo/pato.owl example: 0001998 homepage: https://github.com/pato-ontology/pato/ license: CC-BY-3.0 mappings: aberowl: PATO agroportal: PATO biocontext: PATO bioportal: PATO fairsharing: FAIRsharing.ezwdhz go: PATO miriam: pato n2t: pato obofoundry: pato ols: pato ontobee: PATO prefixcommons: pato name: Phenotype And Trait Ontology namespace_in_lui: true pattern: ^\d{7}$ preferred_prefix: PATO 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/PATO#PATO_$1 publications: - doi: 10.1093/bib/bbx035 pmc: PMC6169674 pubmed: '28387809' title: 'The anatomy of phenotype ontologies: principles, properties and applications.' year: 2018 - doi: 10.1186/gb-2010-11-1-r2 pmc: PMC2847714 pubmed: '20064205' title: Integrating phenotype ontologies across multiple species. year: 2010 - doi: 10.1186/gb-2004-6-1-r8 pmc: PMC549069 pubmed: '15642100' title: Using ontologies to describe mouse phenotypes. year: 2004 repository: https://github.com/pato-ontology/pato uri_format: https://www.ebi.ac.uk/ols/ontologies/pato/terms?obo_id=PATO:$1 version: '2022-08-31' pco: appears_in: - envo contact: email: rlwalls2008@gmail.com github: ramonawalls name: Ramona Walls orcid: 0000-0001-8815-0078 depends_on: - bfo - caro - envo - go - iao - ncbitaxon - pato - ro description: The Population and Community Ontology (PCO) describes material entities, qualities, and processes related to collections of interacting organisms such as populations and communities. It is taxon neutral, and can be used for any species, including humans. The classes in the PCO are useful for describing evolutionary processes, organismal interactions, and ecological experiments. Practical applications of the PCO include community health care, plant pathology, behavioral studies, sociology, and ecology. download_obo: http://purl.obolibrary.org/obo/pco.obo download_owl: http://purl.obolibrary.org/obo/pco.owl example: '0000021' homepage: https://github.com/PopulationAndCommunityOntology/pco license: CC0-1.0 mappings: aberowl: PCO agroportal: PCO biocontext: PCO bioportal: PCO ecoportal: PCO fairsharing: FAIRsharing.vq28qp obofoundry: pco ols: pco ontobee: PCO name: Population and Community Ontology pattern: ^\d{7}$ preferred_prefix: PCO repository: https://github.com/PopulationAndCommunityOntology/pco uri_format: http://purl.obolibrary.org/obo/PCO_$1 version: '2021-05-03' pmc: description: PMC International (PMCI) is a free full-text archive of biomedical and life sciences journal literature. PMCI is a collaborative effort between the U.S. National Institutes of Health and the National Library of Medicine, the publishers whose journal content makes up the PMC archive, and organizations in other countries that share NIH's and NLM's interest in archiving life sciences literature. example: PMC3084216 homepage: http://europepmc.org/ mappings: biocontext: PMCID fairsharing: FAIRsharing.wpt5mp go: PMCID miriam: pmc n2t: pmc prefixcommons: pmc wikidata: P932 name: PMCID pattern: ^PMC\d+$ preferred_prefix: pmc providers: - code: ncbi description: PubMed Central homepage: https://www.ncbi.nlm.nih.gov/pmc/ name: PubMed Central uri_format: https://www.ncbi.nlm.nih.gov/pmc/articles/$1/?tool=pubmed synonyms: - PMC - PMCID uri_format: http://europepmc.org/articles/$1 pr: appears_in: - cl - uberon banana: PR contact: email: dan5@georgetown.edu github: nataled name: Darren Natale orcid: 0000-0001-5809-9523 description: The PRotein Ontology (PRO) has been designed to describe the relationships of proteins and protein evolutionary classes, to delineate the multiple protein forms of a gene locus (ontology for protein forms), and to interconnect