ontologies: - activity_status: active contact: email: alpha.tom.kodamullil@scai.fraunhofer.de github: akodamullil label: Alpha Tom Kodamullil orcid: 0000-0001-9896-3531 dependencies: - id: bfo description: Alzheimer's Disease Ontology is a knowledge-based ontology that encompasses varieties of concepts related to Alzheimer'S Disease, structured by upper level Basic Formal Ontology(BFO). This Ontology is enriched by the interrelated entities that demonstrate the network of the understanding on Alzheimer's disease and can be readily applied for text mining. domain: health homepage: https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO id: ado layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: https://creativecommons.org/licenses/by/4.0/ ontology_purl: http://purl.obolibrary.org/obo/ado.owl preferredPrefix: ADO products: - id: ado.owl ontology_purl: http://purl.obolibrary.org/obo/ado.owl repository: https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO title: Alzheimer's Disease Ontology tracker: https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO/issues - activity_status: active contact: email: mcmelek@msn.com github: Melek-C label: Melek Chaouch orcid: 0000-0001-5868-4204 description: AfPO is an ontology that can be used in the study of diverse populations across Africa. It brings together publicly available demographic, anthropological and genetic data relating to African people in a standardised and structured format. The AfPO can be employed to classify African study participants comprehensively in prospective research studies. It can also be used to classify past study participants by mapping them using a language or ethnicity identifier or synonyms. domain: organisms homepage: https://github.com/h3abionet/afpo id: afpo layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: https://creativecommons.org/licenses/by/4.0/ ontology_purl: http://purl.obolibrary.org/obo/afpo.owl preferredPrefix: AfPO products: - description: The main ontology in OWL. Contains all MP terms and links to other OBO ontologies id: afpo.owl ontology_purl: http://purl.obolibrary.org/obo/afpo.owl title: AfPO (OWL edition) - description: A direct translation of the AfPO (OWL edition) into OBO format id: afpo.obo ontology_purl: http://purl.obolibrary.org/obo/afpo.obo page: https://github.com/h3abionet/afpo title: AfPO (OBO edition) - description: A direct translation of the AfPO (OWL edition) into OBOGraph JSON format id: afpo.json ontology_purl: http://purl.obolibrary.org/obo/afpo.json page: https://github.com/h3abionet/afpo title: AfPO (obographs JSON edition) repository: https://github.com/h3abionet/afpo tags: - ancestry title: African Population Ontology tracker: https://github.com/h3abionet/afpo/issues - activity_status: active contact: email: m.a.laporte@cgiar.org github: marieALaporte label: Marie-Angélique Laporte orcid: 0000-0002-8461-9745 dependencies: - id: bfo - id: envo - id: foodon - id: go - id: iao - id: ncbitaxon - id: obi - id: pato - id: peco - id: po - id: ro - id: to - id: uo - id: xco description: Ontology of agronomic practices, agronomic techniques, and agronomic variables used in agronomic experiments domain: agriculture homepage: https://github.com/AgriculturalSemantics/agro id: agro layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: https://creativecommons.org/licenses/by/4.0/ ontology_purl: http://purl.obolibrary.org/obo/agro.owl preferredPrefix: AGRO products: - description: Contains all AgrO terms and links to other relevant ontologies. id: agro.owl ontology_purl: http://purl.obolibrary.org/obo/agro.owl title: AgrO publications: - id: http://ceur-ws.org/Vol-1747/IT205_ICBO2016.pdf title: 'Data-driven Agricultural Research for Development: A Need for Data Harmonization Via Semantics.' repository: https://github.com/AgriculturalSemantics/agro tags: - agronomy title: Agronomy Ontology tracker: https://github.com/AgriculturalSemantics/agro/issues/ usages: - description: AgroFIMS enables digital collection of agronomic data that is semantically described a priori with agronomic terms from AgrO. user: https://agrofims.org/about - description: AgrO is being used by GARDIAN to facilitate data search within publications and datasets for use in quantitative analyses. user: https://gardian.bigdata.cgiar.org/ - activity_status: active contact: email: entiminae@gmail.com github: JCGiron label: Jennifer C. Girón orcid: 0000-0002-0851-6883 dependencies: - id: bfo - id: bspo - id: caro - id: pato - id: ro - id: uberon description: The AISM contains terms used in insect biodiversity research for describing structures of the exoskeleton and the skeletomuscular system. It aims to serve as the basic backbone of generalized terms to be expanded with order-specific terminology. domain: anatomy and development homepage: https://github.com/insect-morphology/aism id: aism layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: https://creativecommons.org/licenses/by/4.0/ ontology_purl: http://purl.obolibrary.org/obo/aism.owl preferredPrefix: AISM products: - id: aism.owl ontology_purl: http://purl.obolibrary.org/obo/aism.owl - id: aism.obo ontology_purl: http://purl.obolibrary.org/obo/aism.obo - id: aism.json ontology_purl: http://purl.obolibrary.org/obo/aism.json repository: https://github.com/insect-morphology/aism title: Ontology for the Anatomy of the Insect SkeletoMuscular system (AISM) tracker: https://github.com/insect-morphology/aism/issues - activity_status: active contact: email: hescriva@obs-banyuls.fr github: hescriva label: Hector Escriva orcid: 0000-0001-7577-5028 dependencies: - id: uberon description: An ontology for the development and anatomy of Amphioxus (Branchiostoma lanceolatum). domain: anatomy and development homepage: https://github.com/EBISPOT/amphx_ontology id: amphx layout: ontology_detail license: label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/3.0/ ontology_purl: http://purl.obolibrary.org/obo/amphx.owl preferredPrefix: AMPHX products: - id: amphx.owl ontology_purl: http://purl.obolibrary.org/obo/amphx.owl - id: amphx.obo ontology_purl: http://purl.obolibrary.org/obo/amphx.obo repository: https://github.com/EBISPOT/amphx_ontology title: The Amphioxus Development and Anatomy Ontology tracker: https://github.com/EBISPOT/amphx_ontology/issues - activity_status: active contact: email: stacia@stanford.edu github: srengel label: Stacia R Engel orcid: 0000-0001-5472-917X description: A structured controlled vocabulary for the phenotypes of Ascomycete fungi domain: phenotype homepage: http://www.yeastgenome.org/ id: apo layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: https://creativecommons.org/licenses/by/4.0/ ontology_purl: http://purl.obolibrary.org/obo/apo.owl preferredPrefix: APO products: - id: apo.owl ontology_purl: http://purl.obolibrary.org/obo/apo.owl - id: apo.obo ontology_purl: http://purl.obolibrary.org/obo/apo.obo publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/20157474 title: New mutant phenotype data curation system in the Saccharomyces Genome Database repository: https://github.com/obophenotype/ascomycete-phenotype-ontology taxon: id: NCBITaxon:4890 label: Ascomycota title: Ascomycete phenotype ontology tracker: https://github.com/obophenotype/ascomycete-phenotype-ontology/issues - activity_status: active contact: email: hoganwr@gmail.com github: hoganwr label: William Hogan orcid: 0000-0002-9881-1017 description: An OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation. domain: health homepage: https://github.com/ApolloDev/apollo-sv id: apollo_sv layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: https://creativecommons.org/licenses/by/4.0/ ontology_purl: http://purl.obolibrary.org/obo/apollo_sv.owl preferredPrefix: APOLLO_SV products: - id: apollo_sv.owl ontology_purl: http://purl.obolibrary.org/obo/apollo_sv.owl publications: - id: https://doi.org/10.1186/s13326-016-0092-y title: 'The Apollo Structured Vocabulary: an OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation' repository: https://github.com/ApolloDev/apollo-sv title: Apollo Structured Vocabulary tracker: https://github.com/ApolloDev/apollo-sv/issues usages: - description: Apollo-SV terms are used in the new MIDAS portal (https://midasnetwork.us/catalog/) for making data discoverable. examples: - description: A 'hospital stay dataset' reference in the midasnetwork.us resource url: https://midasnetwork.us/ontology/class-oboapollo_sv_00000600.html seeAlso: https://midasnetwork.us/catalog/ type: annotation user: https://midasnetwork.us/ - activity_status: active contact: email: mcarthua@mcmaster.ca github: agmcarthur label: Andrew G. McArthur orcid: 0000-0002-1142-3063 description: Antibiotic resistance genes and mutations domain: microbiology homepage: https://github.com/arpcard/aro id: aro layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: https://creativecommons.org/licenses/by/4.0/ mailing_list: https://mailman.mcmaster.ca/mailman/listinfo/card-l ontology_purl: http://purl.obolibrary.org/obo/aro.owl preferredPrefix: ARO products: - id: aro.owl ontology_purl: http://purl.obolibrary.org/obo/aro.owl publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/31665441 title: 'CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database.' repository: https://github.com/arpcard/aro title: Antibiotic Resistance Ontology tracker: https://github.com/arpcard/aro/issues - activity_status: active contact: email: rlwalls2008@gmail.com github: ramonawalls label: Ramona Walls orcid: 0000-0001-8815-0078 description: An ontology to support the interoperability of biodiversity data, including data on museum collections, environmental/metagenomic samples, and ecological surveys. domain: organisms homepage: https://github.com/BiodiversityOntologies/bco id: bco in_foundry: false layout: ontology_detail license: label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png url: https://creativecommons.org/publicdomain/zero/1.0/ ontology_purl: http://purl.obolibrary.org/obo/bco.owl preferredPrefix: BCO products: - id: bco.owl ontology_purl: http://purl.obolibrary.org/obo/bco.owl publications: - id: https://doi.org/10.1371/journal.pone.0089606 title: 'Semantics in Support of Biodiversity Knowledge Discovery: An Introduction to the Biological Collections Ontology and Related Ontologies' repository: https://github.com/BiodiversityOntologies/bco tags: - biodiversity collections title: Biological Collections Ontology tracker: https://github.com/BiodiversityOntologies/bco/issues - activity_status: active browsers: - label: BioPortal title: BioPortal Browser url: http://bioportal.bioontology.org/ontologies/BFO?p=classes contact: email: phismith@buffalo.edu github: phismith label: Barry Smith orcid: 0000-0003-1384-116X depicted_by: https://avatars2.githubusercontent.com/u/12972134?v=3&s=200 description: The upper level ontology upon which OBO Foundry ontologies are built. domain: upper homepage: http://ifomis.org/bfo/ id: bfo in_foundry_order: 1 layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/4.0/ mailing_list: https://groups.google.com/forum/#!forum/bfo-discuss ontology_purl: http://purl.obolibrary.org/obo/bfo.owl preferredPrefix: BFO products: - id: bfo.owl ontology_purl: http://purl.obolibrary.org/obo/bfo.owl - id: bfo.obo ontology_purl: http://purl.obolibrary.org/obo/bfo.obo repository: https://github.com/BFO-ontology/BFO title: Basic Formal Ontology tracker: https://github.com/BFO-ontology/BFO/issues usages: - description: BFO is imported by multiple OBO ontologies to standardize upper level structure type: owl_import user: http://obofoundry.org - activity_status: active browsers: - label: BioPortal title: BioPortal Ontology Browser url: https://bioportal.bioontology.org/ontologies/BMONT contact: email: alpha.tom.kodamullil@scai.fraunhofer.de github: akodamullil label: Alpha Tom Kodamullil orcid: 0000-0001-9896-3531 description: An application ontology that represents comprehensive knowledge involving a variety of fields of medical and biological aspects. domain: health homepage: https://github.com/SCAI-BIO/BiomarkerOntology id: bmont layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/4.0/ ontology_purl: http://purl.obolibrary.org/obo/bmont.owl preferredPrefix: BMONT products: - description: Includes axioms linking to other ontologies, but no imports of those ontologies id: BMONT.owl ontology_purl: http://purl.obolibrary.org/obo/BMONT.owl repository: https://github.com/SCAI-BIO/BiomarkerOntology title: Biomarker Ontology tracker: https://github.com/SCAI-BIO/BiomarkerOntology/issues - activity_status: active contact: email: cjmungall@lbl.gov github: cmungall label: Chris Mungall orcid: 0000-0002-6601-2165 description: An ontology for representing spatial concepts, anatomical axes, gradients, regions, planes, sides, and surfaces domain: anatomy and development homepage: https://github.com/obophenotype/biological-spatial-ontology id: bspo layout: ontology_detail license: label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/3.0/ ontology_purl: http://purl.obolibrary.org/obo/bspo.owl preferredPrefix: BSPO products: - id: bspo.owl ontology_purl: http://purl.obolibrary.org/obo/bspo.owl - id: bspo.obo ontology_purl: http://purl.obolibrary.org/obo/bspo.obo publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/25140222 title: 'Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology.' repository: https://github.com/obophenotype/biological-spatial-ontology title: Biological Spatial Ontology tracker: https://github.com/obophenotype/biological-spatial-ontology/issues - activity_status: active contact: email: c.dudek@tu-braunschweig.de github: chdudek label: Christian-Alexander Dudek orcid: 0000-0001-9117-7909 description: A structured controlled vocabulary for the source of an enzyme comprising tissues, cell lines, cell types and cell cultures. domain: anatomy and development homepage: http://www.brenda-enzymes.org id: bto layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: https://creativecommons.org/licenses/by/4.0/ ontology_purl: http://purl.obolibrary.org/obo/bto.owl page: https://en.wikipedia.org/wiki/BRENDA_tissue_ontology preferredPrefix: BTO products: - id: bto.owl ontology_purl: http://purl.obolibrary.org/obo/bto.owl - id: bto.obo ontology_purl: http://purl.obolibrary.org/obo/bto.obo - id: bto.json ontology_purl: http://purl.obolibrary.org/obo/bto.json publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/21030441 title: 'The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources' repository: https://github.com/BRENDA-Enzymes/BTO title: BRENDA tissue / enzyme source tracker: https://github.com/BRENDA-Enzymes/BTO/issues - activity_status: active contact: email: balhoff@renci.org github: balhoff label: Jim Balhoff orcid: 0000-0002-8688-6599 description: a formalization of concepts and relations relevant to evolutionary comparative analysis domain: organisms homepage: https://github.com/evoinfo/cdao id: cdao layout: ontology_detail license: label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png url: https://creativecommons.org/publicdomain/zero/1.0/ ontology_purl: http://purl.obolibrary.org/obo/cdao.owl preferredPrefix: CDAO products: - id: cdao.owl ontology_purl: http://purl.obolibrary.org/obo/cdao.owl publications: - id: https://doi.org/10.4137/EBO.S2320 title: Initial Implementation of a Comparative Data Analysis Ontology repository: https://github.com/evoinfo/cdao title: Comparative Data Analysis Ontology tracker: https://github.com/evoinfo/cdao/issues - activity_status: active contact: email: landreshdz@gmail.com github: LilyAndres label: Liliana Andres Hernandez orcid: 0000-0002-7696-731X dependencies: - id: bfo - id: chebi - id: envo - id: pato - id: ro description: CDNO provides structured terminologies to describe nutritional attributes of material entities that contribute to human diet. domain: diet, metabolomics, and nutrition homepage: https://cdno.info/ id: cdno layout: ontology_detail license: label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: https://creativecommons.org/licenses/by/3.0/ ontology_purl: http://purl.obolibrary.org/obo/cdno.owl preferredPrefix: CDNO products: - id: cdno.owl name: Compositional Dietary Nutrition Ontology main release in OWL format ontology_purl: http://purl.obolibrary.org/obo/cdno.owl - id: cdno.obo name: Compositional Dietary Nutrition Ontology additional release in OBO format ontology_purl: http://purl.obolibrary.org/obo/cdno.obo publications: - id: https://doi.org/10.3389/fnut.2022.928837 title: Establishing a Common Nutritional Vocabulary - From Food Production to Diet repository: https://github.com/CompositionalDietaryNutritionOntology/cdno title: Compositional Dietary Nutrition Ontology tracker: https://github.com/CompositionalDietaryNutritionOntology/cdno/issues - activity_status: active browsers: - label: CHEBI title: EBI CHEBI Browser url: http://www.ebi.ac.uk/chebi/chebiOntology.do?treeView=true&chebiId=CHEBI:24431#graphView contact: email: amalik@ebi.ac.uk github: amalik01 label: Adnan Malik orcid: 0000-0001-8123-5351 depicted_by: https://www.ebi.ac.uk/chebi/chebi_logo.svg description: A structured classification of molecular entities of biological interest focusing on 'small' chemical compounds. domain: chemistry and biochemistry homepage: http://www.ebi.ac.uk/chebi id: chebi in_foundry_order: 1 layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: https://creativecommons.org/licenses/by/4.0/ ontology_purl: http://purl.obolibrary.org/obo/chebi.owl page: http://www.ebi.ac.uk/chebi/init.do?toolBarForward=userManual preferredPrefix: CHEBI products: - id: chebi.owl ontology_purl: http://purl.obolibrary.org/obo/chebi.owl - id: chebi.obo ontology_purl: http://purl.obolibrary.org/obo/chebi.obo - id: chebi.json ontology_purl: http://purl.obolibrary.org/obo/chebi.json - id: chebi.owl.gz ontology_purl: http://purl.obolibrary.org/obo/chebi.owl.gz title: chebi, compressed owl - id: chebi/chebi_lite.obo ontology_purl: http://purl.obolibrary.org/obo/chebi/chebi_lite.obo title: chebi_lite, no syns or xrefs - id: chebi/chebi_core.obo ontology_purl: http://purl.obolibrary.org/obo/chebi/chebi_core.obo title: chebi_core, no xrefs publications: - id: https://doi.org/10.1093/nar/gkaf1271 title: 'ChEBI: re-engineered for a sustainable future' - id: https://www.ncbi.nlm.nih.gov/pubmed/26467479 title: 'ChEBI in 2016: Improved services and an expanding collection of metabolites.' repository: https://github.com/ebi-chebi/ChEBI title: Chemical Entities of Biological Interest tracker: https://github.com/ebi-chebi/ChEBI/issues twitter: chebit usages: - description: Rhea uses CHEBI to annotate reaction participants examples: - description: Query for all usages of CHEBI:29748 (chorismate) url: https://www.rhea-db.org/searchresults?q=CHEBI:29748 user: https://www.rhea-db.org/ - description: ZFIN uses CHEBI to annotate experiments examples: - description: A curated zebrafish experiment involving exposure to (5Z,8Z,14Z)-11,12-dihydroxyicosatrienoic acid (CHEBI:63969) url: http://zfin.org/action/expression/experiment?id=ZDB-EXP-190627-10 user: http://zfin.org - activity_status: active contact: email: egon.willighagen@gmail.com github: egonw label: Egon Willighagen orcid: 0000-0001-7542-0286 description: Includes terms for the descriptors commonly used in cheminformatics software applications and the algorithms which generate them. domain: chemistry and biochemistry homepage: https://github.com/semanticchemistry/semanticchemistry id: cheminf layout: ontology_detail license: label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png url: http://creativecommons.org/publicdomain/zero/1.0/ mailing_list: https://groups.google.com/forum/#!forum/cheminf-ontology ontology_purl: http://purl.obolibrary.org/obo/cheminf.owl preferredPrefix: CHEMINF products: - id: cheminf.owl ontology_purl: http://purl.obolibrary.org/obo/cheminf.owl publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/21991315 title: 'The chemical information ontology: provenance and disambiguation for chemical data on the biological semantic web' repository: https://github.com/semanticchemistry/semanticchemistry title: Chemical Information Ontology tracker: https://github.com/semanticchemistry/semanticchemistry/issues usages: - description: ChEMBL uses CHEMINF in the RDF download examples: - description: The RDF is provided as SPARQL endpoint by Maastricht University. url: https://chemblmirror.rdf.bigcat-bioinformatics.org/ user: https://www.ebi.ac.uk/chembl/ - description: PubChem uses CHEMINF in their RDF representation examples: - description: Physicochemical properties are represented as classes that are typed with CHEMINF classes url: https://pubchem.ncbi.nlm.nih.gov/rest/rdf/descriptor/CID161282_Canonical_SMILES user: https://pubchem.ncbi.nlm.nih.gov/ - activity_status: active contact: email: vasilevs@ohsu.edu github: nicolevasilevsky label: Nicole Vasilevsky orcid: 0000-0001-5208-3432 dependencies: - id: chebi - id: go - id: hp - id: mp - id: ncbitaxon - id: pr - id: uberon description: CHEBI provides a distinct role hierarchy. Chemicals in the structural hierarchy are connected via a 'has role' relation. CHIRO provides links from these roles to useful other classes in other ontologies. This will allow direct connection between chemical structures (small molecules, drugs) and what they do. This could be formalized using 'capable of', in the same way Uberon and the Cell Ontology link structures to processes. domain: chemistry and biochemistry homepage: https://github.com/obophenotype/chiro id: chiro layout: ontology_detail license: label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png url: http://creativecommons.org/publicdomain/zero/1.0/ ontology_purl: http://purl.obolibrary.org/obo/chiro.owl preferredPrefix: CHIRO products: - id: chiro.owl name: CHEBI Integrated Role Ontology main release in OWL format ontology_purl: http://purl.obolibrary.org/obo/chiro.owl - id: chiro.obo name: CHEBI Integrated Role Ontology additional release in OBO format ontology_purl: http://purl.obolibrary.org/obo/chiro.obo publications: - id: https://doi.org/10.26434/chemrxiv.12591221 title: Extension of Roles in the ChEBI Ontology repository: https://github.com/obophenotype/chiro title: CHEBI Integrated Role Ontology tracker: https://github.com/obophenotype/chiro/issues - activity_status: active contact: email: batchelorc@rsc.org github: batchelorc label: Colin Batchelor orcid: 0000-0001-5985-7429 description: CHMO, the chemical methods ontology, describes methods used to domain: health homepage: https://github.com/rsc-ontologies/rsc-cmo id: chmo layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/4.0/ mailing_list: chemistry-ontologies@googlegroups.com ontology_purl: http://purl.obolibrary.org/obo/chmo.owl preferredPrefix: CHMO products: - id: chmo.owl ontology_purl: http://purl.obolibrary.org/obo/chmo.owl repository: https://github.com/rsc-ontologies/rsc-cmo title: Chemical Methods Ontology tracker: https://github.com/rsc-ontologies/rsc-cmo/issues - activity_status: active contact: email: yongqunh@med.umich.edu github: yongqunh label: Yongqun Oliver He orcid: 0000-0001-9189-9661 description: The Coronavirus Infectious Disease Ontology (CIDO) aims to ontologically represent and standardize various aspects of coronavirus infectious diseases, including their etiology, transmission, epidemiology, pathogenesis, diagnosis, prevention, and treatment. domain: health homepage: https://github.com/cido-ontology/cido id: cido layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/4.0/ mailing_list: cido-discuss@googlegroups.com ontology_purl: http://purl.obolibrary.org/obo/cido.owl preferredPrefix: CIDO products: - id: cido.owl ontology_purl: http://purl.obolibrary.org/obo/cido.owl publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/36271389 title: 'A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology' repository: https://github.com/cido-ontology/cido title: Coronavirus Infectious Disease Ontology tracker: https://github.com/cido-ontology/cido/issues - activity_status: active contact: email: frederic.bastian@unil.ch github: fbastian label: Frédéric Bastian orcid: 0000-0002-9415-5104 description: An ontology to capture confidence information about annotations. domain: information homepage: https://github.com/BgeeDB/confidence-information-ontology id: cio layout: ontology_detail license: label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png url: https://creativecommons.org/publicdomain/zero/1.0/ ontology_purl: http://purl.obolibrary.org/obo/cio.owl preferredPrefix: CIO products: - id: cio.owl ontology_purl: http://purl.obolibrary.org/obo/cio.owl - id: cio.obo ontology_purl: http://purl.obolibrary.org/obo/cio.obo publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/25957950 title: 'The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations' repository: https://github.com/BgeeDB/confidence-information-ontology title: Confidence Information Ontology tracker: https://github.com/BgeeDB/confidence-information-ontology - activity_status: active contact: email: do12@sanger.ac.uk github: dosumis label: David Osumi-Sutherland orcid: 0000-0002-7073-9172 dependencies: - id: go - id: ncbitaxon - id: omo - id: pato - id: pr - id: ro - id: uberon depicted_by: /images/CL-logo.jpg description: The Cell Ontology is a structured controlled vocabulary for cell types in animals. domain: anatomy and development homepage: https://obophenotype.github.io/cell-ontology/ id: cl layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/4.0/ mailing_list: https://groups.google.com/g/cl_edit ontology_purl: http://purl.obolibrary.org/obo/cl.owl preferredPrefix: CL products: - description: Complete ontology, plus inter-ontology axioms, and imports modules format: owl-rdf/xml id: cl.owl is_canonical: true ontology_purl: http://purl.obolibrary.org/obo/cl.owl title: Main CL OWL edition uses: - go - ncbitaxon - omo - pato - pr - ro - uberon - derived_from: cl.owl description: Complete ontology, plus inter-ontology axioms, and imports modules merged in format: obo id: cl.obo ontology_purl: http://purl.obolibrary.org/obo/cl.obo title: CL obo format edition - derived_from: cl.owl description: Complete ontology, plus inter-ontology axioms, and imports modules merged in format: json id: cl.json ontology_purl: http://purl.obolibrary.org/obo/cl.json title: CL OBOGraph-JSON format edition - description: Basic version, no inter-ontology axioms format: owl-rdf/xml id: cl/cl-basic.owl ontology_purl: http://purl.obolibrary.org/obo/cl/cl-basic.owl title: Basic CL - description: Basic version, no inter-ontology axioms format: obo id: cl/cl-basic.obo ontology_purl: http://purl.obolibrary.org/obo/cl/cl-basic.obo title: Basic CL (OBO version) - description: Basic version, no inter-ontology axioms format: json id: cl/cl-basic.json ontology_purl: http://purl.obolibrary.org/obo/cl/cl-basic.json title: Basic CL (OBOGraph-JSON version) - description: complete CL but with no imports or external axioms format: owl-rdf/xml id: cl/cl-base.owl ontology_purl: http://purl.obolibrary.org/obo/cl/cl-base.owl title: CL base module - description: complete CL but with no imports or external axioms format: obo id: cl/cl-base.obo ontology_purl: http://purl.obolibrary.org/obo/cl/cl-base.obo title: CL base module (OBO version) - description: complete CL but with no imports or external axioms format: json id: cl/cl-base.json ontology_purl: http://purl.obolibrary.org/obo/cl/cl-base.json title: CL base module (OBOGraph-JSON version) publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/27377652 title: 'The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability.' repository: https://github.com/obophenotype/cell-ontology tags: - cells taxon: id: NCBITaxon:33208 label: Metazoa title: Cell Ontology tracker: https://github.com/obophenotype/cell-ontology/issues twitter: CellOntology usages: - description: The BICCN created a high-resolution atlas of cell types in the primary motor based on single cell transcriptomics. These cell types are represented in the brain data standards ontology which anchors to cell types in the cell ontology. examples: - description: cell type card of a cell type linked to a PCL cell type (L2/3 IT primary motor cortex glutamatergic neuron) which is a subclass of cell types in CL (CL:4023041) url: https://knowledge.brain-map.org/celltypes/CCN202002013/CS202002013_193 - description: PCL cell type used in cell type cards linked directly to CL cell types url: https://www.ebi.ac.uk/ols/ontologies/pcl/terms?iri=http://purl.obolibrary.org/obo/PCL_0011193 publications: - id: https://doi.org/10.1101/2021.10.10.463703 title: 'Brain Data Standards Ontology: A data-driven ontology of transcriptomically defined cell types in the primary motor cortex' type: annotation user: https://biccn.org/ - description: HuBMAP develops tools to create an open, global atlas of the human body at the cellular level. The Cell Ontology is used in annotating cell types in the tools developed. examples: - description: ASCT+B reporter showing CL being used to annotate cell types in the heart url: https://hubmapconsortium.github.io/ccf-asct-reporter/vis?selectedOrgans=heart-v1.1&playground=false publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/31597973 title: 'The human body at cellular resolution: the NIH Human Biomolecular Atlas Program.' type: annotation user: https://hubmapconsortium.org/ - description: The single-cell transcriptomics platform CZ CELLxGENE uses CL to annotate all cell types. All datasets on CellXGene are annotated according to a standard schema that specifies the use of CL to record Cell Type. examples: - description: A CELLxGENE Cell Guide entry for 'luminal adaptive secretory precursor cell of mammary gland', which includes the CL ID (CL:4033057), CL definition and a visualizer of CL hierarchy url: https://cellxgene.cziscience.com/cellguide/CL:4033057 publications: - id: https://doi.org/10.1101/2021.04.05.438318 title: 'CELLxGENE: a performant, scalable exploration platform for high dimensional sparse matrices' type: annotation user: https://cellxgene.cziscience.com/ - description: The Human Cell Atlas (HCA) is an international group of researchers using a combination of these new technologies to create cellular reference maps. The HCA use CL to annotate cells in their reference maps. examples: - description: HCA collection studies that are related B cell (CL:0000236) that is filtered through CL annotation url: https://singlecell.broadinstitute.org/single_cell?type=study&page=1&facets=cell_type%3ACL_0000236&scpbr=human-cell-atlas-main-collection publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/29206104 title: The Human Cell Atlas type: annotation user: https://www.humancellatlas.org/ - description: The EBI single cell expression atlas is an extension to EBI expression atlas that displays gene expression in single cells. Cell types in the single cell expression atlas linked with terms from the Cell Ontology. examples: - description: RNA-Seq CAGE (Cap Analysis of Gene Expression) analysis of mice cells in RIKEN FANTOM5 project annotated using cell types from CL url: https://www.ebi.ac.uk/gxa/experiments/E-MTAB-3578/Results publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/31665515 title: 'Expression Atlas update: from tissues to single cells' type: annotation user: https://www.ebi.ac.uk/gxa/home - description: The National Human Genome Research Institute (NHGRI) launched a public research consortium named ENCODE, the Encyclopedia Of DNA Elements, in September 2003, to carry out a project to identify all functional elements in the human genome sequence. The ENCODE DCC uses Uberon to annotate samples publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/25776021 title: Ontology application and use at the ENCODE DCC seeAlso: https://doi.org/10.25504/FAIRsharing.v0hbjs type: annotation user: https://www.encodeproject.org/ - description: FANTOM5 is using Uberon and CL to annotate samples allowing for transcriptome analyses with cell-type and tissue-level specificity. examples: - description: FANTOM5 samples annotated to neuron url: http://fantom.gsc.riken.jp/5/sstar/CL:0000540 type: annotation user: http://fantom5-collaboration.gsc.riken.jp/ - activity_status: active contact: email: lagonzalezmo@unal.edu.co github: luis-gonzalez-m label: Luis González-Montaña orcid: 0000-0002-9136-9932 dependencies: - id: ro description: 'CLAO is an ontology of anatomical terms employed in morphological descriptions for the Class Collembola (Arthropoda: Hexapoda).' domain: anatomy and development homepage: https://github.com/luis-gonzalez-m/Collembola id: clao layout: ontology_detail license: label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png url: http://creativecommons.org/publicdomain/zero/1.0/ ontology_purl: http://purl.obolibrary.org/obo/clao.owl preferredPrefix: CLAO products: - id: clao.owl ontology_purl: http://purl.obolibrary.org/obo/clao.owl - id: clao.obo ontology_purl: http://purl.obolibrary.org/obo/clao.obo pull_request_added: 1337 repository: https://github.com/luis-gonzalez-m/Collembola title: Collembola Anatomy Ontology tracker: https://github.com/luis-gonzalez-m/Collembola/issues - activity_status: active contact: email: zhengj2007@gmail.com github: zhengj2007 label: Jie Zheng orcid: 0000-0002-2999-0103 dependencies: - id: cl - id: doid - id: ncbitaxon - id: uberon description: An ontology to standardize and integrate cell line information and to support computer-assisted reasoning. domain: anatomy and development homepage: https://github.com/CLO-Ontology/CLO id: clo layout: ontology_detail license: label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/3.0/ ontology_purl: http://purl.obolibrary.org/obo/clo.owl preferredPrefix: CLO products: - id: clo.owl ontology_purl: http://purl.obolibrary.org/obo/clo.owl publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/25852852 title: 'CLO: The Cell Line Ontology' repository: https://github.com/CLO-Ontology/CLO title: Cell Line Ontology tracker: https://github.com/CLO-Ontology/CLO/issues - activity_status: active contact: email: lucas.leclere@obs-banyuls.fr github: Leclere-L label: Lucas Leclere orcid: 0000-0002-7440-0467 dependencies: - id: iao - id: ro - id: uberon description: The Clytia hemisphaerica Development and Anatomy Ontology (CLYH) describes the anatomical and developmental features of the Clytia hemisphaerica life cycle. domain: anatomy and development homepage: https://github.com/EBISPOT/clyh_ontology id: clyh layout: ontology_detail license: label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/3.0/ ontology_purl: http://purl.obolibrary.org/obo/clyh.owl preferredPrefix: CLYH products: - id: clyh.owl ontology_purl: http://purl.obolibrary.org/obo/clyh.owl - id: clyh.obo ontology_purl: http://purl.obolibrary.org/obo/clyh.obo pull_request_added: 1205 repository: https://github.com/EBISPOT/clyh_ontology title: Clytia hemisphaerica Development and Anatomy Ontology tracker: https://github.com/EBISPOT/clyh_ontology/issues - activity_status: active browsers: - label: RGD title: RGD Ontology Browser url: http://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=CMO:0000000 contact: email: jrsmith@mcw.edu github: jrsjrs label: Jennifer Smith orcid: 0000-0002-6443-9376 depicted_by: http://rgd.mcw.edu/common/images/rgd_LOGO_blue_rgd.gif description: Morphological and physiological measurement records generated from clinical and model organism research and health programs. domain: health homepage: http://rgd.mcw.edu/rgdweb/ontology/search.html id: cmo layout: ontology_detail license: label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png url: http://creativecommons.org/publicdomain/zero/1.0/ ontology_purl: http://purl.obolibrary.org/obo/cmo.owl page: https://download.rgd.mcw.edu/ontology/clinical_measurement/ preferredPrefix: CMO products: - id: cmo.owl ontology_purl: http://purl.obolibrary.org/obo/cmo.owl - id: cmo.obo ontology_purl: http://purl.obolibrary.org/obo/cmo.obo publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/22654893 title: Three ontologies to define phenotype measurement data. - id: https://www.ncbi.nlm.nih.gov/pubmed/24103152 title: 'The clinical measurement, measurement method and experimental condition ontologies: expansion, improvements and new applications.' repository: https://github.com/rat-genome-database/CMO-Clinical-Measurement-Ontology tags: - clinical title: Clinical measurement ontology tracker: https://github.com/rat-genome-database/CMO-Clinical-Measurement-Ontology/issues - activity_status: active contact: email: bpeters@lji.org github: bpeters42 label: Bjoern Peters orcid: 0000-0002-8457-6693 description: COB brings together key terms from a wide range of OBO projects to improve interoperability. domain: upper homepage: https://obofoundry.org/COB/ id: cob layout: ontology_detail license: label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png url: https://creativecommons.org/publicdomain/zero/1.0/ ontology_purl: http://purl.obolibrary.org/obo/cob.owl preferredPrefix: COB products: - description: Core Ontology for Biology and Biomedicine, main ontology id: cob.owl ontology_purl: http://purl.obolibrary.org/obo/cob.owl title: COB - description: base module for COB id: cob/cob-base.owl ontology_purl: http://purl.obolibrary.org/obo/cob/cob-base.owl title: COB base module - description: COB with native IDs preserved rather than rewired to OBO IDs id: cob/cob-native.owl ontology_purl: http://purl.obolibrary.org/obo/cob/cob-native.owl title: COB native module - id: cob/cob-to-external.owl ontology_purl: http://purl.obolibrary.org/obo/cob/cob-to-external.owl title: COB to external type: BridgeOntology - description: demo of COB including subsets of other ontologies (Experimental, for demo purposes only) id: cob/products/demo-cob.owl ontology_purl: http://purl.obolibrary.org/obo/cob/products/demo-cob.owl status: alpha title: COB demo ontology (experimental) repository: https://github.com/OBOFoundry/COB title: Core Ontology for Biology and Biomedicine tracker: https://github.com/OBOFoundry/COB/issues usages: - description: Ontologies using COB terms examples: - description: List of ontologies using at least one COB term (See section entitled "Which ontologies use it?") url: http://dashboard.obofoundry.org/dashboard/cob/dashboard.html - description: List of ontologies using the term 'organism' (See section entitled "Ontologies that use the Class") url: https://ontobee.org/ontology/COB?iri=http://purl.obolibrary.org/obo/COB_0000022 user: (multiple) - activity_status: active contact: email: entiminae@gmail.com github: JCGiron label: Jennifer C. Giron orcid: 0000-0002-0851-6883 dependencies: - id: aism - id: bfo - id: bspo - id: caro - id: pato - id: ro - id: uberon description: The Coleoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of beetles in biodiversity research. It has been built using the Ontology Develoment Kit, with the Ontology for the Anatomy of the Insect Skeleto-Muscular system (AISM) as a backbone. domain: anatomy and development homepage: https://github.com/insect-morphology/colao id: colao layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: https://creativecommons.org/licenses/by/4.0/ ontology_purl: http://purl.obolibrary.org/obo/colao.owl preferredPrefix: COLAO products: - id: colao.owl ontology_purl: http://purl.obolibrary.org/obo/colao.owl - id: colao.obo ontology_purl: http://purl.obolibrary.org/obo/colao.obo repository: https://github.com/insect-morphology/colao tags: - insect anatomy title: Coleoptera Anatomy Ontology (COLAO) tracker: https://github.com/insect-morphology/colao/issues - activity_status: active contact: email: whimar@ohsu.edu github: marijane label: Marijane White orcid: 0000-0001-5059-4132 description: A classification of the diverse roles performed in the work leading to a published research output in the sciences. Its purpose to provide transparency in contributions to scholarly published work, to enable improved systems of attribution, credit, and accountability. domain: information homepage: https://github.com/data2health/contributor-role-ontology id: cro layout: ontology_detail license: label: CC BY 2.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: https://creativecommons.org/licenses/by/2.0/ ontology_purl: http://purl.obolibrary.org/obo/cro.owl preferredPrefix: CRO products: - id: cro.owl ontology_purl: http://purl.obolibrary.org/obo/cro.owl title: CRO repository: https://github.com/data2health/contributor-role-ontology tags: - scholarly contribution roles title: Contributor Role Ontology tracker: https://github.com/data2health/contributor-role-ontology/issues - activity_status: active contact: email: cjmungall@lbl.gov github: cmungall label: Chris Mungall orcid: 0000-0002-6601-2165 dependencies: - id: ro - id: uberon description: An anatomical and developmental ontology for ctenophores (Comb Jellies) domain: anatomy and development homepage: https://github.com/obophenotype/ctenophore-ontology id: cteno layout: ontology_detail license: label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/3.0/ ontology_purl: http://purl.obolibrary.org/obo/cteno.owl preferredPrefix: CTENO products: - id: cteno.owl ontology_purl: http://purl.obolibrary.org/obo/cteno.owl repository: https://github.com/obophenotype/ctenophore-ontology taxon: id: NCBITaxon:10197 label: Ctenophore title: Ctenophore Ontology tracker: https://github.com/obophenotype/ctenophore-ontology/issues - activity_status: active contact: email: alpha.tom.kodamullil@scai.fraunhofer.de github: akodamullil label: Dr. Alpha Tom Kodamullil orcid: 0000-0001-9896-3531 description: The core Ontology of Clinical Trials (CTO) will serve as a structured resource integrating basic terms and concepts in the context of clinical trials. Thereby covering clinicaltrails.gov. CoreCTO will serve as a basic ontology to generate extended versions for specific applications such as annotation of variables in study documents from clinical trials. domain: health homepage: https://github.com/ClinicalTrialOntology/CTO/ id: cto layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/4.0/ ontology_purl: http://purl.obolibrary.org/obo/cto.owl preferredPrefix: CTO products: - id: cto.owl ontology_purl: http://purl.obolibrary.org/obo/cto.owl repository: https://github.com/ClinicalTrialOntology/CTO title: 'CTO: Core Ontology of Clinical Trials' tracker: https://github.com/ClinicalTrialOntology/CTO/issues - activity_status: active contact: email: paul.fabry@usherbrooke.ca github: pfabry label: Paul Fabry orcid: 0000-0002-3336-2476 description: An ontology to describe entities related to cardiovascular diseases domain: health homepage: https://github.com/OpenLHS/CVDO id: cvdo layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: https://creativecommons.org/licenses/by/4.0/ ontology_purl: http://purl.obolibrary.org/obo/cvdo.owl preferredPrefix: CVDO products: - id: cvdo.owl ontology_purl: http://purl.obolibrary.org/obo/cvdo.owl repository: https://github.com/OpenLHS/CVDO title: Cardiovascular Disease Ontology tracker: https://github.com/OpenLHS/CVDO/issues - activity_status: active contact: email: pfey@northwestern.edu github: pfey03 label: Petra Fey orcid: 0000-0002-4532-2703 description: A structured controlled vocabulary of the anatomy of the slime-mold Dictyostelium discoideum domain: anatomy and development homepage: http://dictybase.org/ id: ddanat layout: ontology_detail license: label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png url: https://creativecommons.org/publicdomain/zero/1.0/ ontology_purl: http://purl.obolibrary.org/obo/ddanat.owl preferredPrefix: DDANAT products: - id: ddanat.owl ontology_purl: http://purl.obolibrary.org/obo/ddanat.owl - id: ddanat.obo ontology_purl: http://purl.obolibrary.org/obo/ddanat.obo publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/18366659 title: An anatomy ontology to represent biological knowledge in Dictyostelium discoideum repository: https://github.com/dictyBase/migration-data taxon: id: NCBITaxon:44689 label: Dictyostelium discoideum title: Dictyostelium discoideum anatomy tracker: https://github.com/dictyBase/migration-data/issues twitter: dictybase - activity_status: active contact: email: pfey@northwestern.edu github: pfey03 label: Petra Fey orcid: 0000-0002-4532-2703 description: A structured controlled vocabulary of phenotypes of the slime-mould Dictyostelium discoideum. domain: anatomy and development homepage: http://dictybase.org/ id: ddpheno layout: ontology_detail license: label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png url: http://creativecommons.org/publicdomain/zero/1.0/ ontology_purl: http://purl.obolibrary.org/obo/ddpheno.owl preferredPrefix: DDPHENO products: - id: ddpheno.owl ontology_purl: http://purl.obolibrary.org/obo/ddpheno.owl - id: ddpheno.obo ontology_purl: http://purl.obolibrary.org/obo/ddpheno.obo publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/31840793 title: dictyBase and the Dicty Stock Center (version 2.0) - a progress report repository: https://github.com/obophenotype/dicty-phenotype-ontology taxon: id: NCBITaxon:44689 label: Dictyostelium discoideum title: Dictyostelium discoideum phenotype ontology tracker: https://github.com/obophenotype/dicty-phenotype-ontology/issues twitter: dictybase - activity_status: active contact: email: mbrochhausen@gmail.com github: mbrochhausen label: Mathias Brochhausen orcid: 0000-0003-1834-3856 description: The Potential Drug-drug Interaction and Potential Drug-drug Interaction Evidence Ontology domain: chemistry and biochemistry homepage: https://github.com/DIDEO/DIDEO id: dideo layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: https://creativecommons.org/licenses/by/4.0/ ontology_purl: http://purl.obolibrary.org/obo/dideo.owl preferredPrefix: DIDEO products: - id: dideo.owl ontology_purl: http://purl.obolibrary.org/obo/dideo.owl repository: https://github.com/DIDEO/DIDEO title: Drug-drug Interaction and Drug-drug Interaction Evidence Ontology tracker: https://github.com/DIDEO/DIDEO/issues - activity_status: active browsers: - label: DO title: DO Browser url: https://disease-ontology.org/ contact: email: lynn.schriml@gmail.com github: lschriml label: Lynn Schriml orcid: 0000-0001-8910-9851 description: Ontology for drivers and triggers of human diseases, built to classify ExO ontology exposure stressors. An application ontology. Built in collaboration with EnvO, ExO, ECTO and ChEBI. domain: health homepage: https://disease-ontology.org/ id: disdriv layout: ontology_detail license: label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png url: https://creativecommons.org/publicdomain/zero/1.0/ ontology_purl: http://purl.obolibrary.org/obo/disdriv.owl preferredPrefix: DISDRIV products: - id: disdriv.owl ontology_purl: http://purl.obolibrary.org/obo/disdriv.owl repository: https://github.com/DiseaseOntology/DiseaseDriversOntology tags: - disease taxon: id: NCBITaxon:9606 label: Homo sapiens title: Disease Drivers Ontology tracker: https://github.com/DiseaseOntology/DiseaseDriversOntology/issues twitter: diseaseontology usages: - description: Human Disease Ontology examples: - description: fetal alcohol syndrome, has exposure stressor some alcohol url: https://disease-ontology.org/?id=DOID:0050665 user: https://disease-ontology.org/ - activity_status: active browsers: - label: DO title: DO Browser url: https://disease-ontology.org/do contact: email: lynn.schriml@gmail.com github: lschriml label: Lynn Schriml orcid: 0000-0001-8910-9851 depicted_by: https://disease-ontology.org/media/images/DO_logo_teal.png description: An ontology for describing the classification of human diseases organized by etiology. domain: health homepage: https://disease-ontology.org id: doid in_foundry_order: 1 layout: ontology_detail license: label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png url: https://creativecommons.org/publicdomain/zero/1.0/ ontology_purl: http://purl.obolibrary.org/obo/doid.owl preferredPrefix: DOID products: - id: doid.owl ontology_purl: http://purl.obolibrary.org/obo/doid.owl title: Disease Ontology, OWL format. This file contains DO's is_a asserted hierarchy plus equivalent axioms to other OBO Foundry ontologies. - id: doid.obo ontology_purl: http://purl.obolibrary.org/obo/doid.obo title: Disease Ontology, OBO format. This file omits the equivalent axioms. publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/25348409 title: 'Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data' - id: https://www.ncbi.nlm.nih.gov/pubmed/34755882 title: The Human Disease Ontology 2022 update repository: https://github.com/DiseaseOntology/HumanDiseaseOntology tags: - disease taxon: id: NCBITaxon:9606 label: Homo sapiens title: Human Disease Ontology tracker: https://github.com/DiseaseOntology/HumanDiseaseOntology/issues twitter: diseaseontology usages: - description: Alliance of Genome Resources - MGD, RGD, SGD, FlyBase, WormBase, ZFIN use DO examples: - description: Human diseases annotated to over 190,000 MOD genes, alleles, disease models and human genes url: https://www.alliancegenome.org/search?category=disease - description: The landing page for Coronavirus Infectious Disease url: https://www.alliancegenome.org/disease/DOID:0080599 user: https://www.alliancegenome.org - description: MGI disease model annotations use DO examples: - description: physical disorder url: https://www.informatics.jax.org/disease/DOID:0080015 user: https://www.informatics.jax.org/disease - description: Immune Epitope Database examples: - description: Antibody and T cell epitopes associated with human diseases url: https://www.iedb.org user: https://www.iedb.org - activity_status: active browsers: - label: FB title: FlyBase Browser url: http://flybase.org/.bin/cvreport.html?cvterm=FBcv:0000347 contact: email: cp390@cam.ac.uk github: Clare72 label: Clare Pilgrim orcid: 0000-0002-1373-1705 description: An ontology of commonly encountered and/or high level Drosophila phenotypes. domain: phenotype homepage: http://purl.obolibrary.org/obo/fbcv id: dpo layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/4.0/ ontology_purl: http://purl.obolibrary.org/obo/dpo.owl preferredPrefix: FBcv products: - id: dpo.owl ontology_purl: http://purl.obolibrary.org/obo/dpo.owl - id: dpo.obo ontology_purl: http://purl.obolibrary.org/obo/dpo.obo - id: dpo.json ontology_purl: http://purl.obolibrary.org/obo/dpo.json publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/24138933 title: The Drosophila phenotype ontology. repository: https://github.com/FlyBase/drosophila-phenotype-ontology taxon: id: NCBITaxon:7227 label: Drosophila title: Drosophila Phenotype Ontology tracker: https://github.com/FlyBase/drosophila-phenotype-ontology/issues usages: - description: FlyBase uses dpo for phenotype data annotation in Drosophila examples: - description: alleles and constructs annotated to pupal lethal in FlyBase url: http://flybase.org/cgi-bin/cvreport.html?rel=is_a&id=FBcv:0002030 user: http://flybase.org - activity_status: active contact: email: hoganwr@gmail.com github: hoganwr label: William Hogan orcid: 0000-0002-9881-1017 description: An ontology to support comparative effectiveness researchers studying claims data. domain: health homepage: https://github.com/ufbmi/dron id: dron layout: ontology_detail license: label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/3.0/ ontology_purl: http://purl.obolibrary.org/obo/dron.owl preferredPrefix: DRON products: - id: dron.owl ontology_purl: http://purl.obolibrary.org/obo/dron.owl publications: - id: https://doi.org/10.1186/s13326-017-0121-5 title: 'Therapeutic indications and other use-case-driven updates in the drug ontology: anti-malarials, anti-hypertensives, opioid analgesics, and a large term request' repository: https://github.com/ufbmi/dron title: The Drug Ontology tracker: https://github.com/ufbmi/dron/issues usages: - description: DrOn is used for the classification of Drugs, in particular, based on RxNorm codes, in the PennTURBO project. examples: - description: 'From the documentation: For example, the text `500 mg Tylenol po tabs` might be mapped to http://purl.obolibrary.org/obo/DRON_00073395, with the label `Acetaminophen 500 MG Oral Tablet [Tylenol]`. DrOn knows that this is a subclass of `Acetaminophen 500 MG Oral Tablet` (through its logical axiomatisation).' url: https://pennturbo.github.io/Turbo-Documentation/medication_text_to_terms_to_roles.html type: annotation user: https://github.com/PennTURBO - activity_status: active contact: email: mcourtot@gmail.com github: mcourtot label: Melanie Courtot orcid: 0000-0002-9551-6370 dependencies: - id: bfo - id: iao description: DUO is an ontology which represent data use conditions. domain: information homepage: https://github.com/EBISPOT/DUO id: duo layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/4.0/ ontology_purl: http://purl.obolibrary.org/obo/duo.owl preferredPrefix: DUO products: - id: duo.owl ontology_purl: http://purl.obolibrary.org/obo/duo.owl repository: https://github.com/EBISPOT/DUO title: Data Use Ontology tracker: https://github.com/EBISPOT/DUO/issues - activity_status: active contact: email: ettensohn@cmu.edu github: ettensohn label: Charles Ettensohn orcid: 0000-0002-3625-0955 dependencies: - id: cl - id: ro - id: uberon description: An ontology for the development and anatomy of the different species of the phylum Echinodermata (NCBITaxon:7586). domain: anatomy and development homepage: https://github.com/echinoderm-ontology/ecao_ontology id: ecao layout: ontology_detail license: label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/3.0/ ontology_purl: http://purl.obolibrary.org/obo/ecao.owl preferredPrefix: ECAO products: - id: ecao.owl ontology_purl: http://purl.obolibrary.org/obo/ecao.owl - id: ecao.obo ontology_purl: http://purl.obolibrary.org/obo/ecao.obo repository: https://github.com/echinoderm-ontology/ecao_ontology title: The Echinoderm Anatomy and Development Ontology tracker: https://github.com/echinoderm-ontology/ecao_ontology/issues - activity_status: active browsers: - label: ECO title: ECO Browser url: https://www.evidenceontology.org/browse contact: email: mgiglio@som.umaryland.edu github: mgiglio99 label: Michelle Giglio orcid: 0000-0001-7628-5565 depicted_by: https://avatars1.githubusercontent.com/u/12802432 description: An ontology for experimental and other evidence statements. domain: investigations funded_by: - id: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1458400 title: NSF ABI-1458400 homepage: https://www.evidenceontology.org id: eco layout: ontology_detail license: label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png url: https://creativecommons.org/publicdomain/zero/1.0/ ontology_purl: http://purl.obolibrary.org/obo/eco.owl preferredPrefix: ECO products: - id: eco.owl ontology_purl: http://purl.obolibrary.org/obo/eco.owl - id: eco.obo ontology_purl: http://purl.obolibrary.org/obo/eco.obo publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/34986598 preferred: true title: 'ECO: the Evidence and Conclusion Ontology, an update for 2022.' - id: https://www.ncbi.nlm.nih.gov/pubmed/30407590 title: 'ECO, the Evidence & Conclusion Ontology: community standard for evidence information.' - id: https://www.ncbi.nlm.nih.gov/pubmed/25052702 title: Standardized description of scientific evidence using the Evidence Ontology (ECO) repository: https://github.com/evidenceontology/evidenceontology title: Evidence and Conclusion Ontology tracker: https://github.com/evidenceontology/evidenceontology/issues usages: - description: ECO is used by the GO consortium for evidence on GO associations examples: - description: annotations to transmembrane transport url: http://amigo.geneontology.org/amigo/term/GO:0055085 type: annotation user: http://geneontology.org - description: ECO is used by the Monarch Initiative for evidence types for disease to phenotype annotations. examples: - description: 'Parkinsonism: Characteristic neurologic anomaly resulting form degeneration of dopamine-generating cells in the substantia nigra, a region of the midbrain, characterized clinically by shaking, rigidity, slowness of movement and difficulty with walking and gait.' url: https://monarchinitiative.org/phenotype/HP%3A0001300#disease publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/27899636 title: 'The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species' type: annotation user: https://monarchinitiative.org/ - activity_status: active contact: email: p.buttigieg@gmail.com github: pbuttigieg label: Pier Luigi Buttigieg orcid: 0000-0002-4366-3088 dependencies: - id: bfo - id: chebi - id: envo - id: go - id: iao - id: pato - id: pco - id: po - id: ro - id: uberon description: Ecocore is a community ontology for the concise and controlled description of ecological traits of organisms. domain: environment homepage: https://github.com/EcologicalSemantics/ecocore id: ecocore layout: ontology_detail license: label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/3.0/ ontology_purl: http://purl.obolibrary.org/obo/ecocore.owl preferredPrefix: ECOCORE products: - id: ecocore.owl ontology_purl: http://purl.obolibrary.org/obo/ecocore.owl - id: ecocore.obo ontology_purl: http://purl.obolibrary.org/obo/ecocore.obo repository: https://github.com/EcologicalSemantics/ecocore tags: - ecological functions - ecological interactions title: An ontology of core ecological entities tracker: https://github.com/EcologicalSemantics/ecocore/issues - activity_status: active contact: email: annethessen@gmail.com github: diatomsRcool label: Anne Thessen orcid: 0000-0002-2908-3327 dependencies: - id: chebi - id: envo - id: exo - id: go - id: iao - id: maxo - id: nbo - id: ncbitaxon - id: ncit - id: pato - id: ro - id: uberon - id: xco depicted_by: https://raw.githubusercontent.com/jmcmurry/closed-illustrations/master/logos/ecto-logos/ecto-logo_black-banner.png description: ECTO describes exposures to experimental treatments of plants and model organisms (e.g. exposures to modification of diet, lighting levels, temperature); exposures of humans or any other organisms to stressors through a variety of routes, for purposes of public health, environmental monitoring etc, stimuli, natural and experimental, any kind of environmental condition or change in condition that can be experienced by an organism or population of organisms on earth. The scope is very general and can include for example plant treatment regimens, as well as human clinical exposures (although these may better be handled by a more specialized ontology). domain: environment homepage: https://github.com/EnvironmentOntology/environmental-exposure-ontology id: ecto layout: ontology_detail license: label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png url: https://creativecommons.org/publicdomain/zero/1.0/ ontology_purl: http://purl.obolibrary.org/obo/ecto.owl preferredPrefix: ECTO products: - id: ecto.owl name: Environmental conditions, treatments and exposures ontology main release in OWL format ontology_purl: http://purl.obolibrary.org/obo/ecto.owl - id: ecto.obo name: Environmental conditions, treatments and exposures ontology additional release in OBO format ontology_purl: http://purl.obolibrary.org/obo/ecto.obo - id: ecto.json name: Environmental conditions, treatments and exposures ontology additional release in OBOJSon format ontology_purl: http://purl.obolibrary.org/obo/ecto.json - id: ecto/ecto-base.owl name: Environmental conditions, treatments and exposures ontology main release in OWL format ontology_purl: http://purl.obolibrary.org/obo/ecto/ecto-base.owl - id: ecto/ecto-base.obo name: Environmental conditions, treatments and exposures ontology additional release in OBO format ontology_purl: http://purl.obolibrary.org/obo/ecto/ecto-base.obo - id: ecto/ecto-base.json name: Environmental conditions, treatments and exposures ontology additional release in OBOJSon format ontology_purl: http://purl.obolibrary.org/obo/ecto/ecto-base.json repository: https://github.com/EnvironmentOntology/environmental-exposure-ontology title: Environmental conditions, treatments and exposures ontology tracker: https://github.com/EnvironmentOntology/environmental-exposure-ontology/issues - activity_status: active contact: email: Terry.Hayamizu@jax.org github: tfhayamizu label: Terry Hayamizu orcid: 0000-0002-0956-8634 description: An ontology for mouse anatomy covering embryonic development and postnatal stages. domain: anatomy and development homepage: http://www.informatics.jax.org/expression.shtml id: emapa layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: https://creativecommons.org/licenses/by/4.0/ ontology_purl: http://purl.obolibrary.org/obo/emapa.owl preferredPrefix: EMAPA products: - id: emapa.owl ontology_purl: http://purl.obolibrary.org/obo/emapa.owl - id: emapa.obo ontology_purl: http://purl.obolibrary.org/obo/emapa.obo publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/9651497 title: An internet-accessible database of mouse developmental anatomy based on a systematic nomenclature - id: https://www.ncbi.nlm.nih.gov/pubmed/23972281 title: 'EMAP/EMAPA ontology of mouse developmental anatomy: 2013 update' - id: https://www.ncbi.nlm.nih.gov/pubmed/26208972 title: 'Mouse Anatomy Ontologies: Enhancements and Tools for Exploring and Integrating Biomedical Data' - id: https://doi.org/10.1016/B978-0-12-800043-4.00023-3 title: 'Textual Anatomics: the Mouse Developmental Anatomy Ontology and the Gene Expression Database for Mouse Development (GXD)' repository: https://github.com/obophenotype/developmental-mouse-anatomy-ontology taxon: id: NCBITaxon:10088 label: Mus title: Mouse Developmental Anatomy Ontology tracker: https://github.com/obophenotype/developmental-mouse-anatomy-ontology/issues usages: - description: GXD seeAlso: https://doi.org/10.25504/FAIRsharing.q9neh8 user: http://www.informatics.jax.org/expression.shtml - activity_status: active contact: email: pier.buttigieg@awi.de github: pbuttigieg label: Pier Luigi Buttigieg orcid: 0000-0002-4366-3088 dependencies: - id: chebi - id: foodon - id: go - id: ncbitaxon - id: pco - id: po - id: ro - id: uberon depicted_by: /images/envo.png description: An ontology of environmental systems, components, and processes. domain: environment homepage: http://environmentontology.org/ id: envo layout: ontology_detail license: label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png url: http://creativecommons.org/publicdomain/zero/1.0/ ontology_purl: http://purl.obolibrary.org/obo/envo.owl page: https://github.com/EnvironmentOntology/envo preferredPrefix: ENVO products: - id: envo.owl ontology_purl: http://purl.obolibrary.org/obo/envo.owl title: main ENVO OWL release - id: envo.json ontology_purl: http://purl.obolibrary.org/obo/envo.json title: ENVO in obographs JSON format - id: envo.obo ontology_purl: http://purl.obolibrary.org/obo/envo.obo title: ENVO in OBO Format. May be lossy - id: envo/subsets/envo-basic.obo ontology_purl: http://purl.obolibrary.org/obo/envo/subsets/envo-basic.obo title: OBO-Basic edition of ENVO - id: envo/subsets/envoEmpo.owl ontology_purl: http://purl.obolibrary.org/obo/envo/subsets/envoEmpo.owl title: Earth Microbiome Project subset - homepage: http://environmentontology.org/downloads id: envo/subsets/EnvO-Lite-GSC.obo ontology_purl: http://purl.obolibrary.org/obo/envo/subsets/EnvO-Lite-GSC.obo title: GSC Lite subset of ENVO publications: - id: https://doi.org/10.1186/2041-1480-4-43 preferred: true title: 'The environment ontology: contextualising biological and biomedical entities' - id: https://doi.org/10.1186/s13326-016-0097-6 title: 'The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation' repository: https://github.com/EnvironmentOntology/envo title: Environment Ontology tracker: https://github.com/EnvironmentOntology/envo/issues/ usages: - description: describing species habitats examples: - description: Pseudobarbus burchelli (Tradou Redfin) is a species of bony fishes in the family Cyprinidae. They are associated with freshwater habitat. Individuals can grow to 13.5 cm. They have sexual reproduction. url: http://eol.org/pages/211700/data type: data-annotation user: http://eol.org - description: describing stomach contents type: data-annotation user: http://globalbioticinteractions.org - description: annotating datasets in data repositories seeAlso: http://blogs.nature.com/scientificdata/2015/12/17/isa-explorer/ type: dataset-description user: http://www.nature.com/sdata/ - description: Samples collected during Tara Oceans expedition are annotated with ENVO examples: - description: Sample collected during the Tara Oceans expedition (2009-2013) at station TARA_004 (latitudeN=36.5533, longitudeE=-6.5669) url: https://www.ebi.ac.uk/metagenomics/projects/ERP001736/samples/ERS487899 user: http://oceans.taraexpeditions.org/en/ - description: Annotation of habitats of microbes examples: - description: Annotation of habitat of Pseudovibrio sp. FO-BEG1 to marine environment url: https://www.ncbi.nlm.nih.gov/nuccore/NC_016642 user: https://www.ncbi.nlm.nih.gov/ - description: Annotation and semantic search over microbial data sets examples: - description: Example metadata of a sample of marine water near Lisboa, taken as part of the Ocean Sampling Day Project (https://www.microb3.eu/osd.html). ENVO is used for the fields environmental feature, material, and biome. url: https://www.planetmicrobe.org/project/#/samples/200 user: https://www.planetmicrobe.org/project/ - activity_status: active contact: email: alpha.tom.kodamullil@scai.fraunhofer.de github: akodamullil label: Alpha Tom Kodamullil orcid: 0000-0001-9896-3531 dependencies: - id: bfo description: A application driven Epilepsy Ontology with official terms from the ILAE. domain: health homepage: https://github.com/SCAI-BIO/EpilepsyOntology id: epio layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/4.0/ ontology_purl: http://purl.obolibrary.org/obo/epio.owl preferredPrefix: EPIO products: - id: epio.owl ontology_purl: http://purl.obolibrary.org/obo/epio.owl - id: EPIO_merged.owl ontology_purl: http://purl.obolibrary.org/obo/EPIO_merged.owl repository: https://github.com/SCAI-BIO/EpilepsyOntology tags: - disease title: Epilepsy Ontology tracker: https://github.com/SCAI-BIO/EpilepsyOntology/issues - activity_status: active contact: email: xyz19940216@163.com github: DarkKnight0-0 label: Xingyun Liu orcid: 0000-0002-9295-2767 description: A core reference ontology built upon BFO about exercise medicine and it contains the related terms for healthy people, people with chronic conditions and people living with diability to exercise. domain: health homepage: https://github.com/Exercise-Medicine-Ontology/EXMO id: exmo layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: https://creativecommons.org/licenses/by/4.0/ ontology_purl: http://purl.obolibrary.org/obo/exmo.owl preferredPrefix: EXMO products: - id: exmo.owl ontology_purl: http://purl.obolibrary.org/obo/exmo.owl publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/39695140 title: Core reference ontology for individualized exercise prescription repository: https://github.com/Exercise-Medicine-Ontology/EXMO title: Exercise Medicine Ontology tracker: https://github.com/Exercise-Medicine-Ontology/EXMO/issues - activity_status: active contact: email: annethessen@gmail.com github: diatomsRcool label: Anne Thessen orcid: 0000-0002-2908-3327 description: Vocabularies for describing exposure data to inform understanding of environmental health. domain: health homepage: https://github.com/CTDbase/exposure-ontology id: exo layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: https://creativecommons.org/licenses/by/4.0/ ontology_purl: http://purl.obolibrary.org/obo/exo.owl preferredPrefix: ExO products: - id: exo.owl ontology_purl: http://purl.obolibrary.org/obo/exo.owl - id: exo.obo ontology_purl: http://purl.obolibrary.org/obo/exo.obo repository: https://github.com/CTDbase/exposure-ontology title: Exposure ontology tracker: https://github.com/CTDbase/exposure-ontology/issues - activity_status: active contact: email: vw253@cam.ac.uk github: ValWood label: Val Wood orcid: 0000-0001-6330-7526 description: A structured controlled vocabulary for the anatomy of fungi. domain: anatomy and development homepage: https://github.com/obophenotype/fungal-anatomy-ontology/ id: fao layout: ontology_detail license: label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png url: http://creativecommons.org/publicdomain/zero/1.0/ ontology_purl: http://purl.obolibrary.org/obo/fao.owl preferredPrefix: FAO products: - id: fao.owl ontology_purl: http://purl.obolibrary.org/obo/fao.owl - id: fao.obo ontology_purl: http://purl.obolibrary.org/obo/fao.obo repository: https://github.com/obophenotype/fungal-anatomy-ontology taxon: id: NCBITaxon:4751 label: Fungal title: Fungal gross anatomy tracker: https://github.com/obophenotype/fungal-anatomy-ontology/issues - activity_status: active browsers: - label: BioPortal title: BioPortal Browser url: https://bioportal.bioontology.org/ontologies/FBbi contact: email: damien@gerbi-gmb.de github: gouttegd label: Damien Goutte-Gattat orcid: 0000-0002-6095-8718 dependencies: - id: iao - id: omo - id: ro description: An ontology for the description of sample preparation, visualization, and imaging methods used in biomedical research. domain: investigations homepage: https://github.com/foundingGIDE/fbbi id: fbbi layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: https://creativecommons.org/licenses/by/4.0/ ontology_purl: http://purl.obolibrary.org/obo/fbbi.owl preferredPrefix: FBbi products: - id: fbbi.owl ontology_purl: http://purl.obolibrary.org/obo/fbbi.owl - id: fbbi.obo ontology_purl: http://purl.obolibrary.org/obo/fbbi.obo - id: fbbi/fbbi-base.owl ontology_purl: http://purl.obolibrary.org/obo/fbbi/fbbi-base.owl - id: fbbi/fbbi-base.obo ontology_purl: http://purl.obolibrary.org/obo/fbbi/fbbi-base.obo repository: https://github.com/foundingGIDE/fbbi tags: - imaging experiments title: Biological Imaging Methods Ontology tracker: https://github.com/foundingGIDE/fbbi/issues usages: - description: FlyBase uses FBbi to annotate its image collection. examples: - description: images annotated to "scanning electron micrograph" url: https://flybase.org/cgi-bin/fbcvquery.pl?mode=subtreehits&cvterm=FBbi:00000257%3EFBim user: https://flybase.org - description: Virtual Fly Brain uses FBbi to annotate images. user: https://virtualflybrain.org - description: The Cell Image Library uses FBbi to annotate images. examples: - description: An image annotate with several terms from FBbi. url: https://www.cellimagelibrary.org/images/13654 user: https://www.cellimagelibrary.org - activity_status: active browsers: - label: FB title: FlyBase Browser url: http://flybase.org/.bin/cvreport.html?cvterm=FBbt:10000000 - label: VFB title: Virtual Fly Brain url: http://www.virtualflybrain.org/site/stacks/index.htm?add=FBbt:00007401 - label: BioPortal title: BioPortal Browser url: http://bioportal.bioontology.org/ontologies/FB-BT?p=classes contact: email: cp390@cam.ac.uk github: Clare72 label: Clare Pilgrim orcid: 0000-0002-1373-1705 description: An ontology representing the gross anatomy of Drosophila melanogaster. domain: anatomy and development homepage: http://purl.obolibrary.org/obo/fbbt id: fbbt layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/4.0/ ontology_purl: http://purl.obolibrary.org/obo/fbbt.owl preferredPrefix: FBbt products: - id: fbbt.owl ontology_purl: http://purl.obolibrary.org/obo/fbbt.owl - id: fbbt.obo ontology_purl: http://purl.obolibrary.org/obo/fbbt.obo - id: fbbt.json ontology_purl: http://purl.obolibrary.org/obo/fbbt.json - id: fbbt/fbbt-simple.owl ontology_purl: http://purl.obolibrary.org/obo/fbbt/fbbt-simple.owl - id: fbbt/fbbt-simple.obo ontology_purl: http://purl.obolibrary.org/obo/fbbt/fbbt-simple.obo publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/24139062 preferred: true title: The Drosophila anatomy ontology - id: https://www.ncbi.nlm.nih.gov/pubmed/22402613 title: A strategy for building neuroanatomy ontologies - id: https://www.ncbi.nlm.nih.gov/pubmed/22180411 title: The Virtual Fly Brain Browser and Query Interface - id: https://www.ncbi.nlm.nih.gov/pubmed/16381917 title: 'FlyBase: anatomical data, images and queries' repository: https://github.com/FlyBase/drosophila-anatomy-developmental-ontology tags: - Drosophilid anatomy taxon: id: NCBITaxon:7227 label: Drosophila title: Drosophila gross anatomy tracker: http://purl.obolibrary.org/obo/fbbt/tracker usages: - description: VFB uses FBbt to annotate brain images examples: - description: Ring neuron R2 in VFB url: http://www.virtualflybrain.org/site/stacks/index.htm?id=FBbt_00003651 - description: genes expressed in ring neuron R2 in VFB url: http://www.virtualflybrain.org/do/gene_list.html?action=geneex&id=FBbt:00003651 user: http://www.virtualflybrain.org/ - description: Flybase uses FBbt for expression and phenotype data annotation in Drosophila examples: - description: alleles, constructs and insertions annotated to neuron in FlyBase url: http://flybase.org/cgi-bin/cvreport.html?rel=is_a&id=FBbt:00005106 user: http://flybase.org - activity_status: active browsers: - label: FB title: FlyBase Browser url: http://flybase.org/.bin/cvreport.html?cvterm=FBcv:0000013 contact: email: cp390@cam.ac.uk github: Clare72 label: Clare Pilgrim orcid: 0000-0002-1373-1705 description: A structured controlled vocabulary used for various aspects of annotation by FlyBase. domain: organisms homepage: http://purl.obolibrary.org/obo/fbcv id: fbcv layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/4.0/ ontology_purl: http://purl.obolibrary.org/obo/fbcv.owl preferredPrefix: FBcv products: - id: fbcv.owl ontology_purl: http://purl.obolibrary.org/obo/fbcv.owl - id: fbcv.obo ontology_purl: http://purl.obolibrary.org/obo/fbcv.obo - id: fbcv.json ontology_purl: http://purl.obolibrary.org/obo/fbcv.json publications: [] repository: https://github.com/FlyBase/flybase-controlled-vocabulary title: FlyBase Controlled Vocabulary tracker: https://github.com/FlyBase/flybase-controlled-vocabulary/issues usages: - description: FlyBase uses FBcv for phenotype data annotation in Drosophila examples: - description: alleles and constructs annotated to bang sensitive in FlyBase url: http://flybase.org/cgi-bin/cvreport.html?rel=is_a&id=FBcv:0000391 user: http://flybase.org - activity_status: active browsers: - label: FB title: FlyBase Browser url: http://flybase.org/.bin/cvreport.html?cvterm=FBdv:00007008 contact: email: cp390@cam.ac.uk github: Clare72 label: Clare Pilgrim orcid: 0000-0002-1373-1705 description: A structured controlled vocabulary of the development of Drosophila melanogaster. domain: anatomy and development homepage: http://purl.obolibrary.org/obo/fbdv id: fbdv layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/4.0/ ontology_purl: http://purl.obolibrary.org/obo/fbdv.owl preferredPrefix: FBdv products: - id: fbdv.owl ontology_purl: http://purl.obolibrary.org/obo/fbdv.owl - id: fbdv.obo ontology_purl: http://purl.obolibrary.org/obo/fbdv.obo - id: fbdv.json ontology_purl: http://purl.obolibrary.org/obo/fbdv.json - id: fbdv/fbdv-simple.owl ontology_purl: http://purl.obolibrary.org/obo/fbdv/fbdv-simple.owl - id: fbdv/fbdv-simple.obo ontology_purl: http://purl.obolibrary.org/obo/fbdv/fbdv-simple.obo publications: [] repository: https://github.com/FlyBase/drosophila-developmental-ontology taxon: id: NCBITaxon:7227 label: Drosophila title: Drosophila development tracker: http://purl.obolibrary.org/obo/fbdv/tracker usages: - description: Used to record stages in expression and phenotype curation examples: - description: Expression of DLP in embryonic/larval midgut primordium at embryonic stage 13 (http://purl.obolibrary.org/obo/FBdv_00005328) (Khare and Baumgartner, 2000) url: https://flybase.org/reports/FBgn0041604#expression user: http://flybase.org - activity_status: active contact: email: georgeta.bordea@u-bordeaux.fr github: getbordea label: Georgeta Bordea orcid: 0000-0001-9921-8234 description: Food-Drug interactions automatically extracted from scientific literature domain: diet, metabolomics, and nutrition homepage: https://gitub.u-bordeaux.fr/erias/fideo id: fideo layout: ontology_detail license: label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png url: https://creativecommons.org/publicdomain/zero/1.0/ ontology_purl: http://purl.obolibrary.org/obo/fideo.owl preferredPrefix: FIDEO products: - id: fideo.owl ontology_purl: http://purl.obolibrary.org/obo/fideo.owl repository: https://gitub.u-bordeaux.fr/erias/fideo title: Food Interactions with Drugs Evidence Ontology tracker: https://gitub.u-bordeaux.fr/erias/fideo/issues - activity_status: active contact: email: robert.hoehndorf@kaust.edu.sa github: leechuck label: Robert Hoehndorf orcid: 0000-0001-8149-5890 description: Traits and phenotypes of flowering plants occurring in digitized Floras domain: phenotype homepage: https://github.com/flora-phenotype-ontology/flopoontology id: flopo layout: ontology_detail license: label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png url: https://creativecommons.org/publicdomain/zero/1.0/ ontology_purl: http://purl.obolibrary.org/obo/flopo.owl preferredPrefix: FLOPO products: - id: flopo.owl ontology_purl: http://purl.obolibrary.org/obo/flopo.owl publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/27842607 title: 'The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants' repository: https://github.com/flora-phenotype-ontology/flopoontology taxon: id: NCBITaxon:33090 label: Viridiplantae title: Flora Phenotype Ontology tracker: https://github.com/flora-phenotype-ontology/flopoontology/issues - activity_status: active contact: email: polcaes@gmail.com github: pcastellanoescuder label: Pol Castellano Escuder orcid: 0000-0001-6466-877X dependencies: - id: chebi - id: foodon description: FOBI (Food-Biomarker Ontology) is an ontology to represent food intake data and associate it with metabolomic data domain: diet, metabolomics, and nutrition homepage: https://github.com/pcastellanoescuder/FoodBiomarkerOntology id: fobi layout: ontology_detail license: label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/3.0/ ontology_purl: http://purl.obolibrary.org/obo/fobi.owl preferredPrefix: FOBI products: - format: owl-rdf/xml id: fobi.owl ontology_purl: http://purl.obolibrary.org/obo/fobi.owl title: FOBI is an ontology to represent food intake data and associate it with metabolomic data publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/32556148 title: 'FOBI: an ontology to represent food intake data and associate it with metabolomic data' - id: https://www.ncbi.nlm.nih.gov/pubmed/34601570 title: 'The fobitools framework: the first steps towards food enrichment analysis' repository: https://github.com/pcastellanoescuder/FoodBiomarkerOntology title: Food-Biomarker Ontology tracker: https://github.com/pcastellanoescuder/FoodBiomarkerOntology/issues - activity_status: active contact: email: damion_dooley@sfu.ca github: ddooley label: Damion Dooley orcid: 0000-0002-8844-9165 dependencies: - id: bfo - id: chebi - id: envo - id: eo - id: ncbitaxon - id: obi - id: ro - id: uberon description: A broadly scoped ontology representing entities which bear a “food role”. It encompasses materials in natural ecosystems and agriculture that are consumed by humans and domesticated animals. This includes any generic (unbranded) raw or processed food material found in processing plants, markets, stores or food distribution points. FoodOn also imports nutritional component and dietary pattern terms from other OBO Foundry ontologies to support interoperability in diet and nutrition research domain: diet, metabolomics, and nutrition homepage: https://foodon.org/ id: foodon layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/4.0/ ontology_purl: http://purl.obolibrary.org/obo/foodon.owl preferredPrefix: FOODON products: - format: owl-rdf/xml id: foodon.owl ontology_purl: http://purl.obolibrary.org/obo/foodon.owl title: FoodOn ontology with import file references and over 9,000 food products - format: owl-rdf/xml id: foodon_core.owl ontology_purl: http://purl.obolibrary.org/obo/foodon_core.owl title: FoodOn core ontology (currently the same as foodon.owl) publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/31304272 title: 'FoodOn: a harmonized food ontology to increase global food traceability, quality control and data integration' repository: https://github.com/FoodOntology/foodon tags: - food title: Food Ontology tracker: https://github.com/FoodOntology/foodon/issues/ usages: - description: FoodData Central nutrition database web portal provided by USDA Agricultural Research Service. examples: - description: An entry for 'Apples, fuji, with skin, raw' from the FoodData Central nutrition database which is annotated with the term FOODON:00002862. url: https://fdc.nal.usda.gov/fdc-app.html#/food-details/1750340/attributes user: https://fdc.nal.usda.gov/ - description: FDA GenomeTrackr surveillance program for reporting foodborne pathogen biosamples. examples: - description: An entry from NCBI Biosample that describes a *Samonella enterica* sample extracted from Chicken and annotated with the term FOODON:03411457. url: https://www.ncbi.nlm.nih.gov/biosample/SAMN03455272 user: https://www.fda.gov/food/whole-genome-sequencing-wgs-program/genometrakr-network - description: Wiki database consolidating over 30 global food composition databases. examples: - description: An entry from WikiFCD that describes Walnuts and is annotated with the term FOODON:03301364. url: https://wikifcd.wikibase.cloud/wiki/Item:Q568877 user: https://wikifcd.wikibase.cloud/wiki/Main_Page - activity_status: active contact: email: meghan.balk@gmail.com github: megbalk label: Meghan Balk orcid: 0000-0003-2699-3066 dependencies: - id: bco - id: bfo - id: bspo - id: iao - id: oba - id: pato - id: ro - id: uberon description: FuTRES Ontology of Vertebrate Traits is an application ontology used to convert vertebrate trait data in spreadsheet to triples. FOVT leverages the BioCollections Ontology (BCO) to link observations of individual specimens to their trait values. Traits are defined in the Ontology of Biological Attributes (OBA). domain: phenotype homepage: https://github.com/futres/fovt id: fovt layout: ontology_detail license: label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png url: https://creativecommons.org/publicdomain/zero/1.0/ ontology_purl: http://purl.obolibrary.org/obo/fovt.owl preferredPrefix: FOVT products: - id: fovt.owl name: FuTRES Ontology of Vertebrate Traits main release in OWL format ontology_purl: http://purl.obolibrary.org/obo/fovt.owl - id: fovt.obo name: FuTRES Ontology of Vertebrate Traits additional release in OBO format ontology_purl: http://purl.obolibrary.org/obo/fovt.obo - id: fovt/fovt-base.owl name: FuTRES Ontology of Vertebrate Traits main release in OWL format ontology_purl: http://purl.obolibrary.org/obo/fovt/fovt-base.owl - id: fovt/fovt-base.obo name: FuTRES Ontology of Vertebrate Traits additional release in OBO format ontology_purl: http://purl.obolibrary.org/obo/fovt/fovt-base.obo repository: https://github.com/futres/fovt tags: - vertebrate traits title: FuTRES Ontology of Vertebrate Traits tracker: https://github.com/futres/fovt/issues - activity_status: active contact: email: vw253@cam.ac.uk github: ValWood label: Val Wood orcid: 0000-0001-6330-7526 depicted_by: https://github.com/pombase/website/blob/master/src/assets/FYPO_logo_tiny.png description: FYPO is a formal ontology of phenotypes observed in fission yeast. domain: phenotype homepage: https://github.com/pombase/fypo id: fypo layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/4.0/ ontology_purl: http://purl.obolibrary.org/obo/fypo.owl preferredPrefix: FYPO products: - id: fypo.owl ontology_purl: http://purl.obolibrary.org/obo/fypo.owl - id: fypo.obo ontology_purl: http://purl.obolibrary.org/obo/fypo.obo publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/23658422 title: 'FYPO: The Fission Yeast Phenotype Ontology.' repository: https://github.com/pombase/fypo taxon: id: NCBITaxon:4896 label: S. pombe title: Fission Yeast Phenotype Ontology tracker: https://github.com/pombase/fypo/issues usages: - description: Pombase uses fypo for phenotype data annotation in fission yeast examples: - description: genotypes annotated to abnormal mitotic cell cycle in fission yeast url: https://www.pombase.org/term/FYPO:0000059 user: https://www.pombase.org - activity_status: active contact: email: adeans@psu.edu github: adeans label: Andy Deans orcid: 0000-0002-2119-4663 dependencies: - id: caro - id: flopo - id: ncbitaxon - id: obi - id: pato - id: po - id: poro - id: ro description: Ontology of plant gall phenotypes. Plant galls are novel plant structures, generated by plants in response to biotic stressors. This ontology is used to annotate gall phenotypes (e.g., their colors, textures, sizes, locations on the plant) in a semantic way, in order to facilitate discoveries about the genetic and physiologic mechanisms responsible for such phenotypes. The ontology can also be used as a controlled vocabulary for natural language descriptions of plant galls. domain: phenotype homepage: https://adeans.github.io/gallont/ id: gallont layout: ontology_detail license: label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png url: https://creativecommons.org/publicdomain/zero/1.0/ ontology_purl: http://purl.obolibrary.org/obo/gallont.owl preferredPrefix: GALLONT products: - id: gallont.owl ontology_purl: http://purl.obolibrary.org/obo/gallont.owl - id: gallont.json ontology_purl: http://purl.obolibrary.org/obo/gallont.json - id: gallont.obo ontology_purl: http://purl.obolibrary.org/obo/gallont.obo repository: https://github.com/adeans/gallont title: Plant Gall Ontology tracker: https://github.com/adeans/gallont/issues - activity_status: active contact: email: lschriml@som.umaryland.edu github: lschriml label: Lynn Schriml orcid: 0000-0001-8910-9851 description: A gazetteer constructed on ontological principles. The countries are actively maintained. domain: environment homepage: http://environmentontology.github.io/gaz/ id: gaz layout: ontology_detail license: label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png url: https://creativecommons.org/publicdomain/zero/1.0/ mailing_list: https://groups.google.com/forum/#!forum/obo-gazetteer ontology_purl: http://purl.obolibrary.org/obo/gaz.owl preferredPrefix: GAZ products: - id: gaz.owl ontology_purl: http://purl.obolibrary.org/obo/gaz.owl - id: gaz.obo ontology_purl: http://purl.obolibrary.org/obo/gaz.obo - description: A country specific subset of the GAZ. id: gaz/gaz-countries.owl ontology_purl: http://purl.obolibrary.org/obo/gaz/gaz-countries.owl title: GAZ countries repository: https://github.com/EnvironmentOntology/gaz title: Gazetteer tracker: https://github.com/EnvironmentOntology/gaz/issues - activity_status: active contact: email: rbca.jackson@gmail.com github: beckyjackson label: Rebecca Jackson orcid: 0000-0003-4871-5569 description: An ontology to represent genomics cohort attributes domain: organisms homepage: https://github.com/IHCC-cohorts/GECKO id: gecko layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: https://creativecommons.org/licenses/by/4.0/ ontology_purl: http://purl.obolibrary.org/obo/gecko.owl preferredPrefix: GECKO products: - id: gecko.owl ontology_purl: http://purl.obolibrary.org/obo/gecko.owl repository: https://github.com/IHCC-cohorts/GECKO tags: - cohort studies title: Genomics Cohorts Knowledge Ontology tracker: https://github.com/IHCC-cohorts/GECKO/issues usages: - description: IHCC uses GECKO to standardize data from various cohorts for the IHCC cohort browser user: https://ihccglobal.org/ - activity_status: active contact: email: damion_dooley@sfu.ca github: ddooley label: Damion Dooley orcid: 0000-0002-8844-9165 dependencies: - id: chebi - id: ncbitaxon - id: po - id: ro - id: uberon description: The Genomic Epidemiology Ontology (GenEpiO) covers vocabulary necessary to identify, document and research foodborne pathogens and associated outbreaks. domain: health homepage: http://genepio.org/ id: genepio layout: ontology_detail license: label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/3.0/ ontology_purl: http://purl.obolibrary.org/obo/genepio.owl page: https://github.com/GenEpiO/genepio preferredPrefix: GENEPIO products: - homepage: http://genepio.github.io/genepio/ id: genepio.owl ontology_purl: http://purl.obolibrary.org/obo/genepio.owl repository: https://github.com/GenEpiO/genepio title: Genomic Epidemiology Ontology tracker: https://github.com/GenEpiO/genepio/issues/ - activity_status: active contact: email: mhb120@gmail.com github: mbrush label: Matthew Brush orcid: 0000-0002-1048-5019 description: An integrated ontology for representing the genetic variations described in genotypes, and their causal relationships to phenotype and diseases. domain: biological systems homepage: https://github.com/monarch-initiative/GENO-ontology/ id: geno layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: https://creativecommons.org/licenses/by/4.0/ ontology_purl: http://purl.obolibrary.org/obo/geno.owl preferredPrefix: GENO products: - id: geno.owl ontology_purl: http://purl.obolibrary.org/obo/geno.owl title: GENO repository: https://github.com/monarch-initiative/GENO-ontology tags: - genotype-to-phenotype associations title: Genotype Ontology tracker: https://github.com/monarch-initiative/GENO-ontology/issues - activity_status: active contact: email: hoganwr@gmail.com github: hoganwr label: Bill Hogan orcid: 0000-0002-9881-1017 description: An ontology of geographical entities domain: environment homepage: https://github.com/ufbmi/geographical-entity-ontology/wiki id: geo layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: https://creativecommons.org/licenses/by/4.0/ ontology_purl: http://purl.obolibrary.org/obo/geo.owl preferredPrefix: GEO products: - id: geo.owl ontology_purl: http://purl.obolibrary.org/obo/geo.owl repository: https://github.com/ufbmi/geographical-entity-ontology title: Geographical Entity Ontology tracker: https://github.com/ufbmi/geographical-entity-ontology/issues - activity_status: active browsers: - label: Structure Browser title: GNOme Glycan Structure Browser url: https://gnome.glyomics.org/StructureBrowser.html?HexNAc=4&Hex=5&dHex=1&NeuAc=2 - label: Composition Browser title: GNOme Glycan Composition Browser url: https://gnome.glyomics.org/CompositionBrowser.html?HexNAc=4&Hex=5&dHex=1&NeuAc=2 contact: email: nje5@georgetown.edu github: edwardsnj label: Nathan Edwards orcid: 0000-0001-5168-3196 description: GlyTouCan provides stable accessions for glycans described at varyious degrees of characterization, including compositions (no linkage) and topologies (no carbon bond positions or anomeric configurations). GNOme organizes these stable accessions for interative browsing, for text-based searching, and for automated reasoning with well-defined characterization levels. domain: chemistry and biochemistry homepage: https://gnome.glyomics.org/ id: gno layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: https://creativecommons.org/licenses/by/4.0/ ontology_purl: http://purl.obolibrary.org/obo/gno.owl preferredPrefix: GNO products: - description: Glycan Naming and Subsumption Ontology, OWL format (primary) id: gno.owl ontology_purl: http://purl.obolibrary.org/obo/gno.owl - description: Glycan Naming and Subsumption Ontology, OBO format (automated conversion from OWL) id: gno.obo ontology_purl: http://purl.obolibrary.org/obo/gno.obo - description: Glycan Naming and Subsumption Ontology, JSON format (automated conversion from OWL) id: gno.json ontology_purl: http://purl.obolibrary.org/obo/gno.json publications: - id: https://doi.org/10.5281/zenodo.6678278 title: GNOme - Glycan Naming and Subsumption Ontology repository: https://github.com/glygen-glycan-data/GNOme tags: - glycan structure title: Glycan Naming and Subsumption Ontology (GNOme) tracker: https://github.com/glygen-glycan-data/GNOme/issues usages: - description: GlyGen - Computational and Informatics Resources for Glycoscience examples: - description: GNOme attributes and related glycans on glycan pages url: https://www.glygen.org/glycan/G00028MO user: https://www.glygen.org/ - description: PRO - Protein Ontology examples: - description: example of PRO use of GNO terms url: http://purl.obolibrary.org/obo/PR_000059585 user: https://proconsortium.org/ - description: ChEBI - Chemical Entities of Biological Interest examples: - description: example of ChEBI use of GNO terms url: http://purl.obolibrary.org/obo/CHEBI_167503 user: https://www.ebi.ac.uk/chebi/init.do - activity_status: active browsers: - label: AmiGO title: Gene Ontology AmiGO 2 Browser url: http://amigo.geneontology.org/amigo/term/GO:0008150#display-lineage-tab contact: email: suzia@stanford.edu github: suzialeksander label: Suzi Aleksander orcid: 0000-0001-6787-2901 dependencies: - id: cl subset: go/extensions/cl_import.owl - connects: - id: nifstd - id: go description: Bridging axioms between nifstd and go id: go/extensions/go-bridge-to-nifstd.owl publications: - id: http://www.ncbi.nlm.nih.gov/pubmed/24093723 title: 'The Gene Ontology (GO) Cellular Component Ontology: integration with SAO (Subcellular Anatomy Ontology) and other recent developments.' title: GO bridge to NIFSTD type: BridgeOntology - id: ncbitaxon subset: go/extensions/ncbitaxon_import.owl - id: ro subset: go/extensions/ro_import.owl - id: uberon subset: go/extensions/uberon_import.owl depicted_by: /images/go_logo.png description: An ontology for describing the function of genes and gene products domain: biological systems homepage: http://geneontology.org/ id: go in_foundry_order: 1 layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: https://creativecommons.org/licenses/by/4.0/ ontology_purl: http://purl.obolibrary.org/obo/go.owl preferredPrefix: GO products: - description: The main ontology in OWL. This is self contained and does not have connections to other OBO ontologies id: go.owl ontology_purl: http://purl.obolibrary.org/obo/go.owl page: http://geneontology.org/page/download-ontology title: GO (OWL edition) - description: Equivalent to go.owl, in obo format id: go.obo ontology_purl: http://purl.obolibrary.org/obo/go.obo page: http://geneontology.org/page/download-ontology title: GO (OBO Format edition) - description: Equivalent to go.owl, in obograph json format id: go.json ontology_purl: http://purl.obolibrary.org/obo/go.json page: https://github.com/geneontology/obographs/ title: GO (JSON edition) - description: The main ontology plus axioms connecting to select external ontologies, with subsets of those ontologies id: go/extensions/go-plus.owl ontology_purl: http://purl.obolibrary.org/obo/go/extensions/go-plus.owl page: http://geneontology.org/page/download-ontology title: GO-Plus - description: The main ontology plus axioms connecting to select external ontologies, excluding the external ontologies themselves id: go/go-base.owl ontology_purl: http://purl.obolibrary.org/obo/go/go-base.owl page: http://geneontology.org/page/download-ontology title: GO Base Module - description: As go-plus.owl, in obographs json format id: go/extensions/go-plus.json ontology_purl: http://purl.obolibrary.org/obo/go/extensions/go-plus.json page: https://github.com/geneontology/obographs/ title: GO-Plus - description: Basic version of the GO, filtered such that the graph is guaranteed to be acyclic and annotations can be propagated up the graph. The relations included are is a, part of, regulates, negatively regulates and positively regulates. This version excludes relationships that cross the 3 GO hierarchies. id: go/go-basic.obo ontology_purl: http://purl.obolibrary.org/obo/go/go-basic.obo page: http://geneontology.org/page/download-ontology title: GO-Basic, Filtered, for use with legacy tools - description: As go-basic.obo, in json format id: go/go-basic.json ontology_purl: http://purl.obolibrary.org/obo/go/go-basic.json page: http://geneontology.org/page/download-ontology title: GO-Basic, Filtered, for use with legacy tools (JSON) - description: Classes added to ncbitaxon for groupings such as prokaryotes id: go/extensions/go-taxon-groupings.owl ontology_purl: http://purl.obolibrary.org/obo/go/extensions/go-taxon-groupings.owl page: http://geneontology.org/page/download-ontology title: GO Taxon Groupings - description: Equivalent to go.owl, but released daily. Note the snapshot release is not archived. id: go/snapshot/go.owl ontology_purl: http://purl.obolibrary.org/obo/go/snapshot/go.owl page: http://geneontology.org/page/download-ontology title: GO (OWL edition), daily snapshot release - description: Equivalent to go.owl, but released daily. Note the snapshot release is not archived. id: go/snapshot/go.obo ontology_purl: http://purl.obolibrary.org/obo/go/snapshot/go.obo page: http://geneontology.org/page/download-ontology title: GO (OBO Format edition), daily snapshot release publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/10802651 title: 'Gene ontology: tool for the unification of biology. The Gene Ontology Consortium' - id: https://www.ncbi.nlm.nih.gov/pubmed/33290552 title: 'The Gene Ontology resource: enriching a GOld mine' repository: https://github.com/geneontology/go-ontology tags: - biology taxon: id: NCBITaxon:1 label: All life title: Gene Ontology tracker: https://github.com/geneontology/go-ontology/issues/ twitter: news4go usages: - description: The GO ontology is used by the GO consortium for functional annotation of genes examples: - description: annotations to transmembrane transport url: http://amigo.geneontology.org/amigo/term/GO:0055085 type: annotation user: http://geneontology.org - description: Uniprot uses GO to show the function of proteins examples: - description: functional annotations of human Sonic hedgehog protein url: https://www.uniprot.org/uniprot/Q15465#function type: annotation user: https://www.uniprot.org - description: Reactome annotates activities, pathways, and cellular localization using GO examples: - description: protein tyrosine kinase activity of an EGFR complex url: https://reactome.org/content/detail/R-HSA-177934 type: annotation user: https://reactome.org - description: The Alliance of Genome Resources uses GO for model organism gene function annotation examples: - description: Functional summary of C elegans nsy-1 gene url: https://www.alliancegenome.org/gene/WB:WBGene00003822#function---go-annotations - description: Gene Ontology Causal Activity Models for C elegans nsy-1 gene url: https://www.alliancegenome.org/gene/WB:WBGene00003822#pathways type: annotation user: https://www.alliancegenome.org - description: Rhea uses GO to describe individual biochemical reactions examples: - description: Glutamine scyllo-inositol transaminase reaction and associated GO term url: https://www.rhea-db.org/rhea/22920 type: mapping user: https://www.rhea-db.org - activity_status: active contact: email: dwelter.ontologist@gmail.com github: daniwelter label: Danielle Welter orcid: 0000-0003-1058-2668 description: The Human Ancestry Ontology (HANCESTRO) provides a systematic description of the ancestry concepts used in the NHGRI-EBI Catalog of published genome-wide association studies. domain: organisms homepage: https://ebispot.github.io/hancestro/ id: hancestro layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: https://creativecommons.org/licenses/by/4.0/ ontology_purl: http://purl.obolibrary.org/obo/hancestro.owl preferredPrefix: HANCESTRO products: - description: The full version of HANCESTRO in OWL format, with BFO upper hierarchy for easier integration with other ontologies id: hancestro.owl ontology_purl: http://purl.obolibrary.org/obo/hancestro.owl title: HANCESTRO - description: Base version of HANCESTRO id: hancestro-base.owl ontology_purl: http://purl.obolibrary.org/obo/hancestro-base.owl title: HANCESTRO Base publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/29448949 title: A standardized framework for representation of ancestry data in genomics studies, with application to the NHGRI-EBI GWAS Catalog repository: https://github.com/EBISPOT/hancestro tags: - ancestry title: Human Ancestry Ontology tracker: https://github.com/EBISPOT/hancestro/issues usages: - description: The Experimental Factor Ontology (EFO) provides a systematic description of many experimental variables available in EBI databases, and for external projects such as the NHGRI GWAS catalogue. It combines parts of several biological ontologies, such as anatomy, disease and chemical compounds. examples: - description: Population category defined using ancestry informative markers (AIMs) based on genetic/genomic data url: https://www.ebi.ac.uk/ols/ontologies/efo/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FHANCESTRO_0004&viewMode=All&siblings=false user: http://www.ebi.ac.uk/efo - description: The Genomic Epidemiology Ontology (GenEpiO) covers vocabulary necessary to identify, document and research foodborne pathogens and associated outbreaks. examples: - description: Population category defined using ancestry informative markers (AIMs) based on genetic/genomic data url: https://www.ebi.ac.uk/ols/ontologies/genepio/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FHANCESTRO_0004&viewMode=All&siblings=false user: https://genepio.org/ - description: FoodOn (http://foodon.org) is a consortium-driven project to build a comprehensive and easily accessible global farm-to-fork ontology about food, that accurately and consistently describes foods commonly known in cultures from around the world. examples: - description: Population category defined using ancestry informative markers (AIMs) based on genetic/genomic data url: https://www.ebi.ac.uk/ols/ontologies/foodon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FHANCESTRO_0004&viewMode=All&siblings=false user: http://foodon.org - activity_status: active contact: email: diapriid@gmail.com github: mjy label: Matt Yoder orcid: 0000-0002-5640-5491 description: A structured controlled vocabulary of the anatomy of the Hymenoptera (bees, wasps, and ants) domain: anatomy and development homepage: http://hymao.org id: hao layout: ontology_detail license: label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png url: https://creativecommons.org/publicdomain/zero/1.0/ ontology_purl: http://purl.obolibrary.org/obo/hao.owl preferredPrefix: HAO products: - id: hao.owl ontology_purl: http://purl.obolibrary.org/obo/hao.owl - id: hao.obo ontology_purl: http://purl.obolibrary.org/obo/hao.obo - id: hao/depictions.owl ontology_purl: http://purl.obolibrary.org/obo/hao/depictions.owl publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/21209921 title: A gross anatomy ontology for hymenoptera repository: https://github.com/hymao/hao taxon: id: NCBITaxon:7399 label: Hymenoptera title: Hymenoptera Anatomy Ontology tracker: https://github.com/hymao/hao/issues - activity_status: active contact: email: bgee@sib.swiss github: fbastian label: Frederic Bastian orcid: 0000-0002-9415-5104 description: This ontology represents concepts related to homology, as well as other concepts used to describe similarity and non-homology. domain: anatomy and development homepage: https://github.com/BgeeDB/homology-ontology id: hom