existing ontologies. download_obo: http://purl.obolibrary.org/obo/pr.obo download_owl: http://purl.obolibrary.org/obo/pr.owl example: '000000024' homepage: http://proconsortium.org license: CC-BY-4.0 mappings: aberowl: PR agroportal: PR biocontext: PR bioportal: PR fairsharing: FAIRsharing.4ndncv go: PR miriam: pr n2t: pr obofoundry: pr ols: pr ontobee: PR prefixcommons: pr uniprot: DB-0181 wikidata: P4926 name: Protein Ontology namespace_in_lui: true pattern: ^\d+$ preferred_prefix: PR publications: - doi: 10.1093/nar/gkw1075 pmc: PMC5210558 pubmed: '27899649' title: 'Protein Ontology (PRO): enhancing and scaling up the representation of protein entities.' year: 2016 - doi: 10.1093/nar/gkt1173 pmc: PMC3964965 pubmed: '24270789' title: 'Protein Ontology: a controlled structured network of protein entities.' year: 2013 - doi: 10.1186/1471-2105-12-371 pmc: PMC3189193 pubmed: '21929785' title: The representation of protein complexes in the Protein Ontology (PRO). year: 2011 - doi: 10.1093/nar/gkq907 pmc: PMC3013777 pubmed: '20935045' title: 'The Protein Ontology: a structured representation of protein forms and complexes.' year: 2010 - doi: 10.1186/1471-2105-8-s9-s1 pmc: PMC2217659 pubmed: '18047702' title: Framework for a protein ontology. year: 2007 repository: https://github.com/PROconsortium/PRoteinOntology synonyms: - PR - PRO uri_format: https://proconsortium.org/app/entry/PR:$1 version: '67.0' pubmed: description: PubMed is a service of the U.S. National Library of Medicine that includes citations from MEDLINE and other life science journals for biomedical articles back to the 1950s. example: '16333295' homepage: https://www.ncbi.nlm.nih.gov/PubMed/ mappings: biocontext: PUBMED cellosaurus: PubMed cheminf: '000302' edam: '1187' fairsharing: FAIRsharing.a5sv8m go: PMID miriam: pubmed n2t: pubmed prefixcommons: pubmed wikidata: P698 name: PubMed ID pattern: ^\d+$ preferred_prefix: pubmed providers: - code: CURATOR_REVIEW description: PubMed through Linkedlife data homepage: http://linkedlifedata.com/ name: PubMed through Linkedlife data uri_format: http://linkedlifedata.com/resource/pubmed/id/$1 - code: epmc description: Europe PMC homepage: http://europepmc.org/ name: Europe PMC uri_format: http://europepmc.org/abstract/MED/$1 - code: hubmed description: HubMed homepage: http://www.hubmed.org/ name: HubMed uri_format: http://www.hubmed.org/display.cgi?uids=$1 - code: pubmed.new description: New-style link for pubmed homepage: https://pubmed.ncbi.nlm.nih.gov name: PubMed (new) uri_format: https://pubmed.ncbi.nlm.nih.gov/$1 - code: scholia description: Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata. homepage: https://scholia.toolforge.org/ name: Scholia uri_format: https://scholia.toolforge.org/pubmed/$1 - code: uniprot.citation description: UniProt mints PURLs for citations identifiers homepage: https://uniprot.org/ name: UniProt uri_format: http://purl.uniprot.org/citations/$1 - code: uniprot.pubmed description: UniProt mints PURLs for PubMed identifiers homepage: https://uniprot.org/ name: UniProt uri_format: http://purl.uniprot.org/pubmed/$1 publications: - doi: 10.1093/nar/gkj158 pmc: PMC1347520 pubmed: '16381840' title: Database resources of the National Center for Biotechnology Information. year: 2006 synonyms: - MEDLINE - PMID - PubMed - pmid uri_format: https://www.ncbi.nlm.nih.gov/pubmed/$1 qudt: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Ontologies that aim to provide semantic specifications for units of measure, quantity kind, dimensions and data types. download_owl: http://aber-owl.net/media/ontologies/QUDT/4/qudt.owl download_rdf: http://qudt.org/schema/qudt/ example: baseDimensionEnumeration homepage: https://qudt.org mappings: aberowl: QUDT bartoc: '18206' biolink: qud bioportal: QUDT fairsharing: FAIRsharing.d3pqw7 name: Quantities, Units, Dimensions, and Types Ontology preferred_prefix: qudt uri_format: http://qudt.org/schema/qudt#$1 rdfs: contact: email: danbri@w3.org github: null name: Dan Brickley orcid: 0000-0002-6450-7041 contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: RDF Schema provides a data-modelling vocabulary for RDF data. RDF Schema is an extension of the basic RDF vocabulary. download_owl: https://triplydb.com/w3c/rdfs/download.trig.gz example: label homepage: https://www.w3.org/TR/rdf-schema/ mappings: aberowl: RDFS biocontext: rdfs bioportal: RDFS fairsharing: FAIRsharing.v9n3gk name: RDF Schema preferred_prefix: rdfs uri_format: http://www.w3.org/2000/01/rdf-schema#$1 ro: appears_in: - cl - envo - foodon - go - maxo - pco banana: RO banana_peel: _ contact: email: cjmungall@lbl.gov github: cmungall name: Chris Mungall orcid: 0000-0002-6601-2165 description: The OBO Relation Ontology provides consistent and unambiguous formal definitions of the relational expressions used in biomedical ontologies. download_json: http://purl.obolibrary.org/obo/ro.json download_obo: http://purl.obolibrary.org/obo/ro.obo download_owl: http://purl.obolibrary.org/obo/ro.owl example: '0002533' homepage: https://oborel.github.io/ license: CC0-1.0 mappings: aberowl: RO agroportal: RO biocontext: RO biolink: RO bioportal: OBOREL fairsharing: FAIRsharing.cp0ybc go: RO miriam: ro n2t: ro obofoundry: ro ols: ro ontobee: RO prefixcommons: ro wikidata: P3590 name: Relation Ontology namespace_in_lui: true pattern: ^\d{7}$ preferred_prefix: RO publications: - doi: 10.1186/2041-1480-5-41 pmc: PMC4177597 pubmed: '25276335' title: 'Structuring research methods and data with the research object model: genomics workflows as a case study.' year: 2014 - doi: 10.1186/gb-2005-6-5-r46 pmc: PMC1175958 pubmed: '15892874' title: Relations in biomedical ontologies. year: 2005 repository: https://github.com/oborel/obo-relations synonyms: - RO_proposed_relation - obo_rel - oborel uri_format: http://purl.obolibrary.org/obo/RO_$1 version: '2022-05-23' sdgio: description: An OBO-compliant ontology representing the entities referenced by the SDGs, their targets, and indicators. download_owl: https://github.com/SDG-InterfaceOntology/sdgio/raw/master/sdgio.owl example: '00020134' homepage: https://github.com/SDG-InterfaceOntology/sdgio mappings: agroportal: SDGIO fairsharing: FAIRsharing.d5ff6e ols: sdgio ontobee: SDGIO name: Sustainable Development Goals Interface Ontology pattern: ^\d{8}$ preferred_prefix: sdgio publications: - doi: 10.1186/s13326-016-0097-6 pmc: PMC5035502 pubmed: '27664130' title: 'The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation.' year: 2016 references: - https://github.com/SDG-InterfaceOntology/sdgio/issues/233 repository: https://github.com/SDG-InterfaceOntology/sdgio uri_format: http://purl.unep.org/sdg/SDGIO_$1 version: '2018-08-10' sio: banana: SIO banana_peel: _ contact: email: michel.dumontier@gmail.com github: micheldumontier name: Michel Dumontier orcid: 0000-0003-4727-9435 description: The semanticscience integrated ontology (SIO) provides a simple, integrated upper level ontology (types, relations) for consistent knowledge representation across physical, processual and informational entities. download_owl: http://semanticscience.org/ontology/sio/v1.53/sio-release.owl example: 000912 homepage: https://github.com/micheldumontier/semanticscience mappings: aberowl: SIO agroportal: SIO biocontext: SIO biolink: SIO bioportal: SIO fairsharing: FAIRsharing.dpkb5f miriam: sio ols: sio ontobee: SIO name: Semanticscience Integrated Ontology pattern: ^\d{6}$ preferred_prefix: sio publications: - doi: 10.1186/2041-1480-5-14 pmc: PMC4015691 pubmed: '24602174' title: The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery. year: 2014 repository: https://github.com/micheldumontier/semanticscience uri_format: https://www.ebi.ac.uk/ols/ontologies/sio/terms?short_form=$1 version: '1.53' skos: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: SKOS is an area of work developing specifications and standards to support the use of knowledge organization systems (KOS) such as thesauri, classification schemes, subject heading lists and taxonomies within the framework of the Semantic Web download_owl: http://aber-owl.net/media/ontologies/skos/1/skos.owl example: prefLabel homepage: https://www.w3.org/2004/02/skos/ mappings: aberowl: skos biocontext: skos name: Simple Knowledge Organization System preferred_prefix: skos uri_format: http://www.w3.org/2004/02/skos/core#$1 so: banana: SO contact: email: keilbeck@genetics.utah.edu github: keilbeck name: Karen Eilbeck orcid: 0000-0002-0831-6427 description: The Sequence Ontology (SO) is a structured controlled vocabulary for the parts of a genomic annotation. It provides a common set of terms and definitions to facilitate the exchange, analysis and management of genomic data. download_obo: https://github.com/The-Sequence-Ontology/SO-Ontologies/raw/master/Ontology_Files/so.obo download_owl: http://purl.obolibrary.org/obo/so.owl example: '0001157' homepage: http://www.sequenceontology.org/ license: CC-BY-4.0 mappings: aberowl: SO agroportal: SO biocontext: SO bioportal: SO fairsharing: FAIRsharing.6bc7h9 go: SO miriam: so n2t: so obofoundry: so ols: so ontobee: SO prefixcommons: so name: Sequence types and features ontology namespace_in_lui: true pattern: ^\d{7}$ preferred_prefix: SO publications: - doi: 10.1186/gb-2010-11-8-r88 pmc: PMC2945790 pubmed: '20796305' title: A standard variation file format for human genome sequences. year: 2010 - doi: 10.1016/j.jbi.2010.03.002 pmc: PMC3052763 pubmed: '20226267' title: Evolution of the Sequence Ontology terms and relationships. year: 2010 - doi: 10.1186/gb-2005-6-5-r44 pmc: PMC1175956 pubmed: '15892872' title: 'The Sequence Ontology: a tool for the unification of genome annotations.' year: 2005 repository: https://github.com/The-Sequence-Ontology/SO-Ontologies uri_format: http://www.sequenceontology.org/miso/current_release/term/SO:$1 version: '2021-11-22' stato: contact: email: alejandra.gonzalez.beltran@gmail.com github: agbeltran name: Alejandra Gonzalez-Beltran orcid: 0000-0003-3499-8262 description: STATO is the statistical methods ontology. It contains concepts and properties related to statistical methods, probability distributions and other concepts related to statistical analysis, including relationships to study designs and plots. download_owl: http://purl.obolibrary.org/obo/stato.owl example: 0000288 homepage: http://stato-ontology.org/ license: CC-BY-3.0 mappings: aberowl: STATO biocontext: STATO bioportal: STATO fairsharing: FAIRsharing.na5xp obofoundry: stato ols: stato ontobee: STATO name: The Statistical Methods Ontology pattern: ^\d{7}$ preferred_prefix: STATO repository: https://github.com/ISA-tools/stato uri_format: http://purl.obolibrary.org/obo/STATO_$1 version: '1.4' symp: contact: email: lynn.schriml@gmail.com github: lschriml name: Lynn Schriml orcid: 0000-0001-8910-9851 description: The Symptom Ontology has been developed as a standardized ontology for symptoms of human diseases. download_json: http://purl.obolibrary.org/obo/symp.json download_obo: http://purl.obolibrary.org/obo/symp.obo download_owl: http://purl.obolibrary.org/obo/symp.owl example: 0019171 homepage: http://symptomontologywiki.igs.umaryland.edu/mediawiki/index.php/Main_Page license: CC0-1.0 mappings: aberowl: SYMP biocontext: SYMP bioportal: SYMP fairsharing: FAIRsharing.ay74mj obofoundry: symp ols: symp ontobee: SYMP prefixcommons: symptom wikidata: P8656 name: Symptom Ontology pattern: ^\d{7}$ preferred_prefix: SYMP publications: - doi: 10.1093/nar/gkab1063 pmc: PMC8728220 pubmed: '34755882' title: The Human Disease Ontology 2022 update. year: 2022 - doi: 10.1093/nar/gkp832 pmc: PMC2808878 pubmed: '19850722' title: GeMInA, Genomic Metadata for Infectious Agents, a geospatial surveillance pathogen database. year: 2009 repository: https://github.com/DiseaseOntology/SymptomOntology synonyms: - SYMP uri_format: http://purl.obolibrary.org/obo/SYMP_$1 version: '2022-07-12' trans: contact: email: lynn.schriml@gmail.com github: lschriml name: Lynn Schriml orcid: 0000-0001-8910-9851 description: The Pathogen Transmission Ontology describes the tranmission methods of human disease pathogens describing how a pathogen is transmitted from one host, reservoir, or source to another host. The pathogen transmission may occur either directly or indirectly and may involve animate vectors or inanimate vehicles. download_obo: http://purl.obolibrary.org/obo/trans.obo download_owl: http://purl.obolibrary.org/obo/trans.owl example: '0000024' homepage: https://github.com/DiseaseOntology/PathogenTransmissionOntology license: CC0-1.0 mappings: aberowl: TRANS biocontext: TRANS bioportal: TRANS fairsharing: FAIRsharing.nygmp7 obofoundry: trans ols: trans ontobee: TRANS prefixcommons: pt name: Pathogen Transmission Ontology pattern: ^\d{7}$ preferred_prefix: TRANS publications: - doi: 10.1093/nar/gkab1063 pmc: PMC8728220 pubmed: '34755882' title: The Human Disease Ontology 2022 update. year: 2022 - doi: 10.1093/nar/gkp832 pmc: PMC2808878 pubmed: '19850722' title: GeMInA, Genomic Metadata for Infectious Agents, a geospatial surveillance pathogen database. year: 2009 repository: https://github.com/DiseaseOntology/PathogenTransmissionOntology uri_format: http://purl.obolibrary.org/obo/TRANS_$1 version: '2020-08-04' uberon: appears_in: - cl - envo - foodon - go - maxo banana: UBERON contact: email: cjmungall@lbl.gov github: cmungall name: Chris Mungall orcid: 0000-0002-6601-2165 depends_on: - chebi - cl - go - pr description: Uberon is an integrated cross-species anatomy ontology representing a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage. The ontology includes comprehensive relationships to taxon-specific anatomical ontologies, allowing integration of functional, phenotype and expression data. download_json: http://purl.obolibrary.org/obo/uberon.json download_obo: http://purl.obolibrary.org/obo/uberon/basic.obo download_owl: http://purl.obolibrary.org/obo/uberon.owl example: '2005080' homepage: http://uberon.org license: CC-BY-3.0 mappings: aberowl: UBERON biocontext: UBERON bioportal: UBERON cellosaurus: UBERON fairsharing: FAIRsharing.4c0b6b go: UBERON miriam: uberon n2t: uberon obofoundry: uberon ols: uberon ontobee: UBERON wikidata: P1554 name: Uber Anatomy Ontology namespace_in_lui: true pattern: ^\d+$ preferred_prefix: UBERON publications: - doi: 10.1186/2041-1480-5-21 pmc: PMC4089931 pubmed: '25009735' title: Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon. year: 2014 - doi: 10.1186/gb-2012-13-1-r5 pmc: PMC3334586 pubmed: '22293552' title: Uberon, an integrative multi-species anatomy ontology. year: 2012 repository: https://github.com/obophenotype/uberon synonyms: - UBERON - Uber-anatomy ontology - Uberon twitter: uberanat uri_format: http://purl.obolibrary.org/obo/UBERON_$1 version: '2022-09-30' uniprot.isoform: description: The UniProt Knowledgebase (UniProtKB) is a comprehensive resource for protein sequence and functional information with extensive cross-references to more than 120 external databases. This collection is a subset of UniProtKB, and provides a means to reference isoform information. example: Q5BJF6-3 homepage: http://www.uniprot.org/ mappings: biocontext: UNIPROT.ISOFORM miriam: uniprot.isoform n2t: uniprot.isoform name: UniProt Isoform part_of: uniprot pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\-\d+)$ preferred_prefix: uniprot.isoform providers: - code: CURATOR_REVIEW description: UniProt Isoform through Universal Protein Resource using Persistent URL system homepage: http://purl.uniprot.org/ name: UniProt Isoform through Universal Protein Resource using Persistent URL system uri_format: http://purl.uniprot.org/uniprot/$1 - code: CURATOR_REVIEW description: UniProt Isoform through UniParc homepage: http://www.uniprot.org/uniparc/ name: UniProt Isoform through UniParc uri_format: http://www.uniprot.org/uniparc/?query=$1 - 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/UniProtKB_$1 synonyms: - UPISO uri_format: http://purl.uniprot.org/isoforms/$1 uo: banana: UO contact: email: g.gkoutos@gmail.com github: gkoutos name: George Gkoutos orcid: 0000-0002-2061-091X description: Ontology of standardized units download_obo: http://purl.obolibrary.org/obo/uo.obo download_owl: http://purl.obolibrary.org/obo/uo.owl example: 0000080 homepage: https://github.com/bio-ontology-research-group/unit-ontology license: CC-BY-3.0 mappings: aberowl: UO biocontext: UO bioportal: UO fairsharing: FAIRsharing.mjnypw miriam: uo n2t: uo obofoundry: uo ols: uo ontobee: UO prefixcommons: uo name: Units of measurement ontology namespace_in_lui: true pattern: ^\d{7}$ preferred_prefix: UO publications: - doi: 10.1093/database/bas033 pmc: PMC3468815 pubmed: '23060432' title: 'The Units Ontology: a tool for integrating units of measurement in science.' year: 2012 repository: https://github.com/bio-ontology-research-group/unit-ontology uri_format: https://www.ebi.ac.uk/ols/ontologies/uo/terms?obo_id=UO:$1 upheno: contact: email: vasilevs@ohsu.edu github: nicolevasilevsky name: Nicole Vasilevsky orcid: 0000-0001-5208-3432 description: The uPheno ontology integrates multiple phenotype ontologies into a unified cross-species phenotype ontology. download_json: https://github.com/obophenotype/upheno/blob/master/upheno.json download_obo: https://github.com/obophenotype/upheno/blob/master/upheno.obo download_owl: https://github.com/obophenotype/upheno/blob/master/upheno.owl homepage: https://github.com/obophenotype/upheno license: CC0-1.0 mappings: aberowl: UPHENO biocontext: UPHENO bioportal: UPHENO fairsharing: FAIRsharing.r41qhx obofoundry: upheno ols: upheno ontobee: UPHENO name: Unified Phenotype Ontology no_own_terms: true preferred_prefix: UPHENO repository: https://github.com/obophenotype/upheno uri_format: http://purl.obolibrary.org/obo/UPHENO_$1 version: '2017-10-31' vario: banana: VariO contact: email: mauno.vihinen@med.lu.se github: null name: Mauno Vihinen orcid: null deprecated: true description: The Variation Ontology (VariO) is an ontology for the standardized, systematic description of effects, consequences and mechanisms of variations. It describes the effects of variations at the DNA, RNA and/or protein level. download_obo: http://purl.obolibrary.org/obo/vario.obo download_owl: http://purl.obolibrary.org/obo/vario.owl example: '0376' homepage: http://variationontology.org mappings: aberowl: VARIO agroportal: VARIO biocontext: VARIO bioportal: VARIO fairsharing: FAIRsharing.65xkbs miriam: vario n2t: vario obofoundry: vario ols: vario ontobee: VariO name: Variation Ontology namespace_in_lui: true pattern: ^\d+$ preferred_prefix: VariO providers: - code: CURATOR_REVIEW description: VariO at Lund University homepage: http://www.variationontology.org/ name: VariO at Lund University uri_format: http://www.ontobee.org/search?ontology=VariO&keywords=VariO_$1&submit=Search+terms publications: - doi: 10.1186/s12864-018-5262-0 pmc: PMC6309100 pubmed: '30591019' title: Systematics for types and effects of DNA variations. year: 2018 - doi: 10.1002/humu.22954 pmc: null pubmed: '26773573' title: VariOtator, a Software Tool for Variation Annotation with the Variation Ontology. year: 2016 - doi: 10.1007/s00439-015-1529-6 pmc: null pubmed: '25616435' title: Types and effects of protein variations. year: 2015 - doi: 10.1186/2041-1480-5-9 pmc: PMC3931275 pubmed: '24533660' title: 'Variation ontology: annotator guide.' year: 2014 - doi: 10.1101/gr.157495.113 pmc: PMC3912426 pubmed: '24162187' title: Variation Ontology for annotation of variation effects and mechanisms. year: 2013 uri_format: http://purl.obolibrary.org/obo/VARIO_$1 version: '2018-11-09' vido: contact: email: johnbeverley2021@u.northwestern.edu github: johnbeve name: John Beverly orcid: 0000-0002-1118-1738 description: The Virus Infectious Disease Ontology (IDO Virus) is an extension of the Infectious Disease Ontology (IDO). IDO Virus follows OBO Foundry guidelines, employs the Basic Formal Ontology as its starting point, and covers epidemiology, classification, pathogenesis, and treatment of terms used by Virologists, i.e. virus, prion, satellite, viroid, etc. download_owl: https://raw.githubusercontent.com/infectious-disease-ontology-extensions/ido-virus/master/ontology/vido.owl example: '0001114' homepage: https://github.com/infectious-disease-ontology-extensions/ido-virus mappings: aberowl: VIDO bioportal: VIDO ols: vido ontobee: VIDO name: The Virus Infectious Disease Ontology pattern: ^\d{7}$ preferred_prefix: vido 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/VIDO_$1 repository: https://github.com/infectious-disease-ontology-extensions/ido-virus uri_format: http://purl.obolibrary.org/obo/VIDO_$1 version: '2020-08-25' vo: contact: email: yongqunh@med.umich.edu github: yongqunh name: Yongqunh He orcid: 0000-0001-9189-9661 description: The Vaccine Ontology (VO) is a biomedical ontology in the domain of vaccine and vaccination. VO aims to standardize vaccine annotation, integrate various vaccine data, and support computer-assisted reasoning. VO supports basic vaccine R&D and clincal vaccine usage. VO is being developed as a community-based ontology with support and collaborations from the vaccine and bio-ontology communities. download_owl: http://purl.obolibrary.org/obo/vo.owl example: 0000093 homepage: http://www.violinet.org/vaccineontology license: CC-BY-3.0 mappings: aberowl: VO biocontext: VO bioportal: VO fairsharing: FAIRsharing.zwtww5 obofoundry: vo ols: vo ontobee: VO prefixcommons: vo wikidata: P1928 name: Vaccine Ontology pattern: ^\d{7}$ preferred_prefix: VO publications: - doi: 10.2174/1381612826666201125112131 pmc: null pubmed: '33238868' title: Ontology-based Precision Vaccinology for Deep Mechanism Understanding and Precision Vaccine Development year: null - doi: 10.1186/2041-1480-3-17 pmc: PMC3639077 pubmed: '23256535' title: Ontology representation and analysis of vaccine formulation and administration and their effects on vaccine immune responses. year: 2012 - doi: 10.1186/2041-1480-2-s2-s8 pmc: PMC3102897 pubmed: '21624163' title: "Mining of vaccine-associated IFN-\u03B3 gene interaction networks using\ \ the Vaccine Ontology." year: 2011 - doi: 10.1186/1745-7580-6-s1-s5 pmc: PMC2946783 pubmed: '20875156' title: Bioinformatics analysis of Brucella vaccines and vaccine targets using VIOLIN. year: 2010 repository: https://github.com/vaccineontology/VO uri_format: http://purl.obolibrary.org/obo/VO_$1 version: 1.1.198 vsmo: contributor: email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: an ontology for vector surveillance and management, focusing on arthropod vectors and vector-borne pathogens with relevance to humans or domestic animals, and with special emphasis on content to support operational activities through inclusion in databases, data management systems, or decision support systems. download_json: https://raw.githubusercontent.com/cthoyt/vsmo/main/vsmo.json download_obo: https://raw.githubusercontent.com/cthoyt/vsmo/main/vsmo.obo download_owl: https://raw.githubusercontent.com/cthoyt/vsmo/main/vsmo.owl example: '0000000' homepage: https://code.google.com/archive/p/vector-surveillance-and-management-ontology/ license: New BSD License name: Ontology for vector surveillance and management preferred_prefix: vsmo publications: - doi: 10.1603/me12169 pmc: PMC3695545 pubmed: '23427646' title: Ontology for vector surveillance and management. year: 2013 uri_format: http://purl.obolibrary.org/obo/VSMO_$1 wikidata: description: Wikidata is a collaboratively edited knowledge base operated by the Wikimedia Foundation. It is intended to provide a common source of certain types of data which can be used by Wikimedia projects such as Wikipedia. Wikidata functions as a document-oriented database, centred on individual items. Items represent topics, for which basic information is stored that identifies each topic. example: Q2207226 homepage: https://www.wikidata.org/ mappings: bartoc: '1940' biocontext: WIKIDATA biolink: WIKIDATA cellosaurus: Wikidata cheminf: '000567' fairsharing: FAIRsharing.6s749p miriam: wikidata n2t: wikidata name: Wikidata pattern: ^(Q|P)\d+$ preferred_prefix: wikidata providers: - code: scholia description: Scholia can generally resolve many Wikidata entries in the biomedical and bibliometric domains homepage: https://scholia.toolforge.org name: Scholia uri_format: https://scholia.toolforge.org/$1 synonyms: - WD_Entity - wd uri_format: http://www.wikidata.org/entity/$1 wikipedia.en: description: Wikipedia is a multilingual, web-based, free-content encyclopedia project based on an openly editable model. It is written collaboratively by largely anonymous Internet volunteers who write without pay. example: SM_UB-81 homepage: http://en.wikipedia.org/wiki/Main_Page mappings: biocontext: WIKIPEDIA.EN go: Wikipedia miriam: wikipedia.en n2t: wikipedia.en prefixcommons: wikipedia name: Wikipedia pattern: ^[A-Za-z-0-9_]+$ preferred_prefix: wikipedia.en providers: - code: CURATOR_REVIEW description: Wikipedia structured content through DBpedia homepage: http://wiki.dbpedia.org/ name: Wikipedia structured content through DBpedia uri_format: http://dbpedia.org/page/$1 - code: volupedia description: A mix of wikipedia and 3d homepage: http://en.volupedia.org name: Volupedia uri_format: http://en.volupedia.org/wiki/$1 synonyms: - wikipedia uri_format: http://en.wikipedia.org/wiki/$1