layout: ontology_detail license: label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png url: https://creativecommons.org/publicdomain/zero/1.0/ ontology_purl: http://purl.obolibrary.org/obo/hom.owl preferredPrefix: HOM products: - id: hom.owl ontology_purl: http://purl.obolibrary.org/obo/hom.owl publications: - id: https://doi.org/10.1016/j.tig.2009.12.012 title: An ontology to clarify homology-related concepts repository: https://github.com/BgeeDB/homology-ontology title: Homology Ontology tracker: https://github.com/BgeeDB/homology-ontology/issues - activity_status: active contact: email: frederic.bastian@unil.ch github: fbastian label: Frédéric Bastian orcid: 0000-0002-9415-5104 description: Life cycle stages for Human domain: anatomy and development homepage: https://github.com/obophenotype/developmental-stage-ontologies/wiki/HsapDv id: hsapdv layout: ontology_detail license: label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/3.0/ ontology_purl: http://purl.obolibrary.org/obo/hsapdv.owl page: https://github.com/obophenotype/developmental-stage-ontologies preferredPrefix: HsapDv products: - id: hsapdv.owl ontology_purl: http://purl.obolibrary.org/obo/hsapdv.owl - id: hsapdv.obo ontology_purl: http://purl.obolibrary.org/obo/hsapdv.obo repository: https://github.com/obophenotype/developmental-stage-ontologies title: Human Developmental Stages tracker: https://github.com/obophenotype/developmental-stage-ontologies/issues - activity_status: active contact: email: fernanda.dorea@sva.se github: nandadorea label: Fernanda Dorea orcid: 0000-0001-8638-8525 dependencies: - id: bfo - id: ncbitaxon - id: obi - id: ro - id: uberon description: The health Surveillance Ontology (HSO) focuses on "surveillance system level data", that is, data outputs from surveillance activities, such as number of samples collected, cases observed, etc. It aims to support One-Health surveillance, covering animal health, public health and food safety surveillance. domain: health homepage: https://w3id.org/hso id: hso layout: ontology_detail license: label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/3.0/ ontology_purl: http://purl.obolibrary.org/obo/hso.owl page: https://github.com/SVA-SE/HSO preferredPrefix: HSO products: - homepage: https://w3id.org/hso id: hso.owl ontology_purl: http://purl.obolibrary.org/obo/hso.owl repository: https://github.com/SVA-SE/HSO title: Health Surveillance Ontology tracker: https://github.com/SVA-SE/HSO/issues/ - activity_status: active contact: email: aellenhicks@gmail.com github: aellenhicks label: Amanda Hicks orcid: 0000-0002-1795-5570 description: An ontology for representing clinical data about hypertension, intended to support classification of patients according to various diagnostic guidelines domain: health homepage: https://github.com/aellenhicks/htn_owl id: htn layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/4.0/ ontology_purl: http://purl.obolibrary.org/obo/htn.owl preferredPrefix: HTN products: - id: htn.owl ontology_purl: http://purl.obolibrary.org/obo/htn.owl title: HTN repository: https://github.com/aellenhicks/htn_owl title: Hypertension Ontology tracker: https://github.com/aellenhicks/htn_owl/issues - activity_status: active contact: email: zhengj2007@gmail.com github: zhengj2007 label: Jie Zheng orcid: 0000-0002-2999-0103 depicted_by: https://avatars0.githubusercontent.com/u/13591168?v=3&s=200 description: An ontology of information entities. domain: information homepage: https://github.com/information-artifact-ontology/IAO/ id: iao layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/4.0/ ontology_purl: http://purl.obolibrary.org/obo/iao.owl preferredPrefix: IAO products: - id: iao.owl ontology_purl: http://purl.obolibrary.org/obo/iao.owl - id: iao/ontology-metadata.owl ontology_purl: http://purl.obolibrary.org/obo/iao/ontology-metadata.owl page: https://github.com/information-artifact-ontology/IAO/wiki/OntologyMetadata title: IAO ontology metadata - id: iao/dev/iao.owl ontology_purl: http://purl.obolibrary.org/obo/iao/dev/iao.owl title: IAO dev - contact: email: mbrochhausen@gmail.com label: Mathias Brochhausen description: An ontology based on a theory of document acts describing what people can do with documents id: iao/d-acts.owl ontology_purl: http://purl.obolibrary.org/obo/iao/d-acts.owl title: ontology of document acts repository: https://github.com/information-artifact-ontology/IAO title: Information Artifact Ontology tracker: https://github.com/information-artifact-ontology/IAO/issues usages: - description: IAO is used widely by multiple OBO ontologies for information representation. type: owl_import user: http://obofoundry.org - activity_status: active contact: email: liumeng94@sjtu.edu.cn github: Lemon-Liu label: Meng LIU orcid: 0000-0003-3781-6962 description: ICEO is an integrated biological ontology for the description of bacterial integrative and conjugative elements (ICEs). domain: microbiology homepage: https://github.com/ontoice/ICEO id: iceo layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/4.0/ ontology_purl: http://purl.obolibrary.org/obo/iceo.owl preferredPrefix: ICEO products: - id: iceo.owl ontology_purl: http://purl.obolibrary.org/obo/iceo.owl publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/35058462 title: ICEO, a biological ontology for representing and analyzing bacterial integrative and conjugative elements repository: https://github.com/ontoice/ICEO title: Integrative and Conjugative Element Ontology tracker: https://github.com/ontoice/ICEO/issues - activity_status: active contact: email: yongqunh@med.umich.edu github: yongqunh label: Yongqun Oliver He orcid: 0000-0001-9189-9661 description: An ontology of clinical informed consents domain: investigations homepage: https://github.com/ICO-ontology/ICO id: ico layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/4.0/ ontology_purl: http://purl.obolibrary.org/obo/ico.owl preferredPrefix: ICO products: - id: ico.owl ontology_purl: http://purl.obolibrary.org/obo/ico.owl repository: https://github.com/ICO-ontology/ICO tags: - informed consent title: Informed Consent Ontology tracker: https://github.com/ICO-ontology/ICO/issues usages: - description: tracking informed consent in the kidney precision medicine project that has over 20 institutes involved. user: http://kpmp.org - activity_status: active contact: email: Lindsay.Cowell@utsouthwestern.edu github: lgcowell label: Lindsay Cowell orcid: 0000-0003-1617-8244 description: A set of interoperable ontologies that will together provide coverage of the infectious disease domain. IDO core is the upper-level ontology that hosts terms of general relevance across the domain, while extension ontologies host terms to specific to a particular part of the domain. domain: health homepage: http://www.bioontology.org/wiki/index.php/Infectious_Disease_Ontology id: ido layout: ontology_detail license: label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: https://creativecommons.org/licenses/by/3.0/ ontology_purl: http://purl.obolibrary.org/obo/ido.owl preferredPrefix: IDO products: - id: ido.owl ontology_purl: http://purl.obolibrary.org/obo/ido.owl publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/34275487 title: The Infectious Disease Ontology in the age of COVID-19 repository: https://github.com/infectious-disease-ontology/infectious-disease-ontology taxon: id: NCBITaxon:9606 label: Homo sapiens title: Infectious Disease Ontology tracker: https://github.com/infectious-disease-ontology/infectious-disease-ontology/issues - activity_status: active contact: email: yongqunh@med.umich.edu github: yongqunh label: Yongqun Oliver He orcid: 0000-0001-9189-9661 description: An ontology of interactions and interaction networks domain: biological systems homepage: https://github.com/INO-ontology/ino id: ino layout: ontology_detail license: label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/3.0/ ontology_purl: http://purl.obolibrary.org/obo/ino.owl preferredPrefix: INO products: - id: ino.owl ontology_purl: http://purl.obolibrary.org/obo/ino.owl publications: - id: https://doi.org/10.1186/2041-1480-6-2 title: Development and application of an Interaction Network Ontology for literature mining of vaccine-associated gene-gene interactions repository: https://github.com/INO-ontology/ino title: Interaction Network Ontology tracker: https://github.com/INO-ontology/ino/issues - activity_status: active contact: email: paul.fabry@usherbrooke.ca github: pfabry label: Paul Fabry orcid: 0000-0002-3336-2476 dependencies: - id: iao - id: obi - id: ogms - id: omiabis - id: omrse - id: opmi description: LABO is an ontology of informational entities formalizing clinical laboratory tests prescriptions and reporting documents. domain: information homepage: https://github.com/OpenLHS/LABO id: labo layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: https://creativecommons.org/licenses/by/4.0/ ontology_purl: http://purl.obolibrary.org/obo/labo.owl preferredPrefix: LABO products: - id: labo.owl ontology_purl: http://purl.obolibrary.org/obo/labo.owl publications: - id: https://doi.org/10.5281/zenodo.6522019 title: 'LABO: An Ontology for Laboratory Test Prescription and Reporting' repository: https://github.com/OpenLHS/LABO tags: - clinical documentation taxon: id: NCBITaxon:9606 label: Homo sapiens title: clinical LABoratory Ontology tracker: https://github.com/OpenLHS/LABO/issues usages: - description: LABO is a part of a core ontological model of medical knowledge in the PARS3 data platform. type: database architecture user: https://griis.ca/ - activity_status: active contact: email: lagonzalezmo@unal.edu.co github: luis-gonzalez-m label: Luis A. Gonzalez-Montana orcid: 0000-0002-9136-9932 dependencies: - id: aism - id: bfo - id: bspo - id: caro - id: pato - id: ro - id: uberon description: The Lepidoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of moths and butterflies in biodiversity research. LEPAO is developed in part by BIOfid (The Specialised Information Service Biodiversity Research). domain: anatomy and development homepage: https://github.com/insect-morphology/lepao id: lepao layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: https://creativecommons.org/licenses/by/4.0/ ontology_purl: http://purl.obolibrary.org/obo/lepao.owl preferredPrefix: LEPAO products: - id: lepao.owl ontology_purl: http://purl.obolibrary.org/obo/lepao.owl - id: lepao.obo ontology_purl: http://purl.obolibrary.org/obo/lepao.obo repository: https://github.com/insect-morphology/lepao tags: - insect anatomy title: Lepidoptera Anatomy Ontology tracker: https://github.com/insect-morphology/lepao/issues - activity_status: active contact: email: Terry.Hayamizu@jax.org github: tfhayamizu label: Terry Hayamizu orcid: 0000-0002-0956-8634 description: A structured controlled vocabulary of the adult anatomy of the mouse (Mus). domain: anatomy and development homepage: https://github.com/obophenotype/adult-mouse-anatomy-ontology id: ma layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: https://creativecommons.org/licenses/by/4.0/ ontology_purl: http://purl.obolibrary.org/obo/ma.owl page: http://www.informatics.jax.org/searches/AMA_form.shtml preferredPrefix: MA products: - id: ma.owl ontology_purl: http://purl.obolibrary.org/obo/ma.owl - id: ma.obo ontology_purl: http://purl.obolibrary.org/obo/ma.obo repository: https://github.com/obophenotype/adult-mouse-anatomy-ontology taxon: id: NCBITaxon:10088 label: Mus title: Mouse adult gross anatomy tracker: https://github.com/obophenotype/adult-mouse-anatomy-ontology/issues usages: - description: GXD seeAlso: https://doi.org/10.25504/FAIRsharing.q9neh8 user: http://www.informatics.jax.org/expression.shtml - activity_status: active contact: email: Leigh.Carmody@jax.org github: LCCarmody label: Leigh Carmody orcid: 0000-0001-7941-2961 dependencies: - id: chebi - id: foodon - id: go - id: hp - id: iao - id: nbo - id: obi - id: ro - id: uberon depicted_by: https://raw.githubusercontent.com/jmcmurry/closed-illustrations/master/logos/maxo-logos/maxo_logo_black-banner.png description: The Medical Action Ontology (MAxO) provides a broad view of medical actions and includes terms for medical procedures, interventions, therapies, treatments, and recommendations. domain: health homepage: https://github.com/monarch-initiative/MAxO id: maxo layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/4.0/ ontology_purl: http://purl.obolibrary.org/obo/maxo.owl preferredPrefix: MAXO products: - id: maxo.owl name: Medical Action Ontology main release in OWL format ontology_purl: http://purl.obolibrary.org/obo/maxo.owl - id: maxo.obo name: Medical Action Ontology additional release in OBO format ontology_purl: http://purl.obolibrary.org/obo/maxo.obo - id: maxo.json name: Medical Action Ontology additional release in OBOJSon format ontology_purl: http://purl.obolibrary.org/obo/maxo.json - id: maxo/maxo-base.owl name: Medical Action Ontology main release in OWL format ontology_purl: http://purl.obolibrary.org/obo/maxo/maxo-base.owl - id: maxo/maxo-base.obo name: Medical Action Ontology additional release in OBO format ontology_purl: http://purl.obolibrary.org/obo/maxo/maxo-base.obo - id: maxo/maxo-base.json name: Medical Action Ontology additional release in OBOJSon format ontology_purl: http://purl.obolibrary.org/obo/maxo/maxo-base.json repository: https://github.com/monarch-initiative/MAxO tags: - medical title: Medical Action Ontology tracker: https://github.com/monarch-initiative/MAxO/issues usages: - description: MAxO is used to capture disease-treatment relations from the scientific literature. examples: - description: Bardet-biedl Syndrome 1 (MONDO:0008854) is treated through dietary interventions (MAXO:0000088) according to Forsyth et al 2003 (PMID:20301537) url: https://hpo.jax.org/data/annotations type: annotation user: https://hpo.jax.org/ - activity_status: active contact: email: citlalli.mejiaalmonte@gmail.com github: citmejia label: Citlalli Mejía-Almonte orcid: 0000-0002-0142-5591 dependencies: - id: bfo - id: chebi - id: cl - id: clo - id: micro - id: ncbitaxon - id: ncit - id: obi - id: omit - id: omp - id: pato - id: peco - id: uberon - id: zeco description: Microbial Conditions Ontology is an ontology... domain: investigations homepage: https://github.com/microbial-conditions-ontology/microbial-conditions-ontology id: mco layout: ontology_detail license: label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/3.0/ ontology_purl: http://purl.obolibrary.org/obo/mco.owl preferredPrefix: MCO products: - id: mco.owl ontology_purl: http://purl.obolibrary.org/obo/mco.owl - id: mco.obo ontology_purl: http://purl.obolibrary.org/obo/mco.obo repository: https://github.com/microbial-conditions-ontology/microbial-conditions-ontology tags: - experimental conditions title: Microbial Conditions Ontology tracker: https://github.com/microbial-conditions-ontology/microbial-conditions-ontology/issues - activity_status: active contact: email: muamith@utmb.edu github: ProfTuan label: Tuan Amith orcid: 0000-0003-4333-1857 dependencies: - id: iao - id: swo description: An ontology representing the structure of model card reports - reports that describe basic characteristics of machine learning models for the public and consumers. domain: information technology homepage: https://github.com/UTHealth-Ontology/MCRO id: mcro layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: https://creativecommons.org/licenses/by/4.0/ ontology_purl: http://purl.obolibrary.org/obo/mcro.owl preferredPrefix: MCRO products: - id: mcro.owl ontology_purl: http://purl.obolibrary.org/obo/mcro.owl publications: - id: https://doi.org/10.1186/s12859-022-04797-6 title: Toward a standard formal semantic representation of the model card report repository: https://github.com/UTHealth-Ontology/MCRO title: Model Card Report Ontology tracker: https://github.com/UTHealth-Ontology/MCRO/issues usages: - description: MCRO used for publishing model cards examples: - description: Demonstration of Java-based library utilizing MCRO to output RDF-based model card reports url: https://github.com/UTHealth-Ontology/MCRO-Software publications: - id: https://doi.org/10.1145/3543873.3587601 title: Application of an ontology for model cards to generate computable artifacts for linking machine learning information from biomedical research user: https://github.com/UTHealth-Ontology/MCRO-Software - activity_status: active contact: email: janna.hastings@gmail.com github: jannahastings label: Janna Hastings orcid: 0000-0002-3469-4923 description: The Mental Functioning Ontology is an overarching ontology for all aspects of mental functioning. domain: health homepage: https://github.com/jannahastings/mental-functioning-ontology id: mf layout: ontology_detail license: label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/3.0/ ontology_purl: http://purl.obolibrary.org/obo/mf.owl preferredPrefix: MF products: - id: mf.owl ontology_purl: http://purl.obolibrary.org/obo/mf.owl repository: https://github.com/jannahastings/mental-functioning-ontology title: Mental Functioning Ontology tracker: https://github.com/jannahastings/mental-functioning-ontology/issues - activity_status: active contact: email: janna.hastings@gmail.com github: jannahastings label: Janna Hastings orcid: 0000-0002-3469-4923 description: An ontology of affective phenomena such as emotions, moods, appraisals and subjective feelings. domain: health homepage: https://github.com/jannahastings/emotion-ontology id: mfoem layout: ontology_detail license: label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/3.0/ ontology_purl: http://purl.obolibrary.org/obo/mfoem.owl preferredPrefix: MFOEM products: - id: mfoem.owl ontology_purl: http://purl.obolibrary.org/obo/mfoem.owl repository: https://github.com/jannahastings/emotion-ontology title: Emotion Ontology tracker: https://github.com/jannahastings/emotion-ontology/issues - activity_status: active contact: email: janna.hastings@gmail.com github: jannahastings label: Janna Hastings orcid: 0000-0002-3469-4923 description: An ontology to describe and classify mental diseases such as schizophrenia, annotated with DSM-IV and ICD codes where applicable domain: health homepage: https://github.com/jannahastings/mental-functioning-ontology id: mfomd layout: ontology_detail license: label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/3.0/ ontology_purl: http://purl.obolibrary.org/obo/mfomd.owl preferredPrefix: MFOMD products: - id: mfomd.owl ontology_purl: http://purl.obolibrary.org/obo/mfomd.owl repository: https://github.com/jannahastings/mental-functioning-ontology title: Mental Disease Ontology tracker: https://github.com/jannahastings/mental-functioning-ontology/issues - activity_status: active contact: email: luana.licata@gmail.com github: luanalicata label: Luana Licata orcid: 0000-0001-5084-9000 description: A structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions. domain: investigations homepage: https://github.com/HUPO-PSI/psi-mi-CV id: mi layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: https://creativecommons.org/licenses/by/4.0/ ontology_purl: http://purl.obolibrary.org/obo/mi.owl page: https://github.com/HUPO-PSI/psi-mi-CV preferredPrefix: MI products: - id: mi.owl ontology_purl: http://purl.obolibrary.org/obo/mi.owl - id: mi.obo ontology_purl: http://purl.obolibrary.org/obo/mi.obo repository: https://github.com/HUPO-PSI/psi-mi-CV title: Molecular Interactions Controlled Vocabulary tracker: https://github.com/HUPO-PSI/psi-mi-CV/issues - activity_status: active contact: email: hilmar.lapp@duke.edu github: hlapp label: Hilmar Lapp orcid: 0000-0001-9107-0714 description: An application ontology to formalize annotation of phylogenetic data. domain: information homepage: http://www.evoio.org/wiki/MIAPA id: miapa layout: ontology_detail license: label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png url: http://creativecommons.org/publicdomain/zero/1.0/ mailing_list: http://groups.google.com/group/miapa-discuss ontology_purl: http://purl.obolibrary.org/obo/miapa.owl preferredPrefix: MIAPA products: - id: miapa.owl ontology_purl: http://purl.obolibrary.org/obo/miapa.owl publications: - id: https://doi.org/10.1089/omi.2006.10.231 title: 'Taking the First Steps towards a Standard for Reporting on Phylogenies: Minimum Information about a Phylogenetic Analysis (MIAPA)' repository: https://github.com/evoinfo/miapa title: MIAPA Ontology tracker: https://github.com/evoinfo/miapa/issues - activity_status: active browsers: - label: RGD title: RGD Ontology Browser url: http://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=MMO:0000000 contact: email: jrsmith@mcw.edu github: jrsjrs label: Jennifer Smith orcid: 0000-0002-6443-9376 description: 'A representation of the variety of methods used to make clinical and phenotype measurements. ' domain: health homepage: https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=MMO:0000000 id: mmo layout: ontology_detail license: label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png url: https://creativecommons.org/publicdomain/zero/1.0/ ontology_purl: http://purl.obolibrary.org/obo/mmo.owl page: https://download.rgd.mcw.edu/ontology/measurement_method/ preferredPrefix: MMO products: - id: mmo.owl ontology_purl: http://purl.obolibrary.org/obo/mmo.owl - id: mmo.obo ontology_purl: http://purl.obolibrary.org/obo/mmo.obo publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/22654893 title: Three ontologies to define phenotype measurement data. - id: https://www.ncbi.nlm.nih.gov/pubmed/24103152 title: 'The clinical measurement, measurement method and experimental condition ontologies: expansion, improvements and new applications.' repository: https://github.com/rat-genome-database/MMO-Measurement-Method-Ontology tags: - clinical title: Measurement method ontology tracker: https://github.com/rat-genome-database/MMO-Measurement-Method-Ontology/issues - activity_status: active contact: email: frederic.bastian@unil.ch github: fbastian label: Frédéric Bastian orcid: 0000-0002-9415-5104 description: Life cycle stages for Mus Musculus domain: anatomy and development homepage: https://github.com/obophenotype/developmental-stage-ontologies/wiki/MmusDv id: mmusdv layout: ontology_detail license: label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/3.0/ ontology_purl: http://purl.obolibrary.org/obo/mmusdv.owl page: https://github.com/obophenotype/developmental-stage-ontologies preferredPrefix: MmusDv products: - id: mmusdv.owl ontology_purl: http://purl.obolibrary.org/obo/mmusdv.owl - id: mmusdv.obo ontology_purl: http://purl.obolibrary.org/obo/mmusdv.obo repository: https://github.com/obophenotype/developmental-stage-ontologies title: Mouse Developmental Stages tracker: https://github.com/obophenotype/developmental-stage-ontologies/issues - activity_status: active contact: email: pierre-alain.binz@chuv.ch github: pabinz label: Pierre-Alain Binz orcid: 0000-0002-0045-7698 description: PSI-MOD is an ontology consisting of terms that describe protein chemical modifications domain: chemistry and biochemistry homepage: http://www.psidev.info/MOD id: mod layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: https://creativecommons.org/licenses/by/4.0/ ontology_purl: http://purl.obolibrary.org/obo/mod.owl preferredPrefix: MOD products: - description: PSI-MOD Ontology, OWL format id: mod.owl ontology_purl: http://purl.obolibrary.org/obo/mod.owl title: PSI-MOD.owl - description: PSI-MOD Ontology, OBO format id: mod.obo ontology_purl: http://purl.obolibrary.org/obo/mod.obo title: PSI-MOD.obo publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/18688235 title: The PSI-MOD community standard for representation of protein modification data repository: https://github.com/HUPO-PSI/psi-mod-CV tags: - proteins title: Protein modification tracker: https://github.com/HUPO-PSI/psi-mod-CV/issues - activity_status: active browsers: - label: Monarch title: Monarch Initiative Disease Browser url: https://monarchinitiative.org/disease/MONDO:0019609 contact: email: Sabrina@tislab.org github: sabrinatoro label: Sabrina Toro orcid: 0000-0002-4142-7153 depicted_by: https://raw.githubusercontent.com/monarch-initiative/mondo/master/docs/images/mondo_logo_black-stacked-small.png description: A global community effort to harmonize multiple disease resources to yield a coherent merged ontology. domain: health homepage: https://monarch-initiative.github.io/mondo id: mondo layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/4.0/ mailing_list: https://groups.google.com/group/mondo-users ontology_purl: http://purl.obolibrary.org/obo/mondo.owl preferredPrefix: MONDO products: - description: Complete ontology with merged imports. format: owl-rdf/xml id: mondo.owl is_canonical: true ontology_purl: http://purl.obolibrary.org/obo/mondo.owl title: Mondo OWL edition - derived_from: mondo.owl description: OBO serialization of mondo.owl. format: obo id: mondo.obo ontology_purl: http://purl.obolibrary.org/obo/mondo.obo title: Mondo OBO Format edition - derived_from: mondo.owl description: Obographs serialization of mondo.owl. format: obo id: mondo.json ontology_purl: http://purl.obolibrary.org/obo/mondo.json title: Mondo JSON edition - description: The main ontology plus axioms connecting to select external ontologies, excluding the external ontologies themselves format: owl id: mondo/mondo-base.owl ontology_purl: http://purl.obolibrary.org/obo/mondo/mondo-base.owl title: Mondo Base Release - description: The main ontology classes and their hierarchies, without references to external terms. format: owl id: mondo/mondo-simple.owl ontology_purl: http://purl.obolibrary.org/obo/mondo/mondo-simple.owl title: Mondo Simple Release publications: - id: https://doi.org/10.1093/genetics/iyaf215 title: 'Mondo: Integrating Disease Terminology Across Communities' - id: https://www.medrxiv.org/content/10.1101/2022.04.13.22273750 title: 'Mondo: Unifying diseases for the world, by the world' repository: https://github.com/monarch-initiative/mondo tags: - disease taxon: id: NCBITaxon:33208 label: Metazoa title: Mondo Disease Ontology tracker: https://github.com/monarch-initiative/mondo/issues usages: - description: Mondo is used by the Monarch Initiative for disease annotations. examples: - description: 'Parkinsonism: Characteristic neurologic anomaly resulting form degeneration of dopamine-generating cells in the substantia nigra, a region of the midbrain, characterized clinically by shaking, rigidity, slowness of movement and difficulty with walking and gait.' url: https://monarchinitiative.org/phenotype/HP:0001300#disease publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/27899636 title: 'The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species ' type: annotation user: https://monarchinitiative.org/ - description: Mondo is used by the ClinGen for disease curations. examples: - description: FBN1 is an autosomal dominant mutation in Marfan syndrome. url: https://search.clinicalgenome.org/kb/conditions/MONDO:0007947 type: annotation user: https://www.clinicalgenome.org/ - description: Mondo is used by the Kids First Data Resource Portal for disease annotations. Note, a login is needed to access the portal and view the Mondo-curated data. type: annotation user: https://portal.kidsfirstdrc.org/ - description: Mondo is used by the Ancestory for some disease curations. examples: - description: Some term names in ancestory.com are curated with Mondo, for ease of use. url: https://support.ancestry.com/s/article/Disease-Condition-Catalog-Powered-by-MONDO type: annotation user: https://www.ancestry.com/ - description: Mondo is used by the Human Cell Atlas for some disease annotations. examples: - description: Disease status specimen is normal, type 2 diabetes mellitus. url: https://data.humancellatlas.org/explore/projects?filter=%5B%7B%22facetName%22:%22organ%22,%22terms%22:%5B%22kidney%22%5D%7D,%7B%22facetName%22:%22donorDisease%22,%22terms%22:%5B%22acoustic%20neuroma%22,%22acute%20kidney%20tubular%20necrosis%22%5D%7D%5D&catalog=dcp1 type: annotation user: https://www.humancellatlas.org/ - activity_status: active contact: email: batchelorc@rsc.org github: batchelorc label: Colin Batchelor orcid: 0000-0001-5985-7429 description: Processes at the molecular level domain: chemistry and biochemistry homepage: https://github.com/rsc-ontologies/rxno id: mop layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: https://creativecommons.org/licenses/by/4.0/ mailing_list: chemistry-ontologies@googlegroups.com ontology_purl: http://purl.obolibrary.org/obo/mop.owl preferredPrefix: MOP products: - id: mop.owl ontology_purl: http://purl.obolibrary.org/obo/mop.owl title: Molecular Process Ontology repository: https://github.com/rsc-ontologies/rxno title: Molecular Process Ontology tracker: https://github.com/rsc-ontologies/rxno/issues - activity_status: active browsers: - label: MGI title: MGI MP Browser url: https://www.informatics.jax.org/vocab/mp_ontology/ - label: RGD title: RGD MP Browser url: https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=MP:0000001 - label: Monarch title: Monarch Phenotype Page url: http://monarchinitiative.org/phenotype/MP:0000001 contact: email: pheno@jax.org github: sbello label: Sue Bello orcid: 0000-0003-4606-0597 depicted_by: https://raw.githubusercontent.com/mgijax/mammalian-phenotype-ontology/main/logo/2024_MP_logo_RGB_ICON_color.png description: Standard terms for annotating mammalian phenotypic data. domain: phenotype homepage: https://www.informatics.jax.org/vocab/mp_ontology/ id: mp layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/4.0/ mailing_list: https://groups.google.com/forum/#!forum/phenotype-ontologies-editors ontology_purl: http://purl.obolibrary.org/obo/mp.owl page: https://github.com/mgijax/mammalian-phenotype-ontology preferredPrefix: MP products: - description: The main ontology in OWL. Contains all MP terms and links to other OBO ontologies. id: mp.owl ontology_purl: http://purl.obolibrary.org/obo/mp.owl page: https://github.com/mgijax/mammalian-phenotype-ontology/releases/tag/current title: MP (OWL edition) - description: A direct translation of the MP (OWL edition) into OBO format. id: mp.obo ontology_purl: http://purl.obolibrary.org/obo/mp.obo page: https://github.com/mgijax/mammalian-phenotype-ontology/releases/tag/current title: MP (OBO edition) - description: For a description of the format see https://github.com/geneontology/obographs. id: mp.json ontology_purl: http://purl.obolibrary.org/obo/mp.json page: https://github.com/mgijax/mammalian-phenotype-ontology/releases/tag/current title: MP (obographs JSON edition) - description: The main ontology plus axioms connecting to select external ontologies, excluding axioms from the the external ontologies themselves. id: mp/mp-base.owl ontology_purl: http://purl.obolibrary.org/obo/mp/mp-base.owl page: https://github.com/mgijax/mammalian-phenotype-ontology/releases/tag/current title: MP Base Module publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/40963406 title: Expanding and refining the Mammalian Phenotype Ontology to enhance disease model discovery - id: https://www.ncbi.nlm.nih.gov/pubmed/22961259 title: The Mammalian Phenotype Ontology as a unifying standard for experimental and high-throughput phenotyping data - id: https://www.ncbi.nlm.nih.gov/pubmed/25825651 title: Expanding the mammalian phenotype ontology to support automated exchange of high throughput mouse phenotyping data generated by large-scale mouse knockout screens repository: https://github.com/mgijax/mammalian-phenotype-ontology taxon: id: NCBITaxon:40674 label: Mammalia title: Mammalian Phenotype Ontology tracker: https://github.com/mgijax/mammalian-phenotype-ontology/issues usages: - description: MGI annotates phenotypes of mouse models using the MP examples: - description: Term browser page for embryonic lethality showing information about the term including definition, placement in the MP hierarchy, and link to mouse models annotated to this term or any of its decendants url: http://www.informatics.jax.org/vocab/mp_ontology/MP:0008762 user: http://www.informatics.jax.org/vocab/mp_ontology - description: RGD annotates phenotypes associated with rat genes and alleles using the MP examples: - description: Term browser page for embryonic lethality showing information about the term including definition, placement in the MP hierarchy, and link to annotations to this term or any of its decendants url: https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=MP:0008762 user: https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=MP:0000001 - description: IMPC annotates abnormal phenotypes of mice carrying null alleles found following the application of a standardised set of physiological tests examples: - description: All IMPC alleles that have been annotated to the MP term 'decreased memory-marker CD4-positive NK T cell number'. url: https://www.mousephenotype.org/data/phenotypes/MP:0013522 user: https://www.mousephenotype.org/ - activity_status: active contact: email: pns12@hermes.cam.ac.uk github: PaulNSchofield label: Paul Schofield orcid: 0000-0002-5111-7263 description: A structured controlled vocabulary of mutant and transgenic mouse pathology phenotypes domain: health homepage: http://www.pathbase.net id: mpath layout: ontology_detail license: label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/3.0/ ontology_purl: http://purl.obolibrary.org/obo/mpath.owl preferredPrefix: MPATH products: - id: mpath.owl ontology_purl: http://purl.obolibrary.org/obo/mpath.owl repository: https://github.com/PaulNSchofield/mpath taxon: id: NCBITaxon:10088 label: Mus title: Mouse pathology ontology tracker: https://github.com/PaulNSchofield/mpath/issues - activity_status: active contact: email: mbrochhausen@uams.edu github: mbrochhausen label: Mathias Brochhausen orcid: 0000-0003-1834-3856 description: An ontology of minimum information regarding potential drug-drug interaction information. domain: health homepage: https://github.com/MPIO-Developers/MPIO id: mpio layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/4.0/ ontology_purl: http://purl.obolibrary.org/obo/mpio.owl preferredPrefix: MPIO products: - id: mpio.owl ontology_purl: http://purl.obolibrary.org/obo/mpio.owl repository: https://github.com/MPIO-Developers/MPIO title: Minimum PDDI Information Ontology tracker: https://github.com/MPIO-Developers/MPIO/issues - activity_status: active contact: email: bpeters@lji.org github: bpeters42 label: Bjoern Peters orcid: 0000-0002-8457-6693 description: An ontology for Major Histocompatibility Complex (MHC) restriction in experiments domain: chemistry and biochemistry homepage: https://github.com/IEDB/MRO id: mro layout: ontology_detail license: label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: https://creativecommons.org/licenses/by/3.0/ ontology_purl: http://purl.obolibrary.org/obo/mro.owl preferredPrefix: MRO products: - id: mro.owl ontology_purl: http://purl.obolibrary.org/obo/mro.owl repository: https://github.com/IEDB/MRO tags: - Major Histocompatibility Complex title: MHC Restriction Ontology tracker: https://github.com/IEDB/MRO/issues usages: - description: MRO is used by the The Immune Epitope Database (IEDB) annotations examples: - description: 'Epitope ID: 59611 based on reference 1003499' url: https://www.iedb.org/assay/1357035 publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/26759709 title: An ontology for major histocompatibility restriction type: annotation user: https://www.iedb.org/ - activity_status: active contact: email: joshua.adam.klein@gmail.com github: mobiusklein label: Joshua Klein orcid: 0000-0003-1279-6838 dependencies: - id: pato - id: uo description: A structured controlled vocabulary for the annotation of experiments concerned with proteomics mass spectrometry. domain: investigations homepage: http://www.psidev.info/groups/controlled-vocabularies id: ms layout: ontology_detail license: label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: https://creativecommons.org/licenses/by/3.0/ mailing_list: psidev-ms-vocab@lists.sourceforge.net ontology_purl: http://purl.obolibrary.org/obo/ms.owl page: http://www.psidev.info/groups/controlled-vocabularies preferredPrefix: MS products: - id: ms.obo ontology_purl: http://purl.obolibrary.org/obo/ms.obo - id: ms.owl ontology_purl: http://purl.obolibrary.org/obo/ms.owl publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/23482073 title: The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary. repository: https://github.com/HUPO-PSI/psi-ms-CV tags: - MS experiments title: Mass spectrometry ontology tracker: https://github.com/HUPO-PSI/psi-ms-CV/issues - activity_status: active browsers: - label: BioPortal title: BioPortal Ontology Browser url: https://bioportal.bioontology.org/ontologies/NBO contact: email: g.gkoutos@bham.ac.uk github: gkoutos label: George Gkoutos orcid: 0000-0002-2061-091X description: An ontology of human and animal behaviours and behavioural phenotypes domain: biological systems homepage: https://github.com/obo-behavior/behavior-ontology/ id: nbo layout: ontology_detail license: label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/3.0/ ontology_purl: http://purl.obolibrary.org/obo/nbo.owl preferredPrefix: NBO products: - id: nbo.owl ontology_purl: http://purl.obolibrary.org/obo/nbo.owl publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/24177753 title: Analyzing gene expression data in mice with the Neuro Behavior Ontology repository: https://github.com/obo-behavior/behavior-ontology tags: - behavior title: Neuro Behavior Ontology tracker: https://github.com/obo-behavior/behavior-ontology/issues - activity_status: active browsers: - label: NCBI title: NCBI Taxonomy Browser url: http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi contact: email: frederic.bastian@unil.ch github: fbastian label: Frederic Bastian orcid: 0000-0002-9415-5104 description: An ontology representation of the NCBI organismal taxonomy domain: organisms homepage: https://github.com/obophenotype/ncbitaxon id: ncbitaxon layout: ontology_detail license: label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png url: https://creativecommons.org/publicdomain/zero/1.0/ ontology_purl: http://purl.obolibrary.org/obo/ncbitaxon.owl page: http://www.ncbi.nlm.nih.gov/taxonomy preferredPrefix: NCBITaxon products: - id: ncbitaxon.owl ontology_purl: http://purl.obolibrary.org/obo/ncbitaxon.owl title: Main release - id: ncbitaxon.obo ontology_purl: http://purl.obolibrary.org/obo/ncbitaxon.obo title: OBO Format version of Main release - id: ncbitaxon.json ontology_purl: http://purl.obolibrary.org/obo/ncbitaxon.json title: OBOGraphs JSON version of Main release - id: ncbitaxon/subsets/taxslim.owl ontology_purl: http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl page: https://github.com/obophenotype/ncbitaxon/blob/master/subsets/README.md title: taxslim - id: ncbitaxon/subsets/taxslim-disjoint-over-in-taxon.owl ontology_purl: http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim-disjoint-over-in-taxon.owl page: https://github.com/obophenotype/ncbitaxon/blob/master/subsets/README.md title: taxslim disjointness axioms repository: https://github.com/obophenotype/ncbitaxon tags: - taxonomy title: NCBI organismal classification tracker: https://github.com/obophenotype/ncbitaxon/issues usages: - description: The Immune Epitope Database (IEDB) is funded by NIAID that catalogs experimental data on antibody and T cell epitopes studied in humans, non-human primates, and other animal species in the context of infectious disease, allergy, autoimmunity and transplantation. examples: - description: A specific assay curated in the IEDB using the NCBITaxon:520 Bordetella pertussis as the source organism. url: http://www.iedb.org/assay/1505273 user: https://www.iedb.org - activity_status: active contact: email: noreply@example.com github: ghost label: None orcid: 0000-0000-0000-0000 description: NCI Thesaurus (NCIt)is a reference terminology that includes broad coverage of the cancer domain, including cancer related diseases, findings and abnormalities. The NCIt OBO Edition aims to increase integration of the NCIt with OBO Library ontologies. NCIt OBO Edition releases should be considered experimental. domain: health homepage: https://github.com/ncit-obo-org/ncit-obo-edition id: ncit layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: https://creativecommons.org/licenses/by/4.0/ ontology_purl: http://purl.obolibrary.org/obo/ncit.owl preferredPrefix: NCIT products: - description: A direct transformation of the standard NCIt content using OBO-style term and ontology IRIs and annotation properties. id: ncit.owl ontology_purl: http://purl.obolibrary.org/obo/ncit.owl title: NCIt OBO Edition OWL format - id: ncit.obo ontology_purl: http://purl.obolibrary.org/obo/ncit.obo title: NCIt OBO Edition OBO format repository: https://github.com/ncit-obo-org/ncit-obo-edition title: NCI Thesaurus OBO Edition tracker: https://github.com/ncit-obo-org/ncit-obo-edition/issues - activity_status: active contact: email: huang@southalabama.edu github: Huang-OMIT label: Jingshan Huang orcid: 0000-0003-2408-2883 description: An ontology for non-coding RNA, both of biological origin, and engineered. domain: investigations homepage: http://omnisearch.soc.southalabama.edu/w/index.php/Ontology id: ncro layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: https://creativecommons.org/licenses/by/4.0/ mailing_list: ncro-devel@googlegroups.com, ncro-discuss@googlegroups.com ontology_purl: http://purl.obolibrary.org/obo/ncro.owl preferredPrefix: NCRO products: - id: ncro/dev/ncro.owl ontology_purl: http://purl.obolibrary.org/obo/ncro/dev/ncro.owl title: NCRO development version repository: https://github.com/OmniSearch/ncro title: Non-Coding RNA Ontology tracker: https://github.com/OmniSearch/ncro/issues - activity_status: active contact: email: dal.alghamdi92@gmail.com github: dalalghamdi label: Dalia Alghamdi orcid: 0000-0002-2801-0767 description: 'The Next Generation Biobanking Ontology (NGBO) is an open application ontology representing contextual data about omics digital assets in biobank. The ontology focuses on capturing the information about three main activities: wet bench analysis used to generate omics data, bioinformatics analysis used to analyze and interpret data, and data management.' domain: investigations homepage: https://github.com/Dalalghamdi/NGBO id: ngbo issue_requested: 1819 layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: https://creativecommons.org/licenses/by/4.0/ ontology_purl: http://purl.obolibrary.org/obo/ngbo.owl preferredPrefix: NGBO products: - id: ngbo.owl ontology_purl: http://purl.obolibrary.org/obo/ngbo.owl pull_request_added: 2214 repository: https://github.com/Dalalghamdi/NGBO title: Next Generation Biobanking Ontology tracker: https://github.com/Dalalghamdi/NGBO/issues - activity_status: active contact: email: diapriid@gmail.com github: mjy label: Matt Yoder orcid: 0000-0002-5640-5491 description: NOMEN is a nomenclatural ontology for biological names (not concepts). It encodes the goverened rules of nomenclature. domain: information funded_by: - id: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1356381 title: NSF ABI-1356381 homepage: https://github.com/SpeciesFileGroup/nomen id: nomen layout: ontology_detail license: label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png url: https://creativecommons.org/publicdomain/zero/1.0/ mailing_list: https://groups.google.com/forum/#!forum/nomen-discuss ontology_purl: http://purl.obolibrary.org/obo/nomen.owl preferredPrefix: NOMEN products: - description: core ontology id: nomen.owl is_canonical: true ontology_purl: http://purl.obolibrary.org/obo/nomen.owl title: NOMEN type: owl:Ontology repository: https://github.com/SpeciesFileGroup/nomen tags: - biological nomenclature title: NOMEN - A nomenclatural ontology for biological names tracker: https://github.com/SpeciesFileGroup/nomen/issues usages: - description: TaxonWorks is an integrated web-based workbench for taxonomists and biodiversity scientists. seeAlso: https://github.com/SpeciesFileGroup/taxonworks type: application user: https://taxonworks.org - activity_status: active contact: email: yongqunh@med.umich.edu github: yongqunh label: Yongqunh He orcid: 0000-0001-9189-9661 description: A biomedical ontology in the domain of adverse events domain: health homepage: https://github.com/OAE-ontology/OAE/ id: oae layout: ontology_detail license: label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/3.0/ ontology_purl: http://purl.obolibrary.org/obo/oae.owl preferredPrefix: OAE products: - id: oae.owl ontology_purl: http://purl.obolibrary.org/obo/oae.owl repository: https://github.com/OAE-ontology/OAE tags: - adverse events title: Ontology of Adverse Events tracker: https://github.com/OAE-ontology/OAE/issues - activity_status: active contact: email: mjyoder@illinois.edu github: mjy label: Matt Yoder orcid: 0000-0002-5640-5491 description: OArCS is an ontology describing the Arthropod ciruclatory system. domain: anatomy and development homepage: https://github.com/aszool/oarcs id: oarcs layout: ontology_detail license: label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/3.0/ ontology_purl: http://purl.obolibrary.org/obo/oarcs.owl preferredPrefix: OARCS products: - id: oarcs.owl ontology_purl: http://purl.obolibrary.org/obo/oarcs.owl repository: https://github.com/aszool/oarcs title: Ontology of Arthropod Circulatory Systems tracker: https://github.com/aszool/oarcs/issues - activity_status: active contact: email: cjmungall@lbl.gov github: cmungall label: Chris Mungall orcid: 0000-0002-6601-2165 description: A collection of biological attributes (traits) covering all kingdoms of life. domain: phenotype homepage: https://github.com/obophenotype/bio-attribute-ontology id: oba layout: ontology_detail license: label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png url: http://creativecommons.org/publicdomain/zero/1.0/ ontology_purl: http://purl.obolibrary.org/obo/oba.owl page: http://wiki.geneontology.org/index.php/Extensions/x-attribute preferredPrefix: OBA products: - id: oba.owl ontology_purl: http://purl.obolibrary.org/obo/oba.owl - id: oba.obo ontology_purl: http://purl.obolibrary.org/obo/oba.obo - id: oba/subsets/oba-basic.obo ontology_purl: http://purl.obolibrary.org/obo/oba/subsets/oba-basic.obo publications: - id: https://doi.org/10.1007/s00335-023-09992-1 title: The Ontology of Biological Attributes (OBA) - computational traits for the life sciences repository: https://github.com/obophenotype/bio-attribute-ontology title: Ontology of Biological Attributes tracker: https://github.com/obophenotype/bio-attribute-ontology/issues usages: - description: OBA terms are used by the NHGRI-EBI GWAS Catalog for phenotypic trait annotation. examples: - description: hip circumference url: https://www.ebi.ac.uk/gwas/efotraits/OBA_1000032 publications: - id: https://doi.org/10.1093/nar/gkae1070 title: 'The NHGRI-EBI GWAS Catalog: standards for reusability, sustainability and diversity' type: annotation user: https://www.ebi.ac.uk/gwas/ - description: OBA trait terms facilitate computational drug target identification via the Open Targets Platform. examples: - description: age of onset of Alzheimer disease url: https://platform.opentargets.org/disease/OBA_2001000/associations publications: - id: https://doi.org/10.1093/nar/gkac1046 title: 'The next-generation Open Targets Platform: reimagined, redesigned, rebuilt' type: Database user: https://platform.opentargets.org - description: The Encyclopedia of Life (EOL) TraitBank takes advantage of the well-axiomatised OBA terms to infer traits in biodiversity data and to improve their search functionality. examples: - description: cell size http://purl.obolibrary.org/obo/OBA_0000055 url: https://eol.org/terms/search_results?tq%5Bf%5D%5B0%5D%5Bp%5D=380&tq%5Br%5D=record publications: - id: https://doi.org/10.3233/SW-150190 title: 'TraitBank: Practical semantics for organism attribute data' type: Database user: https://eol.org/traitbank - description: OBA terms are used by the Functional Trait Resource for Environmental Studies (FuTRES) for the annotation of measurable traits in vertebrates. examples: - description: body length url: https://futres-data-interface.netlify.app/ publications: - id: https://doi.org/10.1016/j.isci.2022.105101 title: A solution to the challenges of interdisciplinary aggregation and use of specimen-level trait data type: annotation user: https://futres.org/ - activity_status: active contact: email: jiezhen@med.umich.edu github: zhengj2007 label: Jie Zheng orcid: 0000-0002-2999-0103 description: A biomedical ontology in the domain of biological and clinical statistics. domain: information technology homepage: https://github.com/obcs/obcs id: obcs in_foundry: false layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/4.0/ ontology_purl: http://purl.obolibrary.org/obo/obcs.owl preferredPrefix: OBCS products: - id: obcs.owl ontology_purl: http://purl.obolibrary.org/obo/obcs.owl repository: https://github.com/obcs/obcs tags: - statistics title: Ontology of Biological and Clinical Statistics tracker: https://github.com/obcs/obcs/issues usages: - description: The Ontology of Biological and Clinical Statistics (OBCS)-based statistical method standardization and meta-analysis of host responses to yellow fever vaccines examples: - description: In Methods, "Both OBCS and the Vaccine Ontology (VO) were used to ontologically model various components and relations ..." url: https://doi.org/10.1007/s40484-017-0122-5 user: https://doi.org/10.1007/s40484-017-0122-5 - activity_status: active browsers: - label: BioPortal title: BioPortal Browser url: http://bioportal.bioontology.org/ontologies/OBI?p=classes contact: email: bpeters@lji.org github: bpeters42 label: Bjoern Peters orcid: 0000-0002-8457-6693 depicted_by: https://svn.code.sf.net/p/obi/code/trunk/web/htdocs/images/obi-lotext.png description: An integrated ontology for the description of life-science and clinical investigations domain: investigations homepage: http://obi-ontology.org id: obi in_foundry_order: 1 layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: https://creativecommons.org/licenses/by/4.0/ mailing_list: http://groups.google.com/group/obi-users ontology_purl: http://purl.obolibrary.org/obo/obi.owl preferredPrefix: OBI products: - description: The full version of OBI in OWL format id: obi.owl ontology_purl: http://purl.obolibrary.org/obo/obi.owl title: OBI - description: The OBO-format version of OBI id: obi.obo ontology_purl: http://purl.obolibrary.org/obo/obi.obo title: OBI in OBO - description: A collection of important high-level terms and their relations from OBI and other ontologies id: obi/obi_core.owl ontology_purl: http://purl.obolibrary.org/obo/obi/obi_core.owl title: OBI Core - description: Base module for OBI id: obi/obi-base.owl ontology_purl: http://purl.obolibrary.org/obo/obi/obi-base.owl title: OBI Base module publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/27128319 title: The Ontology for Biomedical Investigations repository: https://github.com/obi-ontology/obi title: Ontology for Biomedical Investigations tracker: http://purl.obolibrary.org/obo/obi/tracker usages: - description: The Immune Epitope Database (IEDB) is funded by NIAID that catalogs experimental data on antibody and T cell epitopes studied in humans, non-human primates, and other animal species in the context of infectious disease, allergy, autoimmunity and transplantation. examples: - description: A specific assay curated in the IEDB using the OBI:1110180 '3H-thymidine assay measuring epitope specific proliferation of T cells' ('3H-thymidine') url: http://www.iedb.org/assay/1505273 user: https://www.iedb.org - description: ENCODE is a comprehensive parts list of functional elements in the human genome, including elements that act at the protein and RNA levels, and regulatory elements that control cells and circumstances in which a gene is active. examples: - description: A specific assay annotated in ENCODE using OBI:0000716 'ChiP-seq' url: https://www.encodeproject.org/report/?type=Experiment&accession=ENCSR012KGU&accession=ENCSR560MXA&accession=ENCSR803FKU&accession=ENCSR216YPQ&accession=ENCSR115BCB&field=%40id&field=assay_term_name&field=assay_term_id user: https://www.encodeproject.org/ - description: The NASA GeneLab data repository hosts space biology and space-related datasets funded by multiple space agencies around the world. examples: - description: A specific assay annotated in NASA GeneLab using OBI:0001271 'RNA-seq assay' url: https://genelab-data.ndc.nasa.gov/genelab/accession/GLDS-464/ user: https://genelab-data.ndc.nasa.gov/genelab/projects - description: The CFDE is providing a centralized metadata resource to allow search across data coordination centers from multiple Common Fund programs. examples: - description: OBI is used in CFDE to captures types of experiments with assay terms such as OBI:0003094 'fluorescence in-situ hybridization assay' url: https://app.nih-cfde.org/chaise/recordset/#1/CFDE:assay_type@sort(nid) user: https://app.nih-cfde.org/ - description: NIF is a dynamic inventory of Web-based neuroscience resources, data, and tools accessible via any computer connected to the Internet. examples: - description: A specific OBI term used to autocomplete in NIF search OBI:0100026 'organism' url: https://neuinfo.org/data/search?q=organism&l=organism#all user: http://www.neuinfo.org - activity_status: active contact: email: jmwhorton@uams.edu github: jmwhorton label: Justin Whorton orcid: 0009-0003-4268-6207 description: An ontology built for annotation and modeling of biobank repository and biobanking administration domain: investigations homepage: https://github.com/biobanking/biobanking id: obib layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/4.0/ ontology_purl: http://purl.obolibrary.org/obo/obib.owl preferredPrefix: OBIB products: - id: obib.owl ontology_purl: http://purl.obolibrary.org/obo/obib.owl repository: https://github.com/biobanking/biobanking tags: - biobanking - specimens - bio-repository title: Ontology for Biobanking tracker: https://github.com/biobanking/biobanking/issues usages: - description: TURBO ontology supporting the PennTURBO project. examples: - description: Blood draw time url: http://purl.obolibrary.org/obo/OBIB_0000079 user: https://github.com/PennTURBO/turbo-ontology - description: The Minimum Information About BIobank data Sharing (MIABIS) aims to standardize data elements used to describe biobanks, research on samples and associated data. General attributes to describe biobanks, sample collections and studies at an aggregated/metadata level are defined in MIABIS Core 2.0 (Merino-Martinez et al., 2016). user: https://github.com/MIABIS/miabis - description: The National Cancer Institute Biorepositories and Biospecimen Research Branch (BBRB) is an international leader in research and policy activities related to biospecimen collection, processing, and storage, also known as biobanking. user: https://biospecimens.cancer.gov/resources/vocabularies.asp - activity_status: active browsers: - label: BioPortal title: BioPortal Ontology Browser url: https://bioportal.bioontology.org/ontologies/OCCO?p=classes contact: email: zhengj2007@gmail.com github: zhengj2007 label: Jie Zheng orcid: 0000-0002-2999-0103 description: An ontology representing occupations. It is designed to facilitate harmonization of existing occupation standards, such as the US Bureau of Labor Statistics Standard Occupational Classification (US SOC), the International Standard Classification of Occupations (ISCO), the UK National Statistics Standard Occupational Classification (UK SOC), and the European Skills, Competences, Qualifications and Occupations (ESCO) of the European Union. domain: information homepage: https://github.com/Occupation-Ontology/OccO id: occo issue_requested: 2428 layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: https://creativecommons.org/licenses/by/4.0/ ontology_purl: http://purl.obolibrary.org/obo/occo.owl preferredPrefix: OCCO products: - id: occo.owl ontology_purl: http://purl.obolibrary.org/obo/occo.owl repository: https://github.com/Occupation-Ontology/OccO title: Occupation Ontology tracker: https://github.com/Occupation-Ontology/OccO/issues - activity_status: active contact: email: yongqunh@med.umich.edu github: yongqunh label: Yongqun Oliver He orcid: 0000-0001-9189-9661 description: A formal ontology of genes and genomes of biological organisms. domain: biological systems homepage: https://bitbucket.org/hegroup/ogg id: ogg layout: ontology_detail license: label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/3.0/ ontology_purl: http://purl.obolibrary.org/obo/ogg.owl preferredPrefix: OGG products: - id: ogg.owl ontology_purl: http://purl.obolibrary.org/obo/ogg.owl repository: https://bitbucket.org/hegroup/ogg title: The Ontology of Genes and Genomes tracker: https://bitbucket.org/hegroup/ogg/issues/ - activity_status: active contact: email: baeverma@jcvi.org github: BAevermann label: Brian Aevermann orcid: 0000-0003-1346-1327 depicted_by: https://avatars2.githubusercontent.com/u/12973154?s=200&v=4 description: An ontology for representing treatment of disease and diagnosis and on carcinomas and other pathological entities domain: health homepage: https://github.com/OGMS/ogms id: ogms layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/4.0/ ontology_purl: http://purl.obolibrary.org/obo/ogms.owl preferredPrefix: OGMS products: - id: ogms.owl ontology_purl: http://purl.obolibrary.org/obo/ogms.owl publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/21347182 preferred: true title: Toward an ontological treatment of disease and diagnosis - id: https://www.ncbi.nlm.nih.gov/pubmed/25991121 title: Biomarkers in the Ontology for General Medical Science repository: https://github.com/OGMS/ogms tags: - medicine taxon: id: NCBITaxon:9606 label: Homo sapiens title: Ontology for General Medical Science tracker: https://github.com/OGMS/ogms/issues - activity_status: active contact: email: wdduncan@gmail.com github: wdduncan label: Bill Duncan orcid: 0000-0001-9625-1899 description: The Oral Health and Disease Ontology is used for representing the diagnosis and treatment of dental maladies. domain: health homepage: https://purl.obolibrary.org/obo/ohd id: ohd layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/4.0/ ontology_purl: http://purl.obolibrary.org/obo/ohd.owl preferredPrefix: OHD products: - id: ohd.owl ontology_purl: http://purl.obolibrary.org/obo/ohd.owl title: Oral Health and Disease Ontology publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/32819435 title: Structuring, reuse and analysis of electronic dental data using the Oral Health and Disease Ontology repository: https://github.com/oral-health-and-disease-ontologies/ohd-ontology title: Oral Health and Disease Ontology tracker: https://github.com/oral-health-and-disease-ontologies/ohd-ontology/issues - activity_status: active contact: email: yongqunh@med.umich.edu github: yongqunh label: Yongqun Oliver He orcid: 0000-0001-9189-9661 description: The Ontology of Host-Microbiome Interactions aims to ontologically represent and standardize various entities and relations related to microbiomes, microbiome host organisms (e.g., human and mouse), and the interactions between the hosts and microbiomes at different conditions. domain: organisms homepage: https://github.com/ohmi-ontology/ohmi id: ohmi layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/4.0/ mailing_list: http://groups.google.com/group/ohmi-discuss ontology_purl: http://purl.obolibrary.org/obo/ohmi.owl preferredPrefix: OHMI products: - id: ohmi.owl ontology_purl: http://purl.obolibrary.org/obo/ohmi.owl repository: https://github.com/ohmi-ontology/ohmi title: Ontology of Host-Microbiome Interactions tracker: https://github.com/ohmi-ontology/ohmi/issues - activity_status: active contact: email: edong@umich.edu github: e4ong1031 label: Edison Ong orcid: 0000-0002-5159-414X description: OHPI is a community-driven ontology of host-pathogen interactions (OHPI) and represents the virulence factors (VFs) and how the mutants of VFs in the Victors database become less virulence inside a host organism or host cells. It is developed to represent manually curated HPI knowledge available in the PHIDIAS resource. domain: biological systems homepage: https://github.com/OHPI/ohpi id: ohpi layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/4.0/ mailing_list: http://groups.google.com/group/ohpi-discuss ontology_purl: http://purl.obolibrary.org/obo/ohpi.owl preferredPrefix: OHPI products: - id: ohpi.owl ontology_purl: http://purl.obolibrary.org/obo/ohpi.owl publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/30365026 title: 'Victors: a web-based knowledge base of virulence factors in human and animal pathogens' repository: https://github.com/OHPI/ohpi title: Ontology of Host Pathogen Interactions tracker: https://github.com/OHPI/ohpi/issues - activity_status: active contact: email: huang@southalabama.edu github: Huang-OMIT label: Jingshan Huang orcid: 0000-0003-2408-2883 description: Ontology to establish data exchange standards and common data elements in the microRNA (miR) domain domain: chemistry and biochemistry homepage: http://omit.cis.usouthal.edu/ id: omit in_foundry: false layout: ontology_detail license: label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: https://creativecommons.org/licenses/by/3.0/ ontology_purl: http://purl.obolibrary.org/obo/omit.owl page: http://omit.cis.usouthal.edu/ preferredPrefix: OMIT products: - id: omit.owl ontology_purl: http://purl.obolibrary.org/obo/omit.owl repository: https://github.com/OmniSearch/omit title: Ontology for MIRNA Target tracker: https://github.com/OmniSearch/omit/issues - activity_status: active contact: email: cjmungall@lbl.gov github: cmungall label: Chris Mungall orcid: 0000-0002-6601-2165 description: An ontology specifies terms that are used to annotate ontology terms for all OBO ontologies. The ontology was developed as part of Information Artifact Ontology (IAO). domain: information homepage: https://github.com/information-artifact-ontology/ontology-metadata id: omo layout: ontology_detail license: label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png url: https://creativecommons.org/publicdomain/zero/1.0/ ontology_purl: http://purl.obolibrary.org/obo/omo.owl preferredPrefix: OMO products: - id: omo.owl ontology_purl: http://purl.obolibrary.org/obo/omo.owl repository: https://github.com/information-artifact-ontology/ontology-metadata tags: - ontology term annotation title: OBO Metadata Ontology tracker: https://github.com/information-artifact-ontology/ontology-metadata/issues usages: - description: OMO is imported by multiple OBO ontologies for ontology term annotations. type: owl_import user: http://obofoundry.org - activity_status: active contact: email: jimhu@tamu.edu github: jimhu-tamu label: James C. Hu orcid: 0000-0001-9016-2684 description: An ontology of phenotypes covering microbes domain: phenotype homepage: http://microbialphenotypes.org id: omp layout: ontology_detail license: label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/3.0/ ontology_purl: http://purl.obolibrary.org/obo/omp.owl preferredPrefix: OMP products: - id: omp.owl ontology_purl: http://purl.obolibrary.org/obo/omp.owl - id: omp.obo ontology_purl: http://purl.obolibrary.org/obo/omp.obo publications: - id: https://doi.org/10.1186/s12866-014-0294-3 title: An ontology for microbial phenotypes repository: https://github.com/microbialphenotypes/OMP-ontology title: Ontology of Microbial Phenotypes tracker: https://github.com/microbialphenotypes/OMP-ontology/issues - activity_status: active contact: email: hoganwr@gmail.com github: hoganwr label: Bill Hogan orcid: 0000-0002-9881-1017 description: The Ontology for Modeling and Representation of Social Entities (OMRSE) is an OBO Foundry ontology that represents the various entities that arise from human social interactions, such as social acts, social roles, social groups, and organizations. domain: health homepage: https://github.com/mcwdsi/OMRSE/wiki/OMRSE-Overview id: omrse layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: https://creativecommons.org/licenses/by/4.0/ ontology_purl: http://purl.obolibrary.org/obo/omrse.owl preferredPrefix: OMRSE products: - id: omrse.owl ontology_purl: http://purl.obolibrary.org/obo/omrse.owl publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/27406187 title: 'The ontology of medically related social entities: recent developments' repository: https://github.com/mcwdsi/OMRSE tags: - social - behavior taxon: id: NCBITaxon:9606 label: Homo sapiens title: Ontology for Modeling and Representation of Social Entities tracker: https://github.com/mcwdsi/OMRSE/issues usages: - description: OMRSE is used by the CAFÊ and TIPTOE projects examples: - description: The project creates and maintains the Ontology of Organizational Structures of Trauma centers and Trauma systems or OOSTT, which reuses OMRSE terms url: https://www.ebi.ac.uk/ols4/ontologies/oostt/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FOOSTT_00000089 type: owl:Ontology user: https://boar.uams.edu/projects/comparative-assessment-framework-for-environments-of-trauma-care - description: OMRSE is used by the Intervention Setting Ontology component of the Behavior Change Intervention Ontology examples: - description: Several facility classes extend OMRSE's 'facility' url: https://www.ebi.ac.uk/ols4/ontologies/bcio/classes/http%253A%252F%252Fhumanbehaviourchange.org%252Fontology%252FBCIO_026022 publications: - id: https://doi.org/10.12688/wellcomeopenres.15904.1 title: 'Development of an Intervention Setting Ontology for behaviour change: Specifying where interventions take place' type: owl:Ontology user: https://www.humanbehaviourchange.org - activity_status: active contact: email: chenyangnutrition@gmail.com github: cyang0128 label: Chen Yang orcid: 0000-0001-9202-5309 dependencies: - id: foodon - id: obi - id: ons description: An ontology to standardize research output of nutritional epidemiologic studies. domain: diet, metabolomics, and nutrition homepage: https://github.com/cyang0128/Nutritional-epidemiologic-ontologies id: one layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: https://creativecommons.org/licenses/by/4.0/ ontology_purl: http://purl.obolibrary.org/obo/one.owl page: https://github.com/cyang0128/Nutritional-epidemiologic-ontologies preferredPrefix: ONE products: - id: one.owl ontology_purl: http://purl.obolibrary.org/obo/one.owl repository: https://github.com/cyang0128/Nutritional-epidemiologic-ontologies tags: - nutritional epidemiology - observational studies - dietary surveys title: Ontology for Nutritional Epidemiology tracker: https://github.com/cyang0128/Nutritional-epidemiologic-ontologies/issues - activity_status: active contact: email: francesco.vitali@ibba.cnr.it github: FrancescoVit label: Francesco Vitali orcid: 0000-0001-9125-4337 dependencies: - id: bfo - id: chebi - id: envo - id: foodon - id: ncbitaxon - id: obi - id: ro - id: uberon description: An ontology for description of concepts in the nutritional studies domain. domain: diet, metabolomics, and nutrition homepage: https://github.com/enpadasi/Ontology-for-Nutritional-Studies id: ons layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: https://creativecommons.org/licenses/by/4.0/ ontology_purl: http://purl.obolibrary.org/obo/ons.owl page: https://github.com/enpadasi/Ontology-for-Nutritional-Studies preferredPrefix: ONS products: - id: ons.owl ontology_purl: http://purl.obolibrary.org/obo/ons.owl title: ONS latest release publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/29736190 title: 'ONS: an ontology for a standardized description of interventions and observational studies in nutrition' repository: https://github.com/enpadasi/Ontology-for-Nutritional-Studies tags: - nutrition, nutritional studies, nutrition professionals title: Ontology for Nutritional Studies tracker: https://github.com/enpadasi/Ontology-for-Nutritional-Studies/issues - activity_status: active browsers: - label: Human-readable (HTML) title: Ontoavida HTML Browser url: https://owl.fortunalab.org/ontoavida/ contact: email: fortuna@ebd.csic.es github: miguelfortuna label: Miguel A. Fortuna orcid: 0000-0002-8374-1941 dependencies: - id: fbcv - id: gsso - id: ncit - id: ro - id: stato description: OntoAvida develops an integrated vocabulary for the description of the most widely-used computational approach for studying evolution using digital organisms (i.e., self-replicating computer programs that evolve within a user-defined computational environment). domain: simulation homepage: https://gitlab.com/fortunalab/ontoavida id: ontoavida layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: https://creativecommons.org/licenses/by/4.0/ ontology_purl: http://purl.obolibrary.org/obo/ontoavida.owl preferredPrefix: ONTOAVIDA products: - description: The main ontology in OWL id: ontoavida.owl ontology_purl: http://purl.obolibrary.org/obo/ontoavida.owl page: https://gitlab.com/fortunalab/ontoavida/-/raw/master/ontoavida.owl title: OWL - description: Equivalent to ontoavida.owl, in obo format id: ontoavida.obo ontology_purl: http://purl.obolibrary.org/obo/ontoavida.obo page: https://gitlab.com/fortunalab/ontoavida/-/raw/master/ontoavida.obo title: OBO publications: - id: https://doi.org/10.1038/s41597-023-02514-3 title: Ontology for the Avida digital evolution platform repository: https://gitlab.com/fortunalab/ontoavida tags: - digital evolution - artificial life title: 'OntoAvida: ontology for Avida digital evolution platform' tracker: https://gitlab.com/fortunalab/ontoavida/-/issues usages: - description: An R package—avidaR—uses OntoAvida to perform complex queries on an RDF database—avidaDB—containing the genomes, transcriptomes, and phenotypes of more than a million digital organisms examples: - description: 'avidaR: an R library to perform complex queries on an ontology-based database of digital organisms' url: http://doi.org/10.7717/peerj-cs.1568 user: https://cran.r-project.org/package=avidaR - activity_status: active browsers: - label: BioPortal title: BioPortal Browser url: https://bioportal.bioontology.org/ontologies/ONTONEO - label: OntoBee title: OntoBee Browser url: https://ontobee.org/ontology/ONTONEO contact: email: fernanda.farinelli@gmail.com github: FernandaFarinelli label: Fernanda Farinelli orcid: 0000-0003-2338-8872 description: The Obstetric and Neonatal Ontology is a structured controlled vocabulary to provide a representation of the data from electronic health records (EHRs) involved in the care of the pregnant woman, and of her baby. domain: health homepage: https://ontoneo.com/ id: ontoneo layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: https://creativecommons.org/licenses/by/4.0/ mailing_list: http://groups.google.com/group/ontoneo-discuss ontology_purl: http://purl.obolibrary.org/obo/ontoneo.owl preferredPrefix: ONTONEO products: - description: The full version of ONTONEO in OWL format id: ontoneo.owl ontology_purl: http://purl.obolibrary.org/obo/ontoneo.owl title: ONTONEO publications: - id: https://doi.org/10.5281/zenodo.17429771 title: 'OntONeo: The Obstetric and Neonatal Ontology' - id: https://doi.org/10.5281/zenodo.17508651 title: Formal Ontologies in Knowledge Organization within the Obstetric and Neonatal Domain repository: https://github.com/ontoneo-project/Ontoneo title: Obstetric and Neonatal Ontology tracker: https://github.com/ontoneo-project/Ontoneo/issues usages: - description: The ReCOL research group uses OntONeo to model and structure biomedical information, particularly in obstetrics and neonatology. examples: - description: The ontology has been applied in studies on data interoperability and semantic integration, improving access to structured medical information and enabling knowledge sharing between systems. url: https://mba.eci.ufmg.br/wp-content/uploads/Anais_CBIS_2018_FarinelliAlmeidaLouize.pdf user: http://recol.eci.ufmg.br/ - description: OntONeo serves as a knowledge representation framework to support clinical decision-making and data interoperability in healthcare. It is used in information retrieval applications, enabling structured queries over medical databases and facilitating access to critical obstetric and neonatal health information. examples: - description: Demonstrates OntONeo’s application for enabling structured data access and semantic reasoning in clinical contexts. url: https://doi.org/10.56238/devopinterscie-267 user: http://hdl.handle.net/1843/38044 - activity_status: active contact: email: mbrochhausen@gmail.com github: mbrochhausen label: Mathias Brochhausen orcid: 0000-0003-1834-3856 description: An ontology built for representating the organizational components of trauma centers and trauma systems. domain: health homepage: https://github.com/OOSTT/OOSTT id: oostt layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/4.0/ ontology_purl: http://purl.obolibrary.org/obo/oostt.owl preferredPrefix: OOSTT products: - id: oostt.owl ontology_purl: http://purl.obolibrary.org/obo/oostt.owl repository: https://github.com/OOSTT/OOSTT title: Ontology of Organizational Structures of Trauma centers and Trauma systems tracker: https://github.com/OOSTT/OOSTT/issues usages: - description: OOSTT terms, such as OOSTT_00000017 'trauma program' and OOSTT_00000021 'trauma medical director role,' are used in the CAFE questionnaire to assess trauma centers and systems. type: application user: https://cafe-trauma.com/ - description: OOSTT terms, such as OOSTT_00000002 'trauma center' and OOSTT_00000066 'emergency medicine liaison role,' are used in the TIPTOE questionnaire to relate trauma center/system structure to patient outcomes. type: application user: https://tiptoe.apps.dbmi.cloud/tiptoe - description: Terms from OOSTT are imported and used by OMRSE. examples: - description: academic degree url: http://purl.obolibrary.org/obo/OOSTT_00000074 type: owl:Ontology user: https://github.com/mcwdsi/OMRSE - activity_status: active contact: email: zhengj2007@gmail.com github: zhengj2007 label: Jie Zheng orcid: 0000-0002-2999-0103 description: A reference ontology for parasite life cycle stages. domain: organisms homepage: https://github.com/OPL-ontology/OPL id: opl layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: https://creativecommons.org/licenses/by/4.0/ ontology_purl: http://purl.obolibrary.org/obo/opl.owl preferredPrefix: OPL products: - id: opl.owl ontology_purl: http://purl.obolibrary.org/obo/opl.owl repository: https://github.com/OPL-ontology/OPL tags: - life cycle stage - parasite organism title: Ontology for Parasite LifeCycle tracker: https://github.com/OPL-ontology/OPL/issues usages: - description: The ontology for parasite lifecycle is used in the VEuPathDB (Eukaryotic Pathogen, Vector & Host Informatics Resources) for parasite life cycle annotation. type: annotation and query user: https://veupathdb.org - description: The ontology for parasite lifecycle is used in the GeneDB for parasite life cycle annotation. type: annotation and query user: https://www.genedb.org - activity_status: active contact: email: yongqunh@med.umich.edu github: yongqunh label: Yongqun Oliver He orcid: 0000-0001-9189-9661 description: The Ontology of Precision Medicine and Investigation (OPMI) aims to ontologically represent and standardize various entities and relations associated with precision medicine and related investigations at different conditions. domain: investigations homepage: https://github.com/OPMI/opmi id: opmi layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/4.0/ mailing_list: http://groups.google.com/group/opmi-discuss ontology_purl: http://purl.obolibrary.org/obo/opmi.owl preferredPrefix: OPMI products: - id: opmi.owl ontology_purl: http://purl.obolibrary.org/obo/opmi.owl repository: https://github.com/OPMI/opmi title: Ontology of Precision Medicine and Investigation tracker: https://github.com/OPMI/opmi/issues - activity_status: active contact: email: safisher@upenn.edu github: safisher label: Stephen Fisher orcid: 0000-0001-8034-7685 description: An application ontology designed to annotate next-generation sequencing experiments performed on RNA. domain: investigations homepage: http://kim.bio.upenn.edu/software/ornaseq.shtml id: ornaseq layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/4.0/ ontology_purl: http://purl.obolibrary.org/obo/ornaseq.owl preferredPrefix: ORNASEQ products: - id: ornaseq.owl ontology_purl: http://purl.obolibrary.org/obo/ornaseq.owl repository: https://github.com/safisher/ornaseq title: Ontology of RNA Sequencing tracker: https://github.com/safisher/ornaseq/issues - activity_status: active contact: email: yongqunh@med.umich.edu github: yongqunh label: Yongqunh He orcid: 0000-0001-9189-9661 description: A biomedical ontology in the domain of vaccine adverse events. domain: health homepage: http://www.violinet.org/ovae/ id: ovae layout: ontology_detail license: label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/3.0/ ontology_purl: http://purl.obolibrary.org/obo/ovae.owl preferredPrefix: OVAE products: - id: ovae.owl ontology_purl: http://purl.obolibrary.org/obo/ovae.owl repository: https://github.com/OVAE-Ontology/ovae title: Ontology of Vaccine Adverse Events tracker: https://github.com/OVAE-Ontology/ovae/issues - activity_status: active browsers: - label: BioPortal title: BioPortal Ontology Browser url: https://bioportal.bioontology.org/ontologies/PATO contact: email: g.gkoutos@gmail.com github: gkoutos label: George Gkoutos orcid: 0000-0002-2061-091X description: An ontology of phenotypic qualities (properties, attributes or characteristics) domain: phenotype homepage: https://github.com/pato-ontology/pato/ id: pato in_foundry_order: 1 layout: ontology_detail license: label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/3.0/ ontology_purl: http://purl.obolibrary.org/obo/pato.owl preferredPrefix: PATO products: - id: pato.owl ontology_purl: http://purl.obolibrary.org/obo/pato.owl - id: pato.obo ontology_purl: http://purl.obolibrary.org/obo/pato.obo - id: pato.json ontology_purl: http://purl.obolibrary.org/obo/pato.json - description: Includes axioms linking to other ontologies, but no imports of those ontologies id: pato/pato-base.owl ontology_purl: http://purl.obolibrary.org/obo/pato/pato-base.owl publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/28387809 title: 'The anatomy of phenotype ontologies: principles, properties and applications' - id: https://www.ncbi.nlm.nih.gov/pubmed/15642100 title: Using ontologies to describe mouse phenotypes repository: https://github.com/pato-ontology/pato title: Phenotype And Trait Ontology tracker: https://github.com/pato-ontology/pato/issues usages: - description: PATO is used by the Human Phenotype Ontology (HPO) for logical definitions of phenotypes that facilitate cross-species integration. examples: - description: An abnormality in a cellular process. url: https://www.ebi.ac.uk/ols/ontologies/hp/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FHP_0011017&viewMode=All&siblings=false publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/30476213 title: Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources type: annotation user: https://hpo.jax.org/app/ - activity_status: active browsers: - label: BioPortal title: BioPortal Ontology Browser url: https://bioportal.bioontology.org/ontologies/pbpko contact: email: saurav.kumar@iispv.cat github: Crispae label: Saurav Kumar orcid: 0000-0003-0593-2598 description: An ontology for modeling and understanding of pharmacokinetics in biological systems. domain: chemistry and biochemistry homepage: https://github.com/InSilicoVida-Research-Lab/pbpko id: pbpko in_foundry_order: 1 layout: ontology_detail license: label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/3.0/ ontology_purl: http://purl.obolibrary.org/obo/pbpko.owl preferredPrefix: PBPKO products: - id: pbpko.owl ontology_purl: http://purl.obolibrary.org/obo/pbpko.owl - id: pbpko.obo ontology_purl: http://purl.obolibrary.org/obo/pbpko.obo - id: pbpko.json ontology_purl: http://purl.obolibrary.org/obo/pbpko.json repository: https://github.com/InSilicoVida-Research-Lab/pbpko title: Physiologically-Based Pharmacokinetic Ontology tracker: https://github.com/InSilicoVida-Research-Lab/pbpko/issues usages: - description: PBPKO is used for annotation of kinetic model in SBML description format. user: https://github.com/InSilicoVida-Research-Lab - activity_status: active contact: email: davidos@ebi.ac.uk github: dosumis label: David Osumi-Sutherland orcid: 0000-0002-7073-9172 dependencies: - id: bfo - id: chebi - id: cl - id: go - id: nbo - id: ncbitaxon - id: omo - id: pato - id: pr - id: ro - id: so - id: uberon description: Cell types that are provisionally defined by experimental techniques such as single cell or single nucleus transcriptomics rather than a straightforward & coherent set of properties. domain: phenotype homepage: https://github.com/obophenotype/provisional_cell_ontology id: pcl layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/4.0/ ontology_purl: http://purl.obolibrary.org/obo/pcl.owl preferredPrefix: PCL products: - id: pcl.owl ontology_purl: http://purl.obolibrary.org/obo/pcl.owl - id: pcl.obo ontology_purl: http://purl.obolibrary.org/obo/pcl.obo - id: pcl.json ontology_purl: http://purl.obolibrary.org/obo/pcl.json - id: pcl-base.owl ontology_purl: http://purl.obolibrary.org/obo/pcl-base.owl - id: pcl-base.obo ontology_purl: http://purl.obolibrary.org/obo/pcl-base.obo - id: pcl-base.json ontology_purl: http://purl.obolibrary.org/obo/pcl-base.json - id: pcl-full.owl ontology_purl: http://purl.obolibrary.org/obo/pcl-full.owl - id: pcl-full.obo ontology_purl: http://purl.obolibrary.org/obo/pcl-full.obo - id: pcl-full.json ontology_purl: http://purl.obolibrary.org/obo/pcl-full.json - id: pcl-simple.owl ontology_purl: http://purl.obolibrary.org/obo/pcl-simple.owl - id: pcl-simple.obo ontology_purl: http://purl.obolibrary.org/obo/pcl-simple.obo - id: pcl-simple.json ontology_purl: http://purl.obolibrary.org/obo/pcl-simple.json repository: https://github.com/obophenotype/provisional_cell_ontology title: Provisional Cell Ontology tracker: https://github.com/obophenotype/provisional_cell_ontology/issues - activity_status: active contact: email: rlwalls2008@gmail.com github: ramonawalls label: Ramona Walls orcid: 0000-0001-8815-0078 dependencies: - id: bfo - id: caro - id: envo - id: go - id: iao - id: ncbitaxon - id: pato - id: ro description: An ontology about groups of interacting organisms such as populations and communities domain: environment homepage: https://github.com/PopulationAndCommunityOntology/pco id: pco layout: ontology_detail license: label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png url: http://creativecommons.org/publicdomain/zero/1.0/ ontology_purl: http://purl.obolibrary.org/obo/pco.owl preferredPrefix: PCO products: - id: pco.owl ontology_purl: http://purl.obolibrary.org/obo/pco.owl repository: https://github.com/PopulationAndCommunityOntology/pco tags: - collections of organisms title: Population and Community Ontology tracker: https://github.com/PopulationAndCommunityOntology/pco/issues - activity_status: active contact: email: paul.fabry@usherbrooke.ca github: pfabry label: Paul Fabry orcid: 0000-0002-3336-2476 description: An ontology to describe entities related to prescription of drugs domain: information homepage: https://github.com/OpenLHS/PDRO id: pdro layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: https://creativecommons.org/licenses/by/4.0/ ontology_purl: http://purl.obolibrary.org/obo/pdro.owl preferredPrefix: PDRO products: - id: pdro.owl ontology_purl: http://purl.obolibrary.org/obo/pdro.owl publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/34831777 title: 'The Prescription of Drug Ontology 2.0 (PDRO): More Than the Sum of Its Parts' repository: https://github.com/OpenLHS/PDRO tags: - clinical documentation title: The Prescription of Drugs Ontology tracker: https://github.com/OpenLHS/PDRO/issues - activity_status: active contact: email: jaiswalp@science.oregonstate.edu github: jaiswalp label: Pankaj Jaiswal orcid: 0000-0002-1005-8383 depicted_by: https://raw.githubusercontent.com/Planteome/plant-ontology/refs/heads/master/Planteome_profile.jpg description: A structured, controlled vocabulary which describes the treatments, growing conditions, and/or study types used in plant biology experiments. domain: investigations homepage: http://planteome.org/ id: peco layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: https://creativecommons.org/licenses/by/4.0/ ontology_purl: http://purl.obolibrary.org/obo/peco.owl page: http://browser.planteome.org/amigo/term/PECO:0007359 preferredPrefix: PECO products: - id: peco.owl ontology_purl: http://purl.obolibrary.org/obo/peco.owl - id: peco.obo ontology_purl: http://purl.obolibrary.org/obo/peco.obo publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/29186578 title: 'The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics.' repository: https://github.com/Planteome/plant-experimental-conditions-ontology tags: - experimental conditions title: Plant Experimental Conditions Ontology tracker: https://github.com/Planteome/plant-experimental-conditions-ontology/issues - activity_status: active contact: email: alayne.cuzick@rothamsted.ac.uk github: CuzickA label: Alayne Cuzick orcid: 0000-0001-8941-3984 dependencies: - id: pato description: PHIPO is a formal ontology of species-neutral phenotypes observed in pathogen-host interactions. domain: phenotype homepage: https://github.com/PHI-base/phipo id: phipo layout: ontology_detail license: label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/3.0/ ontology_purl: http://purl.obolibrary.org/obo/phipo.owl preferredPrefix: PHIPO products: - id: phipo.owl ontology_purl: http://purl.obolibrary.org/obo/phipo.owl - id: phipo.obo ontology_purl: http://purl.obolibrary.org/obo/phipo.obo publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/34788826 title: 'PHI-base in 2022: a multi-species phenotype database for Pathogen-Host Interactions' repository: https://github.com/PHI-base/phipo title: Pathogen Host Interaction Phenotype Ontology tracker: https://github.com/PHI-base/phipo/issues - activity_status: active contact: email: smr@stowers.org github: srobb1 label: Sofia Robb orcid: 0000-0002-3528-5267 dependencies: - id: ro - id: uberon description: PLANA, the planarian anatomy ontology, encompasses the anatomy and life cycle stages for both __Schmidtea mediterranea__ biotypes. domain: anatomy and development homepage: https://github.com/obophenotype/planaria-ontology id: plana layout: ontology_detail license: label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/3.0/ ontology_purl: http://purl.obolibrary.org/obo/plana.owl preferredPrefix: PLANA products: - id: plana.owl ontology_purl: http://purl.obolibrary.org/obo/plana.owl - id: plana.obo ontology_purl: http://purl.obolibrary.org/obo/plana.obo publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/34318308 title: 'Planarian Anatomy Ontology: a resource to connect data within and across experimental platforms' repository: https://github.com/obophenotype/planaria-ontology title: planaria-ontology tracker: https://github.com/obophenotype/planaria-ontology/issues usages: - description: Planosphere's PAGE database uses PLANA to annotate gene expression locations examples: - description: The user can get an overview of the genes expressed in the planarian epidermis url: https://planosphere.stowers.org/ontology/PLANA_0000034 user: https://planosphere.stowers.org/ - activity_status: active contact: email: smr@stowers.org github: srobb1 label: Sofia Robb orcid: 0000-0002-3528-5267 dependencies: - id: go - id: pato - id: plana - id: ro description: Planarian Phenotype Ontology is an ontology of phenotypes observed in the planarian Schmidtea mediterranea. domain: phenotype homepage: https://github.com/obophenotype/planarian-phenotype-ontology id: planp layout: ontology_detail license: label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/3.0/ ontology_purl: http://purl.obolibrary.org/obo/planp.owl preferredPrefix: PLANP products: - id: planp.owl ontology_purl: http://purl.obolibrary.org/obo/planp.owl - id: planp.obo ontology_purl: http://purl.obolibrary.org/obo/planp.obo repository: https://github.com/obophenotype/planarian-phenotype-ontology title: Planarian Phenotype Ontology tracker: https://github.com/obophenotype/planarian-phenotype-ontology/issues - activity_status: active browsers: - label: Planteome title: Planteome browser url: http://browser.planteome.org/amigo contact: email: jaiswalp@science.oregonstate.edu github: jaiswalp label: Pankaj Jaiswal orcid: 0000-0002-1005-8383 depicted_by: https://raw.githubusercontent.com/Planteome/plant-ontology/refs/heads/master/Planteome_profile.jpg description: The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data. domain: anatomy and development homepage: http://browser.planteome.org/amigo id: po in_foundry_order: 1 layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: https://creativecommons.org/licenses/by/4.0/ ontology_purl: http://purl.obolibrary.org/obo/po.owl page: https://github.com/Planteome/plant-ontology preferredPrefix: PO products: - id: po.owl ontology_purl: http://purl.obolibrary.org/obo/po.owl - id: po.obo ontology_purl: http://purl.obolibrary.org/obo/po.obo publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/23220694 title: The plant ontology as a tool for comparative plant anatomy and genomic analyses. - id: https://www.ncbi.nlm.nih.gov/pubmed/29186578 title: 'The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics.' repository: https://github.com/Planteome/plant-ontology taxon: id: NCBITaxon:33090 label: Viridiplantae title: Plant Ontology tracker: https://github.com/Planteome/plant-ontology/issues twitter: planteome usages: - description: Planteome uses PO to describe location of tissue expression for genes in viridiplantae examples: - description: Genes and proteins annotate to leaf url: http://browser.planteome.org/amigo/term/PO:0025034 user: http://planteome.org/ - description: Maize CELL genomics DB uses PO to annotate images examples: - description: LhG4 Promoter Drivers url: http://maize.jcvi.org/cellgenomics/geneDB_list.php?filter=3 user: http://maize.jcvi.org/ - description: MaizeGDB uses PO for annotation of genes examples: - description: Introduced in gene model set 5b in assembly version RefGen_v2. url: http://maizegdb.org/gene_center/gene/GRMZM5G863962 user: http://maizegdb.org/ - description: Gramene uses PO for the annotation of plant genes examples: - description: Gramene annotations to leaf from Arabidopsis url: http://archive.gramene.org/db/ontology/search?id=PO:0025034 user: http://gramene.org/ - activity_status: active contact: email: robert.thacker@stonybrook.edu github: bobthacker label: Bob Thacker orcid: 0000-0002-9654-0073 dependencies: - id: ro - id: uberon description: An ontology covering the anatomy of the taxon Porifera (sponges) domain: anatomy and development homepage: https://github.com/obophenotype/porifera-ontology id: poro layout: ontology_detail license: label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/3.0/ ontology_purl: http://purl.obolibrary.org/obo/poro.owl preferredPrefix: PORO products: - id: poro.owl ontology_purl: http://purl.obolibrary.org/obo/poro.owl - id: poro.obo ontology_purl: http://purl.obolibrary.org/obo/poro.obo publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/25276334 title: 'The Porifera Ontology (PORO): enhancing sponge systematics with an anatomy ontology' repository: https://github.com/obophenotype/porifera-ontology taxon: id: NCBITaxon:6040 label: Porifera title: Porifera Ontology tracker: https://github.com/obophenotype/porifera-ontology/issues - activity_status: active contact: email: rlwalls2008@gmail.com github: ramonawalls label: Ramona Walls orcid: 0000-0001-8815-0078 description: An ontology for describing the phenology of individual plants and populations of plants, and for integrating plant phenological data across sources and scales. domain: phenotype homepage: https://github.com/PlantPhenoOntology/PPO id: ppo layout: ontology_detail license: label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/3.0/ mailing_list: ppo-discuss@googlegroups.com ontology_purl: http://purl.obolibrary.org/obo/ppo.owl preferredPrefix: PPO products: - id: ppo.owl ontology_purl: http://purl.obolibrary.org/obo/ppo.owl repository: https://github.com/PlantPhenoOntology/PPO tags: - plant phenotypes taxon: id: NCBITaxon:33090 label: Viridiplantae title: Plant Phenology Ontology tracker: https://github.com/PlantPhenoOntology/PPO/issues - activity_status: active browsers: - label: BioPortal title: BioPortal Browser url: http://bioportal.bioontology.org/ontologies/PR?p=classes&conceptid=http://purl.obolibrary.org/obo/PR_000000001 - label: PRO title: PRO Home url: http://proconsortium.org contact: email: dan5@georgetown.edu github: nataled label: Darren Natale orcid: 0000-0001-5809-9523 depicted_by: https://raw.githubusercontent.com/PROconsortium/logo/master/PROlogo_small.png description: An ontological representation of protein-related entities domain: chemistry and biochemistry homepage: http://proconsortium.org id: pr in_foundry_order: 1 layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/4.0/ ontology_purl: http://purl.obolibrary.org/obo/pr.owl preferredPrefix: PR products: - description: PRO after reasoning has been applied, OWL format. Add '.gz' for compressed. id: pr.owl ontology_purl: http://purl.obolibrary.org/obo/pr.owl title: pro_reasoned.owl - description: PRO after reasoning has been applied, OBO format. id: pr.obo ontology_purl: http://purl.obolibrary.org/obo/pr.obo title: pro_reasoned.obo - description: PRO without reasoning applied, OWL format. Add '.gz' for compressed. id: pr-asserted.owl ontology_purl: http://purl.obolibrary.org/obo/pr-asserted.owl title: pro_nonreasoned.owl - description: PRO without reasoning applied, OBO format. id: pr-asserted.obo ontology_purl: http://purl.obolibrary.org/obo/pr-asserted.obo title: pro_nonreasoned.obo publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/27899649 title: 'Protein Ontology (PRO): enhancing and scaling up the representation of protein entities' repository: https://github.com/PROconsortium/PRoteinOntology tags: - proteins title: PRotein Ontology (PRO) tracker: https://github.com/PROconsortium/PRoteinOntology/issues usages: - description: Colorado Richly Annotated Full-Text (CRAFT) Corpus; PRO is used for entity tagging and annotation examples: - description: Tagged entities (requires download) url: https://github.com/UCDenver-ccp/CRAFT/releases/tag/v4.0.1 user: https://github.com/UCDenver-ccp/CRAFT - description: Cell Ontology is a structured controlled vocabulary for cell types in animals; PRO is used for cell type definitions examples: - description: A B cell that is CD19-positive (uses the PRO term for non-species-specific CD19 molecule, PR:000001002) url: http://purl.obolibrary.org/obo/CL_0001201 user: http://www.obofoundry.org/ontology/cl.html - activity_status: active contact: email: wes_schafer@merck.com github: schaferw label: Wes Schafer orcid: 0000-0002-8786-1756 dependencies: - id: chebi - id: cheminf - id: obi - id: pato - id: ro - id: sbo description: PROCO covers process chemistry, the chemical field concerned with scaling up laboratory syntheses to commercially viable processes. domain: chemistry and biochemistry homepage: https://github.com/proco-ontology/PROCO id: proco layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: https://creativecommons.org/licenses/by/4.0/ ontology_purl: http://purl.obolibrary.org/obo/proco.owl preferredPrefix: PROCO products: - id: proco.owl ontology_purl: http://purl.obolibrary.org/obo/proco.owl repository: https://github.com/proco-ontology/PROCO title: Process Chemistry Ontology tracker: https://github.com/proco-ontology/PROCO/issues - activity_status: active contact: email: zachll@umich.edu github: zachll label: Zach Landis-Lewis orcid: 0000-0002-9117-9338 dependencies: - id: bfo - id: iao - id: ro - id: stato description: Ontology to reproducibly study visualizations of clinical performance domain: information homepage: https://github.com/Display-Lab/psdo id: psdo layout: ontology_detail license: label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/3.0/ ontology_purl: http://purl.obolibrary.org/obo/psdo.owl preferredPrefix: PSDO products: - id: psdo.owl ontology_purl: http://purl.obolibrary.org/obo/psdo.owl repository: https://github.com/Display-Lab/psdo tags: - learning systems title: Performance Summary Display Ontology tracker: https://github.com/Display-Lab/psdo/issues - activity_status: active contact: email: cooperl@oregonstate.edu github: cooperl09 label: Laurel Cooper orcid: 0000-0002-6379-8932 dependencies: - id: ro depicted_by: https://raw.githubusercontent.com/Planteome/plant-ontology/refs/heads/master/Planteome_profile.jpg description: The Plant Stress Ontology describes biotic and abiotic stresses that a plant may encounter. domain: agriculture homepage: https://github.com/Planteome/plant-stress-ontology id: pso layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/4.0/ ontology_purl: http://purl.obolibrary.org/obo/pso.owl preferredPrefix: PSO products: - id: pso.owl ontology_purl: http://purl.obolibrary.org/obo/pso.owl - id: pso.obo ontology_purl: http://purl.obolibrary.org/obo/pso.obo publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/29186578 title: 'The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics.' repository: https://github.com/Planteome/plant-stress-ontology tags: - plant disease - abiotic stress title: Plant Stress Ontology tracker: https://github.com/Planteome/plant-stress-ontology/issues - activity_status: active browsers: - label: RGD title: RGD Ontology Browser url: http://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=PW:0000001 contact: email: gthayman@mcw.edu github: gthayman label: G. Thomas Hayman orcid: 0000-0002-9553-7227 depicted_by: http://rgd.mcw.edu/common/images/rgd_LOGO_blue_rgd.gif description: A controlled vocabulary for annotating gene products to pathways. domain: biological systems homepage: http://rgd.mcw.edu/rgdweb/ontology/search.html id: pw layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: https://creativecommons.org/licenses/by/4.0/ ontology_purl: http://purl.obolibrary.org/obo/pw.owl page: https://download.rgd.mcw.edu/ontology/pathway/ preferredPrefix: PW products: - id: pw.owl ontology_purl: http://purl.obolibrary.org/obo/pw.owl - id: pw.obo ontology_purl: http://purl.obolibrary.org/obo/pw.obo publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/21478484 title: The Rat Genome Database pathway portal. - id: https://www.ncbi.nlm.nih.gov/pubmed/24499703 title: The pathway ontology - updates and applications. repository: https://github.com/rat-genome-database/PW-Pathway-Ontology tags: - biological process title: Pathway ontology tracker: https://github.com/rat-genome-database/PW-Pathway-Ontology/issues - activity_status: active contact: email: daniel.c.berrios@nasa.gov github: DanBerrios label: Daniel C. Berrios orcid: 0000-0003-4312-9552 dependencies: - id: bfo - id: chmo - id: envo - id: obi - id: pato - id: ro - id: uo description: RBO is an ontology for the effects of radiation on biota in terrestrial and space environments. domain: environment homepage: https://github.com/Radiobiology-Informatics-Consortium/RBO id: rbo layout: ontology_detail license: label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/3.0/ ontology_purl: http://purl.obolibrary.org/obo/rbo.owl preferredPrefix: RBO products: - id: rbo.owl name: Radiation Biology Ontology main release in OWL format ontology_purl: http://purl.obolibrary.org/obo/rbo.owl - id: rbo.obo name: Radiation Biology Ontology additional release in OBO format ontology_purl: http://purl.obolibrary.org/obo/rbo.obo - id: rbo.json name: Radiation Biology Ontology additional release in OBOJSon format ontology_purl: http://purl.obolibrary.org/obo/rbo.json - id: rbo/rbo-base.owl name: Radiation Biology Ontology main release in OWL format ontology_purl: http://purl.obolibrary.org/obo/rbo/rbo-base.owl - id: rbo/rbo-base.obo name: Radiation Biology Ontology additional release in OBO format ontology_purl: http://purl.obolibrary.org/obo/rbo/rbo-base.obo - id: rbo/rbo-base.json name: Radiation Biology Ontology additional release in OBOJSon format ontology_purl: http://purl.obolibrary.org/obo/rbo/rbo-base.json repository: https://github.com/Radiobiology-Informatics-Consortium/RBO tags: - radiation biology title: Radiation Biology Ontology tracker: https://github.com/Radiobiology-Informatics-Consortium/RBO/issues - activity_status: active contact: email: cjmungall@lbl.gov github: cmungall label: Chris Mungall orcid: 0000-0002-6601-2165 description: Relationship types shared across multiple ontologies domain: upper homepage: https://oborel.github.io/ id: ro layout: ontology_detail license: label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png url: http://creativecommons.org/publicdomain/zero/1.0/ mailing_list: https://groups.google.com/forum/#!forum/obo-relations ontology_purl: http://purl.obolibrary.org/obo/ro.owl preferredPrefix: RO products: - description: Canonical edition id: ro.owl ontology_purl: http://purl.obolibrary.org/obo/ro.owl title: Relation Ontology - description: The obo edition is less expressive than the OWL, and has imports merged in id: ro.obo ontology_purl: http://purl.obolibrary.org/obo/ro.obo title: Relation Ontology in obo format - id: ro.json ontology_purl: http://purl.obolibrary.org/obo/ro.json title: Relation Ontology in obojson format - description: Minimal subset intended to work with BFO-classes id: ro/core.owl ontology_purl: http://purl.obolibrary.org/obo/ro/core.owl page: https://github.com/oborel/obo-relations/wiki/ROCore title: RO Core relations - description: Axioms defined within RO and to be used in imports for other ontologies id: ro/ro-base.owl ontology_purl: http://purl.obolibrary.org/obo/ro/ro-base.owl page: https://github.com/INCATools/ontology-development-kit/issues/50 title: RO base ontology - description: For use in ecology and environmental science id: ro/subsets/ro-interaction.owl ontology_purl: http://purl.obolibrary.org/obo/ro/subsets/ro-interaction.owl title: Interaction relations - id: ro/subsets/ro-eco.owl ontology_purl: http://purl.obolibrary.org/obo/ro/subsets/ro-eco.owl title: Ecology subset - description: For use in neuroscience id: ro/subsets/ro-neuro.owl ontology_purl: http://purl.obolibrary.org/obo/ro/subsets/ro-neuro.owl page: http://bioinformatics.oxfordjournals.org/content/28/9/1262.long title: Neuroscience subset repository: https://github.com/oborel/obo-relations tags: - relations title: Relation Ontology tracker: https://github.com/oborel/obo-relations/issues usages: - description: RO is used for annotation extensions in the GO and GO Causal Activity Models. examples: - description: wg_biogenesis_FlyBase url: http://model.geneontology.org/56d1143000003402 publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/24885854 title: A method for increasing expressivity of Gene Ontology annotations using a compositional approach type: annotation user: http://geneontology.org - activity_status: active browsers: - label: RGD title: RGD Ontology Browser url: http://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=RS:0000457 contact: email: sjwang@mcw.edu github: shurjenw label: Shur-Jen Wang orcid: 0000-0001-5256-8683 depicted_by: http://rgd.mcw.edu/common/images/rgd_LOGO_blue_rgd.gif description: Ontology of rat strains domain: organisms homepage: http://rgd.mcw.edu/rgdweb/search/strains.html id: rs layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: https://creativecommons.org/licenses/by/4.0/ ontology_purl: http://purl.obolibrary.org/obo/rs.owl page: https://download.rgd.mcw.edu/ontology/rat_strain/ preferredPrefix: RS products: - id: rs.owl ontology_purl: http://purl.obolibrary.org/obo/rs.owl - id: rs.obo ontology_purl: http://purl.obolibrary.org/obo/rs.obo publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/24267899 title: 'Rat Strain Ontology: structured controlled vocabulary designed to facilitate access to strain data at RGD.' repository: https://github.com/rat-genome-database/RS-Rat-Strain-Ontology taxon: id: NCBITaxon:10114 label: Rattus title: Rat Strain Ontology tracker: https://github.com/rat-genome-database/RS-Rat-Strain-Ontology/issues - activity_status: active contact: email: batchelorc@rsc.org github: batchelorc label: Colin Batchelor orcid: 0000-0001-5985-7429 description: Connects organic name reactions to their roles in an organic synthesis and to processes in MOP domain: chemistry and biochemistry homepage: https://github.com/rsc-ontologies/rxno id: rxno layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: https://creativecommons.org/licenses/by/4.0/ mailing_list: chemistry-ontologies@googlegroups.com ontology_purl: http://purl.obolibrary.org/obo/rxno.owl preferredPrefix: RXNO products: - id: rxno.owl ontology_purl: http://purl.obolibrary.org/obo/rxno.owl title: Name Reaction Ontology repository: https://github.com/rsc-ontologies/rxno title: Name Reaction Ontology tracker: https://github.com/rsc-ontologies/rxno/issues - activity_status: active contact: email: mhb120@gmail.com github: mbrush label: Matthew Brush orcid: 0000-0002-1048-5019 depicted_by: https://raw.githubusercontent.com/jmcmurry/closed-illustrations/master/logos/SEPIO-LOGOS/sepio_logo_black-banner.png description: An ontology for representing the provenance of scientific claims and the evidence that supports them. domain: investigations homepage: https://github.com/monarch-initiative/SEPIO-ontology id: sepio layout: ontology_detail license: label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: https://creativecommons.org/licenses/by/3.0/ ontology_purl: http://purl.obolibrary.org/obo/sepio.owl preferredPrefix: SEPIO products: - id: sepio.owl ontology_purl: http://purl.obolibrary.org/obo/sepio.owl title: SEPIO repository: https://github.com/monarch-initiative/SEPIO-ontology tags: - scientific claims - evidence title: Scientific Evidence and Provenance Information Ontology tracker: https://github.com/monarch-initiative/SEPIO-ontology/issues - activity_status: active browsers: - label: BioPortal title: BioPortal Ontology Browser url: https://bioportal.bioontology.org/ontologies/SLSO contact: email: daniel.c.berrios@nasa.gov github: DanBerrios label: Dan Berrios orcid: 0000-0003-4312-9552 description: The Space Life Sciences Ontology is an application ontology and is intended to support the operation of NASA's Life Sciences Data Archive and other systems that contain space life science research data. domain: investigations homepage: https://github.com/nasa/LSDAO id: slso layout: ontology_detail license: label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/3.0/ ontology_purl: http://purl.obolibrary.org/obo/slso.owl preferredPrefix: SLSO products: - id: slso.owl ontology_purl: http://purl.obolibrary.org/obo/slso.owl - id: slso.obo ontology_purl: http://purl.obolibrary.org/obo/slso.obo - id: slso.json ontology_purl: http://purl.obolibrary.org/obo/slso.json - description: Includes axioms linking to other ontologies, but no imports of those ontologies id: slso-base.owl ontology_purl: http://purl.obolibrary.org/obo/slso-base.owl repository: https://github.com/nasa/LSDAO title: Space Life Sciences Ontology tracker: https://github.com/nasa/LSDAO/issues - activity_status: active contact: email: keilbeck@genetics.utah.edu github: keilbeck label: Karen Eilbeck orcid: 0000-0002-0831-6427 depicted_by: /images/so_logo.png description: A structured controlled vocabulary for sequence annotation, for the exchange of annotation data and for the description of sequence objects in databases. domain: chemistry and biochemistry homepage: http://www.sequenceontology.org/ id: so layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: https://creativecommons.org/licenses/by/4.0/ mailing_list: https://sourceforge.net/p/song/mailman/song-devel/ ontology_purl: http://purl.obolibrary.org/obo/so.owl page: https://en.wikipedia.org/wiki/Sequence_Ontology preferredPrefix: SO products: - id: so.owl ontology_purl: http://purl.obolibrary.org/obo/so.owl title: Main SO OWL release - id: so.obo ontology_purl: http://purl.obolibrary.org/obo/so.obo title: Main SO release in OBO Format - description: This subset includes only locatable sequence features and is designed for use in such outputs as GFF3 id: so/subsets/SOFA.owl ontology_purl: http://purl.obolibrary.org/obo/so/subsets/SOFA.owl title: Sequence Ontology Feature Annotation (SOFA) subset (OWL) - description: This subset includes only locatable sequence features and is designed for use in such outputs as GFF3 id: so/subsets/SOFA.obo ontology_purl: http://purl.obolibrary.org/obo/so/subsets/SOFA.obo title: Sequence Ontology Feature Annotation (SOFA) subset (OBO Format) publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/15892872 title: 'The Sequence Ontology: a tool for the unification of genome annotations.' - id: https://www.ncbi.nlm.nih.gov/pubmed/20226267 title: Evolution of the Sequence Ontology terms and relationships. repository: https://github.com/The-Sequence-Ontology/SO-Ontologies tags: - biological sequence title: Sequence types and features ontology tracker: https://github.com/The-Sequence-Ontology/SO-Ontologies/issues - activity_status: active contact: email: ramirez@macn.gov.ar github: martinjramirez label: Martin Ramirez orcid: 0000-0002-0358-0130 description: An ontology for spider comparative biology including anatomical parts (e.g. leg, claw), behavior (e.g. courtship, combing) and products (i.g. silk, web, borrow). domain: anatomy and development homepage: http://research.amnh.org/atol/files/ id: spd layout: ontology_detail license: label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: https://creativecommons.org/licenses/by/3.0/ ontology_purl: http://purl.obolibrary.org/obo/spd.owl preferredPrefix: SPD products: - id: spd.owl ontology_purl: http://purl.obolibrary.org/obo/spd.owl publications: - id: https://doi.org/10.3390/d11100202 title: The Spider Anatomy Ontology (SPD)—A Versatile Tool to Link Anatomy with Cross-Disciplinary Data repository: https://github.com/obophenotype/spider-ontology taxon: id: NCBITaxon:6893 label: spiders title: Spider Ontology tracker: https://github.com/obophenotype/spider-ontology/issues - activity_status: active contact: email: proccaserra@gmail.com github: proccaserra label: Philippe Rocca-Serra orcid: 0000-0001-9853-5668 depicted_by: https://raw.githubusercontent.com/ISA-tools/stato/dev/images/stato-logo-3.png description: STATO is a general-purpose STATistics Ontology. Its aim is to provide coverage for processes such as statistical tests, their conditions of application, and information needed or resulting from statistical methods, such as probability distributions, variables, spread and variation metrics. STATO also covers aspects of experimental design and description of plots and graphical representations commonly used to provide visual cues of data distribution or layout and to assist review of the results. domain: information technology homepage: http://stato-ontology.org/ id: stato in_foundry: false layout: ontology_detail license: label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/3.0/ ontology_purl: http://purl.obolibrary.org/obo/stato.owl preferredPrefix: STATO products: - id: stato.owl ontology_purl: http://purl.obolibrary.org/obo/stato.owl publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/31831744 title: Experiment design driven FAIRification of omics data matrices, an exemplar - id: https://www.ncbi.nlm.nih.gov/pubmed/32109232 title: Semantic concept schema of the linear mixed model of experimental observations repository: https://github.com/ISA-tools/stato tags: - statistics title: The Statistical Methods Ontology tracker: https://github.com/ISA-tools/stato/issues usages: - description: struct (Statistics in R using Class-based Templates), Struct integrates with the STATistics Ontology to ensure consistent reporting and maximizes semantic interoperability publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/33325493 title: 'struct: an R/Bioconductor-based framework for standardized metabolomics data analysis and beyond' type: annotation user: https://bioconductor.org/packages/release/bioc/html/struct.html - description: Scientific Evidence Code System (SEVCO) on the FEvIR platform. The FEvIR Platform includes many Builder Tools to create FHIR Resources without requiring expertise in FHIR or JSON, and Converter Tools to convert structured data to FHIR Resources publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/33486066 title: 'Making science computable: Developing code systems for statistics, study design, and risk of bias' type: annotation user: https://fevir.net/resources/CodeSystem/27270#STATO:0000039 - description: OBCS publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/27627881 title: The Ontology of Biological and Clinical Statistics (OBCS) for standardized and reproducible statistical analysis type: annotation user: https://github.com/obcs/obcs - activity_status: active contact: email: allyson.lister@oerc.ox.ac.uk github: allysonlister label: Allyson Lister orcid: 0000-0002-7702-4495 description: The Software Ontology (SWO) is a resource for describing software tools, their types, tasks, versions, provenance and associated data. It contains detailed information on licensing and formats as well as software applications themselves, mainly (but not limited) to the bioinformatics community. domain: information technology homepage: https://github.com/allysonlister/swo id: swo layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: https://creativecommons.org/licenses/by/4.0/ ontology_purl: http://purl.obolibrary.org/obo/swo.owl preferredPrefix: SWO products: - id: swo.owl ontology_purl: http://purl.obolibrary.org/obo/swo.owl - id: swo.json ontology_purl: http://purl.obolibrary.org/obo/swo.json publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/25068035 title: 'The Software Ontology (SWO): a resource for reproducibility in biomedical data analysis, curation and digital preservation' repository: https://github.com/allysonlister/swo tags: - software title: Software ontology tracker: https://github.com/allysonlister/swo/issues - activity_status: active contact: email: lynn.schriml@gmail.com github: lschriml label: Lynn Schriml orcid: 0000-0001-8910-9851 description: An ontology of disease symptoms, with symptoms encompasing perceived changes in function, sensations or appearance reported by a patient indicative of a disease. domain: health homepage: https://github.com/DiseaseOntology/SymptomOntology id: symp layout: ontology_detail license: label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png url: https://creativecommons.org/publicdomain/zero/1.0/ ontology_purl: http://purl.obolibrary.org/obo/symp.owl preferredPrefix: SYMP products: - id: symp.owl ontology_purl: http://purl.obolibrary.org/obo/symp.owl - id: symp.obo ontology_purl: http://purl.obolibrary.org/obo/symp.obo publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/19850722 title: GeMInA, Genomic Metadata for Infectious Agents, a geospatial surveillance pathogen database - id: https://www.ncbi.nlm.nih.gov/pubmed/34755882 title: The Human Disease Ontology 2022 update repository: https://github.com/DiseaseOntology/SymptomOntology tags: - disease taxon: id: NCBITaxon:9606 label: Homo sapiens title: Symptom Ontology tracker: https://github.com/DiseaseOntology/SymptomOntology/issues usages: - description: Symptoms of human diseases in the DO examples: - description: symptoms of human diseases url: https://disease-ontology.org/?id=DOID:0060164 user: https://disease-ontology.org/ - activity_status: active contact: email: allyson.lister@oerc.ox.ac.uk github: allysonlister label: Allyson Lister orcid: 0000-0002-7702-4495 description: A terminology for the skills necessary to make data FAIR and to keep it FAIR. domain: information homepage: https://github.com/terms4fairskills/FAIRterminology id: t4fs issue_requested: 1520 layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: https://creativecommons.org/licenses/by/4.0/ ontology_purl: http://purl.obolibrary.org/obo/t4fs.owl preferredPrefix: T4FS products: - id: t4fs.owl ontology_purl: http://purl.obolibrary.org/obo/t4fs.owl - id: t4fs.obo ontology_purl: http://purl.obolibrary.org/obo/t4fs.obo - id: t4fs.json ontology_purl: http://purl.obolibrary.org/obo/t4fs.json - id: t4fs-community.owl ontology_purl: http://purl.obolibrary.org/obo/t4fs-community.owl title: This community view of T4FS makes the ontology available in OWL without upper-level ontology (ULO) terms to give the user community a simpler view of the term hierarchy. - id: t4fs-community.obo ontology_purl: http://purl.obolibrary.org/obo/t4fs-community.obo title: This community view of T4FS makes the ontology available in OBO format without upper-level ontology (ULO) terms to give the user community a simpler view of the term hierarchy. - id: t4fs-community.json ontology_purl: http://purl.obolibrary.org/obo/t4fs-community.json title: This community view of T4FS makes the ontology available in JSON format without upper-level ontology (ULO) terms to give the user community a simpler view of the term hierarchy. publications: - id: https://doi.org/10.5281/zenodo.4705219 title: 'EOSC Co-creation funded project 074: Delivery of a proof of concept for terms4FAIRskills: Technical report' pull_request_added: 2140 repository: https://github.com/terms4fairskills/FAIRterminology title: terms4FAIRskills tracker: https://github.com/terms4fairskills/FAIRterminology/issues usages: - description: Semaphora integrates terms4FAIRskills, allowing users to annotate training materials with the ontology. user: http://t4fs.esciencedatafactory.com/ - description: FAIRassist is designed to offer personalised guidance to all stakeholders to enable the discovery of standards and repositories in FAIRsharing, which should be used to make data FAIR, as well as to signpost FAIR assessment resources. user: https://fairassist.org - description: FAIRsFAIR Competence Centre (project wp6) will provide a platform for training materials resulting from project training activities, annot user: https://www.fairsfair.eu/ - activity_status: active contact: email: balhoff@renci.org github: balhoff label: Jim Balhoff orcid: 0000-0002-8688-6599 description: A vocabulary of taxonomic ranks (species, family, phylum, etc) domain: organisms homepage: https://github.com/phenoscape/taxrank id: taxrank layout: ontology_detail license: label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png url: http://creativecommons.org/publicdomain/zero/1.0/ ontology_purl: http://purl.obolibrary.org/obo/taxrank.owl preferredPrefix: TAXRANK products: - id: taxrank.owl ontology_purl: http://purl.obolibrary.org/obo/taxrank.owl - id: taxrank.obo ontology_purl: http://purl.obolibrary.org/obo/taxrank.obo publications: - id: https://doi.org/10.1186/2041-1480-4-34 title: 'The vertebrate taxonomy ontology: a framework for reasoning across model organism and species phenotypes' repository: https://github.com/phenoscape/taxrank tags: - taxonomy title: Taxonomic rank vocabulary tracker: https://github.com/phenoscape/taxrank/issues - activity_status: active browsers: - label: Planteome title: Planteome browser url: http://browser.planteome.org/amigo/term/TO:0000387#display-lineage-tab contact: email: jaiswalp@science.oregonstate.edu github: jaiswalp label: Pankaj Jaiswal orcid: 0000-0002-1005-8383 depicted_by: https://raw.githubusercontent.com/Planteome/plant-ontology/refs/heads/master/Planteome_profile.jpg description: A controlled vocabulary to describe phenotypic traits in plants. domain: phenotype homepage: http://browser.planteome.org/amigo id: to layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: https://creativecommons.org/licenses/by/4.0/ ontology_purl: http://purl.obolibrary.org/obo/to.owl page: http://browser.planteome.org/amigo/term/TO:0000387#display-lineage-tab preferredPrefix: TO products: - id: to.owl ontology_purl: http://purl.obolibrary.org/obo/to.owl - id: to.obo ontology_purl: http://purl.obolibrary.org/obo/to.obo publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/29186578 title: 'The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics.' repository: https://github.com/Planteome/plant-trait-ontology taxon: id: NCBITaxon:33090 label: Viridiplantae title: Plant Trait Ontology tracker: https://github.com/Planteome/plant-trait-ontology/issues usages: - description: Planteome uses TO to describe traits for genes and germplasm examples: - description: Genes and proteins annotated to submergence tolerance, including SUB1 url: http://browser.planteome.org/amigo/term/TO:0000286 user: http://planteome.org/ - description: Gramene uses PO for the annotation of plant genes and QTLs examples: - description: Gramene annotations to submergence tolerance url: http://archive.gramene.org/db/ontology/search?id=TO:0000286 user: http://gramene.org/ - activity_status: active contact: email: lynn.schriml@gmail.com github: lschriml label: Lynn Schriml orcid: 0000-0001-8910-9851 description: An ontology representing the disease transmission process during which the pathogen is transmitted directly or indirectly from its natural reservoir, a susceptible host or source to a new host. domain: health homepage: https://github.com/DiseaseOntology/PathogenTransmissionOntology id: trans layout: ontology_detail license: label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png url: https://creativecommons.org/publicdomain/zero/1.0/ ontology_purl: http://purl.obolibrary.org/obo/trans.owl preferredPrefix: TRANS products: - id: trans.owl ontology_purl: http://purl.obolibrary.org/obo/trans.owl - id: trans.obo ontology_purl: http://purl.obolibrary.org/obo/trans.obo publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/19850722 title: GeMInA, Genomic Metadata for Infectious Agents, a geospatial surveillance pathogen database - id: https://www.ncbi.nlm.nih.gov/pubmed/34755882 title: The Human Disease Ontology 2022 update repository: https://github.com/DiseaseOntology/PathogenTransmissionOntology tags: - disease title: Pathogen Transmission Ontology tracker: https://github.com/DiseaseOntology/PathogenTransmissionOntology/issues usages: - description: Methods of transmission of human diseases in the DO examples: - description: methods of transmission of human diseases url: https://disease-ontology.org/?id=DOID:12365 user: https://disease-ontology.org/ - activity_status: active contact: email: balhoff@renci.org github: balhoff label: Jim Balhoff orcid: 0000-0002-8688-6599 description: An ontology covering the taxonomy of teleosts (bony fish) domain: organisms homepage: https://github.com/phenoscape/teleost-taxonomy-ontology id: tto layout: ontology_detail license: label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png url: http://creativecommons.org/publicdomain/zero/1.0/ ontology_purl: http://purl.obolibrary.org/obo/tto.owl preferredPrefix: TTO products: - id: tto.obo ontology_purl: http://purl.obolibrary.org/obo/tto.obo - id: tto.owl ontology_purl: http://purl.obolibrary.org/obo/tto.owl publications: - id: https://doi.org/10.1038/npre.2010.4629.1 title: The Teleost Taxonomy Ontology repository: https://github.com/phenoscape/teleost-taxonomy-ontology tags: - taxonomy taxon: id: NCBITaxon:32443 label: Teleostei title: Teleost taxonomy ontology tracker: https://github.com/phenoscape/teleost-taxonomy-ontology/issues - activity_status: active browsers: - label: BioPortal title: BioPortal Browser url: http://bioportal.bioontology.org/ontologies/TXPO?p=classes - label: TOXPILOT title: TOXPILOT url: https://toxpilot.nibiohn.go.jp/ contact: email: yuki.yamagata@riken.jp github: yuki-yamagata label: Yuki Yamagata orcid: 0000-0002-9673-1283 description: TOXic Process Ontology (TXPO) systematizes a wide variety of terms involving toxicity courses and processes. The first version of TXPO focuses on liver toxicity. domain: chemistry and biochemistry homepage: https://toxpilot.nibiohn.go.jp/ id: txpo layout: ontology_detail license: label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: https://creativecommons.org/licenses/by/3.0/ ontology_purl: http://purl.obolibrary.org/obo/txpo.owl preferredPrefix: TXPO products: - id: txpo.owl ontology_purl: http://purl.obolibrary.org/obo/txpo.owl publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/32883995 title: Ontological approach to the knowledge systematization of a toxic process and toxic course representation framework for early drug risk management repository: https://github.com/txpo-ontology/TXPO tags: - toxicity title: Toxic Process Ontology tracker: https://github.com/txpo-ontology/TXPO/issues - activity_status: active browsers: - label: RGD title: Gene Ontology AmiGO 2 Browser url: http://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=UBERON:0001062 - label: AmiGO (SUBSET) title: Gene Ontology AmiGO 2 Browser url: http://amigo.geneontology.org/amigo/term/UBERON:0001062#display-lineage-tab - label: Bgee (gene expression) title: Bgee gene expression queries url: http://bgee.org/?page=gene - label: FANTOM5 title: FANTOM5 Data Portal url: http://fantom.gsc.riken.jp/5/sstar/UBERON:0001890 - label: KnowledgeSpace title: INCF KnowledgeSpace Portal url: https://knowledge-space.org/index.php/pages/view/UBERON:0000061 contact: email: cjmungall@lbl.gov github: cmungall label: Chris Mungall orcid: 0000-0002-6601-2165 dependencies: - id: bfo - id: bspo - id: chebi - id: cl - id: envo - id: go - id: nbo - id: ncbitaxon - id: omo - id: pato - id: pr - id: ro depicted_by: https://raw.githubusercontent.com/jmcmurry/closed-illustrations/master/logos/uberon-logos/uberon_logo_black-banner.png description: An integrated cross-species anatomy ontology covering animals and bridging multiple species-specific ontologies domain: anatomy and development funded_by: - id: https://taggs.hhs.gov/Detail/AwardDetail?arg_AwardNum=R24OD011883&arg_ProgOfficeCode=205 title: NIH R24-OD011883 - id: https://grantome.com/grant/NIH/R01-HG004838 title: NIH R01-HG004838 - id: https://taggs.hhs.gov/Detail/AwardDetail?arg_AwardNum=P41HG002273&arg_ProgOfficeCode=55 title: NIH P41-HG002273 - id: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0956049 title: NSF DEB-0956049 homepage: http://uberon.org id: uberon layout: ontology_detail license: label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/3.0/ mailing_list: https://lists.sourceforge.net/lists/listinfo/obo-anatomy ontology_purl: http://purl.obolibrary.org/obo/uberon.owl page: http://en.wikipedia.org/wiki/Uberon preferredPrefix: UBERON products: - description: core ontology id: uberon.owl is_canonical: true ontology_purl: http://purl.obolibrary.org/obo/uberon.owl title: Uberon type: owl:Ontology - description: Axioms defined within Uberon and to be used in imports for other ontologies id: uberon/uberon-base.owl ontology_purl: http://purl.obolibrary.org/obo/uberon/uberon-base.owl page: https://github.com/INCATools/ontology-development-kit/issues/50 title: Uberon base ontology - description: Uberon edition that excludes external ontologies and most relations format: obo id: uberon/uberon-basic.obo ontology_purl: http://purl.obolibrary.org/obo/uberon/uberon-basic.obo title: Uberon basic type: obo-basic-ontology - description: Uberon plus all metazoan ontologies id: uberon/collected-metazoan.owl ontology_purl: http://purl.obolibrary.org/obo/uberon/collected-metazoan.owl page: https://obophenotype.github.io/uberon/combined_multispecies/ taxon: Metazoa title: Uberon collected metazoan ontology type: MergedOntology - description: Uberon and all metazoan ontologies with redundant species-specific terms removed id: uberon/composite-metazoan.owl ontology_purl: http://purl.obolibrary.org/obo/uberon/composite-metazoan.owl page: https://obophenotype.github.io/uberon/combined_multispecies/ taxon: Metazoa title: Uberon composite metazoan ontology type: MergedOntology - id: uberon/composite-vertebrate.owl mireots_from: - zfa - xao - fbbt - wbbt - ma - fma - emapa - ehdaa2 ontology_purl: http://purl.obolibrary.org/obo/uberon/composite-vertebrate.owl page: https://obophenotype.github.io/uberon/combined_multispecies/ taxon: Vertebrata title: Uberon composite vertebrate ontology type: MergedOntology publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/22293552 title: Uberon, an integrative multi-species anatomy ontology - id: https://www.ncbi.nlm.nih.gov/pubmed/25009735 title: Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon repository: https://github.com/obophenotype/uberon taxon: id: NCBITaxon:33208 label: Metazoa title: Uberon multi-species anatomy ontology tracker: https://github.com/obophenotype/uberon/issues twitter: uberanat usages: - description: Bgee is a database to retrieve and compare gene expression patterns between animal species. Bgee in using Uberon to annotate the site of expression, and Bgee curators one the major contributors to the ontology. examples: - description: Uberon terms used to annotate expression of human hemoglobin subunit beta url: http://bgee.org/?page=gene&gene_id=ENSG00000244734 seeAlso: https://doi.org/10.25504/FAIRsharing.x6d6sx type: annotation user: http://bgee.org/ - description: The National Human Genome Research Institute (NHGRI) launched a public research consortium named ENCODE, the Encyclopedia Of DNA Elements, in September 2003, to carry out a project to identify all functional elements in the human genome sequence. The ENCODE DCC users Uberon to annotate samples publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/25776021 title: Ontology application and use at the ENCODE DCC seeAlso: https://doi.org/10.25504/FAIRsharing.v0hbjs type: annotation user: https://www.encodeproject.org/ - description: FANTOM5 is using Uberon and CL to annotate samples allowing for transcriptome analyses with cell-type and tissue-level specificity. examples: - description: FANTOM5 samples annotated to telencephalon or its parts url: http://fantom.gsc.riken.jp/5/sstar/UBERON:0001893 type: annotation user: http://fantom5-collaboration.gsc.riken.jp/ - description: Querying expression and phenotype data type: query user: https://monarchinitiative.org/ - description: GO Database is used for querying for functional annotations relevant to a tissue examples: - description: GO annotations relevant to the uberon class for brain url: http://amigo.geneontology.org/amigo/term/UBERON:0000955 type: query user: https://geneontology.org/ - description: The Phenoscape project is both a major driver of and contributor to Uberon, contibuting thousands of terms. The teleost (bony fishes) component of Uberon was derived from the Teleost Anatomy Ontology, developed by the Phenoscape group. Most of the high level design of the skeletal system comes from the Vertebrate Skeletal Anatomy Ontology (VSAO), also created by the Phenoscape group. Phenoscape curators continue to extend the ontology, covering a wide variety of tetrapod structures, with an emphasis on the appendicular system. user: http://phenoscape.org - description: Searchable collection of neuroscience data and ontology for neuroscience type: Database user: https://neuinfo.org/ - description: cooperative data platform to be used by diverse communities in making data more FAIR. type: Database user: https://scicrunch.org/ - description: SCPortalen publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/29045713 title: 'SCPortalen: human and mouse single-cell centric database' type: Database user: http://single-cell.clst.riken.jp/ - description: ChEMBL uses Uberon to describe organ/tissue information in assays publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/30398643 title: 'ChEMBL: towards direct deposition of bioassay data' type: Database user: https://www.ebi.ac.uk/chembl/ - activity_status: active contact: email: g.gkoutos@gmail.com github: gkoutos label: George Gkoutos orcid: 0000-0002-2061-091X description: Metrical units for use in conjunction with PATO domain: phenotype homepage: https://github.com/bio-ontology-research-group/unit-ontology id: uo in_foundry: false layout: ontology_detail license: label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/3.0/ ontology_purl: http://purl.obolibrary.org/obo/uo.owl preferredPrefix: UO products: - id: uo.owl ontology_purl: http://purl.obolibrary.org/obo/uo.owl - id: uo.obo ontology_purl: http://purl.obolibrary.org/obo/uo.obo - id: uo.json ontology_purl: http://purl.obolibrary.org/obo/uo.json publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/23060432 title: 'The Units Ontology: a tool for integrating units of measurement in science' repository: https://github.com/bio-ontology-research-group/unit-ontology title: Units of measurement ontology tracker: https://github.com/bio-ontology-research-group/unit-ontology/issues - activity_status: active contact: email: jmcl@ebi.ac.uk github: jamesamcl label: James McLaughlin orcid: 0000-0002-8361-2795 description: The uPheno ontology integrates multiple phenotype ontologies into a unified cross-species phenotype ontology. domain: phenotype homepage: https://github.com/obophenotype/upheno id: upheno layout: ontology_detail license: label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png url: https://creativecommons.org/publicdomain/zero/1.0/ mailing_list: https://groups.google.com/forum/#!forum/phenotype-ontologies-editors ontology_purl: http://purl.obolibrary.org/obo/upheno.owl preferredPrefix: UPHENO products: - description: uPheno 1 is no longer actively maintained, please start using uPheno 2 (see below). id: upheno.owl ontology_purl: http://purl.obolibrary.org/obo/upheno.owl page: https://github.com/obophenotype/upheno title: uPheno 1 (inactive) - description: No longer actively maintained. id: upheno/mp-hp-view.owl ontology_purl: http://purl.obolibrary.org/obo/upheno/mp-hp-view.owl page: https://github.com/obophenotype/upheno/tree/master/hp-mp title: uPheno MP-HP equivalence axioms - description: The new version of uPheno, along with species independent phenotypes and additional phenotype relations. The ontology is still in Beta status, but we recommend users to migrate their infrastructures to uPheno 2 as uPheno 1 is no longer actively maintained. id: upheno/v2/upheno.owl ontology_purl: http://purl.obolibrary.org/obo/upheno/v2/upheno.owl page: https://github.com/obophenotype/upheno-dev title: uPheno 2 publications: - id: https://doi.org/10.1101/2024.09.18.613276 title: 'The Unified Phenotype Ontology (uPheno): A framework for cross-species integrative phenomics' - id: https://zenodo.org/record/2382757 title: Phenotype Ontologies Traversing All The Organisms (POTATO) workshop aims to reconcile logical definitions across species - id: https://zenodo.org/record/3352149 title: 'Phenotype Ontologies Traversing All The Organisms (POTATO) workshop: 2nd edition' repository: https://github.com/obophenotype/upheno title: Unified Phenotype Ontology (uPheno) tracker: https://github.com/obophenotype/upheno/issues usages: - description: uPheno is used by the Monarch Initiative for cross-species inference. examples: - description: Characteristic neurologic anomaly resulting form degeneration of dopamine-generating cells in the substantia nigra, a region of the midbrain, characterized clinically by shaking, rigidity, slowness of movement and difficulty with walking and gait. url: https://monarchinitiative.org/phenotype/HP:0001300#disease publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/27899636 title: 'The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species ' type: analysis user: https://monarchinitiative.org/ - activity_status: active contact: email: Sabrina@tislab.org github: sabrinatoro label: Sabrina Toro orcid: 0000-0002-4142-7153 dependencies: - id: ncbitaxon depicted_by: https://raw.githubusercontent.com/tis-lab/closed-illustrations/master/logos/vbo-logo/VBO-black-logo-stackedv2.png description: Vertebrate Breed Ontology is an ontology created to serve as a single computable resource for vertebrate breed names. domain: organisms homepage: https://github.com/monarch-initiative/vertebrate-breed-ontology id: vbo layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: https://creativecommons.org/licenses/by/4.0/ mailing_list: https://groups.google.com/group/VBO-users ontology_purl: http://purl.obolibrary.org/obo/vbo.owl preferredPrefix: VBO products: - id: vbo.owl name: Vertebrate Breed Ontology main release in OWL format ontology_purl: http://purl.obolibrary.org/obo/vbo.owl - id: vbo.obo name: Vertebrate Breed Ontology additional release in OBO format ontology_purl: http://purl.obolibrary.org/obo/vbo.obo - id: vbo.json name: Vertebrate Breed Ontology additional release in OBOJSon format ontology_purl: http://purl.obolibrary.org/obo/vbo.json - id: vbo/vbo-base.owl name: Vertebrate Breed Ontology main release in OWL format ontology_purl: http://purl.obolibrary.org/obo/vbo/vbo-base.owl - id: vbo/vbo-base.obo name: Vertebrate Breed Ontology additional release in OBO format ontology_purl: http://purl.obolibrary.org/obo/vbo/vbo-base.obo - id: vbo/vbo-base.json name: Vertebrate Breed Ontology additional release in OBOJSon format ontology_purl: http://purl.obolibrary.org/obo/vbo/vbo-base.json publications: - id: https://doi.org/10.1111/jvim.70133 title: 'The Vertebrate Breed Ontology: Toward Effective Breed Data Standardization' repository: https://github.com/monarch-initiative/vertebrate-breed-ontology title: Vertebrate Breed Ontology tracker: https://github.com/monarch-initiative/vertebrate-breed-ontology/issues usages: - description: VBO is used in the Online Mendelian Inheritance in Animals (OMIA) for breed annotations. examples: - description: Urticaria pigmentosa affects the Sphynx (Cat) (VBO:0100230) breed. url: https://www.omia.org/OMIA001289/9685/ type: annotation user: https://omia.org/home/ - description: VBO is used in Cellosaurus for breed/subspecies of origin of cell lines. examples: - description: The cell line AG07906 derived from the Thoroughbred (VBO:0001083) breed of Equuus caballus (Horse). url: https://www.cellosaurus.org/CVCL_2L83 type: annotation user: https://www.cellosaurus.org/index.html - activity_status: active contact: email: yongqunh@med.umich.edu github: yongqunh label: Yongqunh He orcid: 0000-0001-9189-9661 description: VO is a biomedical ontology in the domain of vaccine and vaccination. domain: health homepage: https://violinet.org/vaccineontology id: vo layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/4.0/ ontology_purl: http://purl.obolibrary.org/obo/vo.owl preferredPrefix: VO products: - id: vo.owl ontology_purl: http://purl.obolibrary.org/obo/vo.owl publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/23256535 title: Ontology representation and analysis of vaccine formulation and administration and their effects on vaccine immune responses - id: https://www.ncbi.nlm.nih.gov/pubmed/21624163 title: Mining of vaccine-associated IFN-γ gene interaction networks using the Vaccine Ontology repository: https://github.com/vaccineontology/VO title: Vaccine Ontology tracker: https://github.com/vaccineontology/VO/issues usages: - description: VIOLIN uses VO to standardize vaccine information examples: - description: VIOLIN using VO grouped all SARS-CoV-2 vaccines url: https://violinet.org/canvaxkb/vaccine_detail.php?c_vaccine_id=5339 - description: A specific vaccine ‘Allogeneic Tumor Cell Vaccine’ curated in VO for VIOLIN vaccine record url: https://violinet.org/vaxquery/query_detail.php?c_pathogen_id=321#vaccine_5878 user: https://violinet.org - description: Vaccine Adjuvant Compendium (VAC) uses Vaccine Ontology to standard vaccine adjuvants developed by NIH examples: - description: A specific vaccine adjuvant, such as CaPNP (CaPtivant)(TM), in Vaccine Adjuvant Compendium, uses VO_0005295 ‘CaPNP (CaPtivant)(TM) vaccine adjuvant’ url: https://vac.niaid.nih.gov/view?id=11 user: https://www.niaid.nih.gov/research/vaccine-adjuvant-compendium-vac - description: ImmPort uses Vaccine Ontology to standardize vaccine recorded collected in NIH funded ImmPort studies examples: - description: ImmPort data used VO for annotation shown in its dataModel url: https://www.immport.org/shared/dataModel user: https://www.immport.org/ - description: Human Immunology Project Consortium (HIPC) uses VO to standardize vaccine records examples: - description: Influenza Vaccine Live, Intranasal used VO_0000044 url: http://www.hipc-dashboard.org/#vaccine/vo-0000044 user: https://immunespace.org/ - activity_status: active contact: email: caripark@iastate.edu github: caripark label: Carissa Park orcid: 0000-0002-2346-5201 description: An ontology of traits covering vertebrates domain: phenotype homepage: https://github.com/AnimalGenome/vertebrate-trait-ontology id: vt layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: https://creativecommons.org/licenses/by/4.0/ ontology_purl: http://purl.obolibrary.org/obo/vt.owl preferredPrefix: VT products: - id: vt.owl ontology_purl: http://purl.obolibrary.org/obo/vt.owl repository: https://github.com/AnimalGenome/vertebrate-trait-ontology title: Vertebrate trait ontology tracker: https://github.com/AnimalGenome/vertebrate-trait-ontology/issues usages: - description: The Animal Quantitative Trait Loci (QTL) Database (Animal QTLdb) annotates trait mapping data for livestock animals using the VTO examples: - description: Links to cattle QTL associated with the VTO term gastrointestinal system morphology trait or its descendants url: https://www.animalgenome.org/cgi-bin/QTLdb/BT/traitsrch?tword=Gastrointestinal%20tract%20weight user: https://www.animalgenome.org/cgi-bin/QTLdb/index - description: The Rat Genome Database (RGD) uses the VTO to annotate rat QTL examples: - description: Annotations of rat QTL associated with the VTO term cholesterol amount or its descendants url: https://rgd.mcw.edu/rgdweb/ontology/annot.html?acc_id=VT:0003947&species=Rat user: https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=VT:0000001 - description: The Mouse Phenome Database (MPD) uses the VTO to annotate mouse strain traits examples: - description: Studies in the MPD database that have measurements related to the VTO term spleen size trait or its descendants url: https://phenome.jax.org/ontologies/VT:0002224 user: https://phenome.jax.org/ontologies/navigate/VT:0000001 - activity_status: active contact: email: balhoff@renci.org github: balhoff label: Jim Balhoff orcid: 0000-0002-8688-6599 description: Comprehensive hierarchy of extinct and extant vertebrate taxa. domain: organisms homepage: https://github.com/phenoscape/vertebrate-taxonomy-ontology id: vto layout: ontology_detail license: label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png url: http://creativecommons.org/publicdomain/zero/1.0/ ontology_purl: http://purl.obolibrary.org/obo/vto.owl preferredPrefix: VTO products: - id: vto.owl ontology_purl: http://purl.obolibrary.org/obo/vto.owl - id: vto.obo ontology_purl: http://purl.obolibrary.org/obo/vto.obo publications: - id: https://doi.org/10.1186/2041-1480-4-34 title: 'The vertebrate taxonomy ontology: a framework for reasoning across model organism and species phenotypes' repository: https://github.com/phenoscape/vertebrate-taxonomy-ontology title: Vertebrate Taxonomy Ontology tracker: https://github.com/phenoscape/vertebrate-taxonomy-ontology/issues usages: - description: Phenoscape uses VTO to annotate systematics data user: http://phenoscape.org - activity_status: active contact: email: raymond@caltech.edu github: raymond91125 label: Raymond Lee orcid: 0000-0002-8151-7479 description: A structured controlled vocabulary of the anatomy of Caenorhabditis elegans. domain: anatomy and development homepage: https://github.com/obophenotype/c-elegans-gross-anatomy-ontology id: wbbt layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: https://creativecommons.org/licenses/by/4.0/ ontology_purl: http://purl.obolibrary.org/obo/wbbt.owl preferredPrefix: WBbt products: - id: wbbt.owl ontology_purl: http://purl.obolibrary.org/obo/wbbt.owl - id: wbbt.obo ontology_purl: http://purl.obolibrary.org/obo/wbbt.obo publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/18629098 title: Building a cell and anatomy ontology of Caenorhabditis elegans repository: https://github.com/obophenotype/c-elegans-gross-anatomy-ontology taxon: id: NCBITaxon:6237 label: Caenorhabditis title: C. elegans Gross Anatomy Ontology tracker: https://github.com/obophenotype/c-elegans-gross-anatomy-ontology/issues usages: - description: WormBase uses WBbt to curate anatomical expression patterns and anatomy function annotations, and to allow search and indexing on the WormBase site examples: - description: Expression for gene daf-16 with WormBase ID WBGene00000912 url: http://www.wormbase.org/db/get?name=WBGene00000912;class=Gene;widget=expression publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/31642470 title: 'WormBase: a modern Model Organism Information Resource' type: annotation user: https://www.wormbase.org/ - activity_status: active contact: email: cgrove@caltech.edu github: chris-grove label: Chris Grove orcid: 0000-0001-9076-6015 description: A structured controlled vocabulary of the development of Caenorhabditis elegans. domain: anatomy and development homepage: https://github.com/obophenotype/c-elegans-development-ontology id: wbls layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: https://creativecommons.org/licenses/by/4.0/ ontology_purl: http://purl.obolibrary.org/obo/wbls.owl preferredPrefix: WBls products: - id: wbls.owl ontology_purl: http://purl.obolibrary.org/obo/wbls.owl - id: wbls.obo ontology_purl: http://purl.obolibrary.org/obo/wbls.obo publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/31642470 title: 'WormBase: a modern Model Organism Information Resource' repository: https://github.com/obophenotype/c-elegans-development-ontology tags: - developemental life stage taxon: id: NCBITaxon:6237 label: Caenorhabditis title: C. elegans development ontology tracker: https://github.com/obophenotype/c-elegans-development-ontology/issues usages: - description: WormBase uses WBls to curate temporal expression patterns, and to allow search and indexing on the WormBase site examples: - description: Expression for daf-16 gene with WormBase ID WBGene00000912. url: http://www.wormbase.org/db/get?name=WBGene00000912;class=Gene;widget=expression publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/31642470 title: 'WormBase: a modern Model Organism Information Resource' type: annotation user: https://www.wormbase.org/ - activity_status: active contact: email: cgrove@caltech.edu github: chris-grove label: Chris Grove orcid: 0000-0001-9076-6015 description: A structured controlled vocabulary of Caenorhabditis elegans phenotypes domain: phenotype homepage: https://github.com/obophenotype/c-elegans-phenotype-ontology id: wbphenotype layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/4.0/ ontology_purl: http://purl.obolibrary.org/obo/wbphenotype.owl preferredPrefix: WBPhenotype products: - id: wbphenotype.owl ontology_purl: http://purl.obolibrary.org/obo/wbphenotype.owl - id: wbphenotype.obo ontology_purl: http://purl.obolibrary.org/obo/wbphenotype.obo - id: wbphenotype/wbphenotype-base.owl ontology_purl: http://purl.obolibrary.org/obo/wbphenotype/wbphenotype-base.owl publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/21261995 title: 'Worm Phenotype Ontology: integrating phenotype data within and beyond the C. elegans community.' repository: https://github.com/obophenotype/c-elegans-phenotype-ontology taxon: id: NCBITaxon:6237 label: Caenorhabditis title: C. elegans phenotype tracker: https://github.com/obophenotype/c-elegans-phenotype-ontology/issues usages: - description: WormBase uses WBPhenotype to curate worm phenotypes, and to allow search and indexing on the WormBase site examples: - description: Expression for daf-16 gene with WormBase ID WBGene00000912. url: http://www.wormbase.org/db/get?name=WBGene00000912;class=Gene;widget=expression publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/31642470 title: 'WormBase: a modern Model Organism Information Resource' type: annotation user: https://www.wormbase.org/ - description: Monarch integrates phenotype annotations from sources such as WormBase, and allows for querying using the WBPhenotype ontology. examples: - description: 'Egg long: The fertilized oocytes have a greater than standard length measured end to end compared to control.' url: https://monarchinitiative.org/phenotype/WBPhenotype%3A0000370 publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/27899636 title: 'The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species ' type: annotation user: https://monarchinitiative.org/ - activity_status: active contact: email: Erik.Segerdell@cchmc.org github: seger label: Erik Segerdell orcid: 0000-0002-9611-1279 description: XAO represents the anatomy and development of the African frogs Xenopus laevis and tropicalis. domain: anatomy and development homepage: http://www.xenbase.org/anatomy/xao.do?method=display id: xao in_foundry_order: 1 layout: ontology_detail license: label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/3.0/ ontology_purl: http://purl.obolibrary.org/obo/xao.owl preferredPrefix: XAO products: - id: xao.owl ontology_purl: http://purl.obolibrary.org/obo/xao.owl - id: xao.obo ontology_purl: http://purl.obolibrary.org/obo/xao.obo publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/18817563 title: An ontology for Xenopus anatomy and development. - id: https://www.ncbi.nlm.nih.gov/pubmed/24139024 title: 'Enhanced XAO: the ontology of Xenopus anatomy and development underpins more accurate annotation of gene expression and queries on Xenbase.' repository: https://github.com/xenopus-anatomy/xao taxon: id: NCBITaxon:8353 label: Xenopus title: Xenopus Anatomy Ontology tracker: https://github.com/xenopus-anatomy/xao/issues usages: - description: Xenbase uses XAO to annotate gene expression. examples: - description: Xenopus genes expressed in the pronephric kidney. url: http://www.xenbase.org/anatomy/showanatomy.do?method=displayAnatomySummary&anatomyId=463 user: http://www.xenbase.org - activity_status: active browsers: - label: RGD title: RGD Ontology Browser url: http://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=XCO:0000000 contact: email: jrsmith@mcw.edu github: jrsjrs label: Jennifer Smith orcid: 0000-0002-6443-9376 depicted_by: http://rgd.mcw.edu/common/images/rgd_LOGO_blue_rgd.gif description: Conditions under which physiological and morphological measurements are made both in the clinic and in studies involving humans or model organisms. domain: health homepage: https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=XCO:0000000 id: xco layout: ontology_detail license: label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png url: https://creativecommons.org/publicdomain/zero/1.0/ ontology_purl: http://purl.obolibrary.org/obo/xco.owl page: https://download.rgd.mcw.edu/ontology/experimental_condition/ preferredPrefix: XCO products: - id: xco.owl ontology_purl: http://purl.obolibrary.org/obo/xco.owl - id: xco.obo ontology_purl: http://purl.obolibrary.org/obo/xco.obo publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/22654893 title: Three ontologies to define phenotype measurement data. - id: https://www.ncbi.nlm.nih.gov/pubmed/24103152 title: 'The clinical measurement, measurement method and experimental condition ontologies: expansion, improvements and new applications.' repository: https://github.com/rat-genome-database/XCO-experimental-condition-ontology tags: - clinical title: Experimental condition ontology tracker: https://github.com/rat-genome-database/XCO-experimental-condition-ontology/issues - activity_status: active contact: email: lutz.fischer@tu-berlin.de github: lutzfischer label: Lutz Fischer orcid: 0000-0003-4978-0864 description: A structured controlled vocabulary for cross-linking reagents used with proteomics mass spectrometry. domain: chemistry and biochemistry homepage: http://www.psidev.info/groups/controlled-vocabularies id: xlmod layout: ontology_detail license: label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: https://creativecommons.org/licenses/by/3.0/ mailing_list: psidev-ms-vocab@lists.sourceforge.net ontology_purl: http://purl.obolibrary.org/obo/xlmod.owl page: http://www.psidev.info/groups/controlled-vocabularies preferredPrefix: XLMOD products: - id: xlmod.obo ontology_purl: http://purl.obolibrary.org/obo/xlmod.obo - id: xlmod.owl ontology_purl: http://purl.obolibrary.org/obo/xlmod.owl repository: https://github.com/HUPO-PSI/xlmod-CV tags: - MS cross-linker reagents title: HUPO-PSI cross-linking and derivatization reagents controlled vocabulary tracker: https://github.com/HUPO-PSI/xlmod-CV/issues - activity_status: active contact: email: Erik.Segerdell@cchmc.org github: seger label: Erik Segerdell orcid: 0000-0002-9611-1279 dependencies: - id: bfo - id: chebi - id: cl - id: go - id: iao - id: pato - id: ro - id: xao description: XPO represents anatomical, cellular, and gene function phenotypes occurring throughout the development of the African frogs Xenopus laevis and tropicalis. domain: phenotype homepage: https://github.com/obophenotype/xenopus-phenotype-ontology id: xpo layout: ontology_detail license: label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/3.0/ ontology_purl: http://purl.obolibrary.org/obo/xpo.owl preferredPrefix: XPO products: - id: xpo.owl ontology_purl: http://purl.obolibrary.org/obo/xpo.owl - id: xpo.obo ontology_purl: http://purl.obolibrary.org/obo/xpo.obo publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/35317743 title: 'The Xenopus phenotype ontology: bridging model organism phenotype data to human health and development.' repository: https://github.com/obophenotype/xenopus-phenotype-ontology taxon: id: NCBITaxon:8353 label: Xenopus title: Xenopus Phenotype Ontology tracker: https://github.com/obophenotype/xenopus-phenotype-ontology/issues - activity_status: active contact: email: ybradford@zfin.org github: ybradford label: Yvonne Bradford orcid: 0000-0002-9900-7880 description: Experimental conditions applied to zebrafish, developed to facilitate experiment condition annotation at ZFIN domain: environment homepage: https://github.com/ybradford/zebrafish-experimental-conditions-ontology id: zeco layout: ontology_detail license: label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/3.0/ ontology_purl: http://purl.obolibrary.org/obo/zeco.owl preferredPrefix: ZECO products: - id: zeco.obo ontology_purl: http://purl.obolibrary.org/obo/zeco.obo - id: zeco.owl ontology_purl: http://purl.obolibrary.org/obo/zeco.owl - id: zeco.json ontology_purl: http://purl.obolibrary.org/obo/zeco.json repository: https://github.com/ybradford/zebrafish-experimental-conditions-ontology taxon: id: NCBITaxon:7954 label: Danio title: Zebrafish Experimental Conditions Ontology tracker: https://github.com/ybradford/zebrafish-experimental-conditions-ontology/issues - activity_status: active contact: email: van_slyke@zfin.org github: cerivs label: Ceri Van Slyke orcid: 0000-0002-2244-7917 description: A structured controlled vocabulary of the anatomy and development of the Zebrafish domain: anatomy and development homepage: https://wiki.zfin.org/display/general/Anatomy+Atlases+and+Resources id: zfa in_foundry_order: 1 layout: ontology_detail license: label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/3.0/ ontology_purl: http://purl.obolibrary.org/obo/zfa.owl preferredPrefix: ZFA products: - id: zfa.owl ontology_purl: http://purl.obolibrary.org/obo/zfa.owl - id: zfa.obo ontology_purl: http://purl.obolibrary.org/obo/zfa.obo publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/24568621 title: 'The zebrafish anatomy and stage ontologies: representing the anatomy and development of Danio rerio.' repository: https://github.com/cerivs/zebrafish-anatomical-ontology taxon: id: NCBITaxon:7954 label: Danio title: Zebrafish anatomy and development ontology tracker: https://github.com/cerivs/zebrafish-anatomical-ontology/issues usages: - description: ZFIN uses ZFA to annotate gene expression and phenotype examples: - description: zebrafish genes expressed in hindbrain and genotypes with hindbrain phenotype url: http://zfin.org/ZFA:0000029 user: http://zfin.org - activity_status: active contact: email: van_slyke@zfin.org github: cerivs label: Ceri Van Slyke orcid: 0000-0002-2244-7917 description: Developmental stages of the Zebrafish domain: anatomy and development homepage: https://wiki.zfin.org/display/general/Anatomy+Atlases+and+Resources id: zfs in_foundry: false layout: ontology_detail license: label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/3.0/ ontology_purl: http://purl.obolibrary.org/obo/zfs.owl page: https://github.com/obophenotype/developmental-stage-ontologies/wiki/ZFS preferredPrefix: ZFS products: - id: zfs.owl ontology_purl: http://purl.obolibrary.org/obo/zfs.owl - id: zfs.obo ontology_purl: http://purl.obolibrary.org/obo/zfs.obo repository: https://github.com/cerivs/zebrafish-anatomical-ontology taxon: id: NCBITaxon:7954 label: Danio title: Zebrafish developmental stages ontology tracker: https://github.com/cerivs/zebrafish-anatomical-ontology/issues - activity_status: active contact: email: ybradford@zfin.org github: ybradford label: Yvonne Bradford orcid: 0000-0002-9900-7880 dependencies: - id: bfo - id: bspo - id: go - id: pato - id: ro - id: uberon - id: zfa description: The Zebrafish Phenotype Ontology formally defines all phenotypes of the Zebrafish model organism. domain: phenotype homepage: https://github.com/obophenotype/zebrafish-phenotype-ontology id: zp layout: ontology_detail license: label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/3.0/ ontology_purl: http://purl.obolibrary.org/obo/zp.owl preferredPrefix: ZP products: - id: zp.owl ontology_purl: http://purl.obolibrary.org/obo/zp.owl - id: zp.obo ontology_purl: http://purl.obolibrary.org/obo/zp.obo repository: https://github.com/obophenotype/zebrafish-phenotype-ontology title: Zebrafish Phenotype Ontology tracker: https://github.com/obophenotype/zebrafish-phenotype-ontology/issues usages: - description: Monarch integrates phenotype annotations from sources such as ZFIIN, and allows for querying using the ZP ontology. examples: - description: 'adaxial cell absent, abnormal: Abnormal(ly) absent (of) adaxial cell.' url: https://monarchinitiative.org/phenotype/ZP:0005692 publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/27899636 title: 'The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species' type: annotation user: https://monarchinitiative.org/ - activity_status: active contact: email: kronkcj@mail.uc.edu github: Superraptor label: Clair Kronk orcid: 0000-0001-8397-8810 description: The Gender, Sex, and Sexual Orientation (GSSO) ontology has terms for annotating interdisciplinary information concerning gender, sex, and sexual orientation for primary usage in the biomedical and adjacent sciences. domain: organisms homepage: https://gsso.research.cchmc.org/ id: gsso layout: ontology_detail license: label: Apache 2.0 License url: http://www.apache.org/licenses/LICENSE-2.0 ontology_purl: http://purl.obolibrary.org/obo/gsso.owl preferredPrefix: GSSO products: - id: gsso.owl ontology_purl: http://purl.obolibrary.org/obo/gsso.owl - id: gsso.obo ontology_purl: http://purl.obolibrary.org/obo/gsso.obo - id: gsso.json ontology_purl: http://purl.obolibrary.org/obo/gsso.json repository: https://github.com/Superraptor/GSSO title: Gender, Sex, and Sexual Orientation (GSSO) ontology tracker: https://github.com/Superraptor/GSSO/issues - activity_status: active browsers: - label: HPO title: JAX HPO Browser url: https://hpo.jax.org/app/ - label: Monarch title: Monarch Phenotype Page url: http://monarchinitiative.org/phenotype/HP:0000118 contact: email: dr.sebastian.koehler@gmail.com github: drseb label: Sebastian Koehler orcid: 0000-0002-5316-1399 depicted_by: https://raw.githubusercontent.com/obophenotype/human-phenotype-ontology/master/logo/HPO-logo-black_small.png description: The Human Phenotype Ontology (HPO) is a structured and controlled vocabulary for the phenotypic features encountered in human hereditary and other disease. domain: phenotype homepage: http://www.human-phenotype-ontology.org/ id: hp layout: ontology_detail license: label: hpo url: https://hpo.jax.org/app/license mailing_list: https://groups.io/g/human-phenotype-ontology ontology_purl: http://purl.obolibrary.org/obo/hp.owl preferredPrefix: HP products: - derived_from: hp/hp-simple-non-classified.owl description: Simple, manually curated version of the ontology without the use of a reasoner, and without any imported terms, in obographs JSON format. format: json id: hp.json ontology_purl: http://purl.obolibrary.org/obo/hp.json title: Official HPO release in obographs JSON format - derived_from: hp/hp-simple-non-classified.owl description: Simple, manually curated version of the ontology without the use of a reasoner, and without any imported terms, in OBO file format. format: obo id: hp.obo ontology_purl: http://purl.obolibrary.org/obo/hp.obo title: Official HPO release in OBO format - description: Manually classified version of the ontology without the use of a reasoner, with imported terms, in OWL format (RDF/XML). format: owl id: hp.owl ontology_purl: http://purl.obolibrary.org/obo/hp.owl title: Official HPO release in OWL - derived_from: hp/hp-base.owl description: Manually curated version of the ontology without the use of a reasoner, with references to imported terms, in obographs JSON file format. format: obo id: hp/hp-base.json ontology_purl: http://purl.obolibrary.org/obo/hp/hp-base.json title: HPO base release in obographs JSON format - derived_from: hp/hp-base.owl description: Manually curated version of the ontology without the use of a reasoner, with references to imported terms, in OBO file format. format: obo id: hp/hp-base.obo ontology_purl: http://purl.obolibrary.org/obo/hp/hp-base.obo title: HPO base release in OBO format - description: Manually curated version of the ontology without the use of a reasoner, with references to imported terms, in OWL (RDF/XML) file format. format: owl id: hp/hp-base.owl ontology_purl: http://purl.obolibrary.org/obo/hp/hp-base.owl title: HPO base release in OWL format - derived_from: hp/hp-full.owl description: Version of the ontology automatically classified with the use of a reasoner, including all imported terms, in obographs JSON file format. format: json id: hp/hp-full.json ontology_purl: http://purl.obolibrary.org/obo/hp/hp-full.json title: HPO full release in obographs JSON format - derived_from: hp/hp-full.owl description: Version of the ontology automatically classified with the use of a reasoner, including all imported terms, in OBO file format. format: obo id: hp/hp-full.obo ontology_purl: http://purl.obolibrary.org/obo/hp/hp-full.obo title: HPO full release in OBO format - description: Version of the ontology automatically classified with the use of a reasoner, including all imported terms, in OWL (RDF/XML) file format. format: owl id: hp/hp-full.owl ontology_purl: http://purl.obolibrary.org/obo/hp/hp-full.owl title: HPO full release in OWL format - derived_from: hp/hp-international.owl description: Version of the ontology corresponding to the primary release (hp.owl), with translated labels, synonyms, and definitions, in obographs JSON file format. format: json id: hp/hp-international.json ontology_purl: http://purl.obolibrary.org/obo/hp/hp-international.json title: HPO International Edition in obographs JSON format - derived_from: hp/hp-international.owl description: Version of the ontology corresponding to the primary release (hp.owl), with translated labels, synonyms, and definitions, in OBO file format. format: obo id: hp/hp-international.obo ontology_purl: http://purl.obolibrary.org/obo/hp/hp-international.obo title: HPO International Edition in OBO format - description: Version of the ontology corresponding to the primary release (hp.owl), with translated labels, synonyms, and definitions, in OWL (RDF/XML) file format. format: owl id: hp/hp-international.owl ontology_purl: http://purl.obolibrary.org/obo/hp/hp-international.owl title: HPO International Edition in OWL format - derived_from: hp/hp-simple-non-classified.owl description: Simple, manually curated version of the ontology without the use of a reasoner, and without any imported terms, in obographs JSON file format. format: json id: hp/hp-simple-non-classified.json ontology_purl: http://purl.obolibrary.org/obo/hp/hp-simple-non-classified.json title: HPO simple, manually classified, without imports in obographs JSON format - derived_from: hp/hp-simple-non-classified.owl description: Simple, manually curated version of the ontology without the use of a reasoner, and without any imported terms, in OBO file format. format: obo id: hp/hp-simple-non-classified.obo ontology_purl: http://purl.obolibrary.org/obo/hp/hp-simple-non-classified.obo title: HPO simple, manually classified, without imports in OBO format - description: Simple, manually curated version of the ontology without the use of a reasoner, and without any imported terms, in OWL (RDF/XML) file format. format: owl id: hp/hp-simple-non-classified.owl ontology_purl: http://purl.obolibrary.org/obo/hp/hp-simple-non-classified.owl title: HPO simple, manually classified, without imports in OWL format - description: https://hpo.jax.org/app/data/annotations format: tsv id: hp/phenotype.hpoa ontology_purl: http://purl.obolibrary.org/obo/hp/phenotype.hpoa title: HPO Annotations (Phenotype to Disease) - description: https://hpo.jax.org/app/data/annotations format: tsv id: hp/phenotype_to_genes.txt ontology_purl: http://purl.obolibrary.org/obo/hp/phenotype_to_genes.txt title: HPO phenotype to gene annotations - description: https://hpo.jax.org/app/data/annotations format: tsv id: hp/genes_to_phenotype.txt ontology_purl: http://purl.obolibrary.org/obo/hp/genes_to_phenotype.txt title: HPO gene to phenotype annotations publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/18950739 title: 'The Human Phenotype Ontology: a tool for annotating and analyzing human hereditary disease.' - id: https://www.ncbi.nlm.nih.gov/pubmed/26119816 title: 'The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease.' - id: https://www.ncbi.nlm.nih.gov/pubmed/24217912 title: 'The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data.' - id: https://www.ncbi.nlm.nih.gov/pubmed/30476213 title: Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources. repository: https://github.com/obophenotype/human-phenotype-ontology taxon: id: NCBITaxon:9606 label: Homo sapiens title: Human Phenotype Ontology (HPO) tracker: https://github.com/obophenotype/human-phenotype-ontology/issues/ twitter: hp_ontology usages: - description: HPO is used by the Monarch Initiative for phenotype annotations. examples: - url: https://monarchinitiative.org/phenotype/HP:0001300 reference: https://academic.oup.com/nar/article/45/D1/D712/2605791 type: annotation user: https://monarchinitiative.org/ - activity_status: active browsers: - label: OLS title: Ontology Lookup Service url: https://www.ebi.ac.uk/ols/ontologies/kisao - label: BioPortal title: BioPortal url: https://bioportal.bioontology.org/ontologies/KISAO - label: OntoBee title: OntoBee url: https://www.ontobee.org/ontology/KISAO contact: email: jonrkarr@gmail.com github: jonrkarr label: Jonathan Karr orcid: 0000-0002-2605-5080 description: A classification of algorithms for simulating biology, their parameters, and their outputs domain: simulation funded_by: - id: https://grantome.com/search?q=P41EB023912 title: NIH P41EB023912 - id: https://grantome.com/search?q=R35GM119771 title: NIH R35GM119771 homepage: https://github.com/SED-ML/KiSAO id: kisao layout: ontology_detail license: label: Artistic License 2.0 url: http://opensource.org/licenses/Artistic-2.0 ontology_purl: http://purl.obolibrary.org/obo/kisao.owl preferredPrefix: KISAO products: - id: kisao.owl ontology_purl: http://purl.obolibrary.org/obo/kisao.owl publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/22027554 title: Controlled vocabularies and semantics in systems biology repository: https://github.com/SED-ML/KiSAO tags: - systems biology - computational biology - mathematical modeling - numerical simulation - simulation algorithms title: Kinetic Simulation Algorithm Ontology tracker: https://github.com/SED-ML/KiSAO/issues usages: - description: The Simulation Experiment Description Markup Language (SED-ML) is a language for describing simulations and visualizations of their results. examples: - description: Several examples of simulations encoded in SED-ML url: https://sed-ml.org/examples.html type: annotation user: https://sed-ml.org/ - description: BioSimulations is a repository of biosimulation projects. examples: - description: Simulation of a synthetic oscillatory biochemical network url: https://biosimulations.org/projects/Repressilator-Elowitz-Nature-2000 type: annotation user: https://biosimulations.org/ - description: runBioSimulations is a web application for execution biological simulations. examples: - description: Example simulation runs url: https://run.biosimulations.org/runs?try=1 type: annotation user: https://run.biosimulations.org/ - description: BioSimulators is a registry of biosimulation tools. examples: - description: tellurium is a software tool for kinetic simulation of biochemical networks url: https://biosimulators.org/simulators/tellurium/latest#tab=algorithms seeAlso: https://arxiv.org/abs/2203.06732 type: annotation user: https://biosimulators.org/ - activity_status: active contact: email: sheriff@ebi.ac.uk github: rsmsheriff label: Rahuman Sheriff orcid: 0000-0003-0705-9809 description: Terms commonly used in Systems Biology, and in particular in computational modeling. domain: chemistry and biochemistry homepage: http://www.ebi.ac.uk/sbo/ id: sbo layout: ontology_detail license: label: Artistic License 2.0 url: http://opensource.org/licenses/Artistic-2.0 ontology_purl: http://purl.obolibrary.org/obo/sbo.owl preferredPrefix: SBO products: - id: sbo.owl ontology_purl: http://purl.obolibrary.org/obo/sbo.owl repository: https://github.com/EBI-BioModels/SBO title: Systems Biology Ontology tracker: https://github.com/EBI-BioModels/SBO/issues - activity_status: active contact: email: giant.plankton@gmail.com github: JadeHotchkiss label: Jade Hotchkiss orcid: 0000-0002-2193-0704 dependencies: - id: apollo_sv - id: aro - id: chebi - id: chmo - id: cmo - id: doid - id: dron - id: duo - id: envo - id: eupath - id: exo - id: gaz - id: gsso - id: hp - id: hsapdv - id: ico - id: ido - id: idomal - id: mp - id: nbo - id: ncit - id: obi - id: ogms - id: opmi - id: pr - id: sbo - id: stato - id: symp - id: uo - id: vo - id: vt description: An ontology for the standardization of terminology and integration of knowledge about Sickle Cell Disease. domain: health homepage: https://scdontology.h3abionet.org/ id: scdo layout: ontology_detail license: label: GPL-3.0 url: https://www.gnu.org/licenses/gpl-3.0.en.html ontology_purl: http://purl.obolibrary.org/obo/scdo.owl preferredPrefix: SCDO products: - id: scdo.owl ontology_purl: http://purl.obolibrary.org/obo/scdo.owl - id: scdo.obo ontology_purl: http://purl.obolibrary.org/obo/scdo.obo publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/35363306 title: 'The Sickle Cell Disease Ontology: recent development and expansion of the universal sickle cell knowledge representation.' - id: https://www.ncbi.nlm.nih.gov/pubmed/33021900 title: 'The Sickle Cell Disease Ontology: Enabling Collaborative Research and Co-Designing of New Planetary Health Applications.' - id: https://www.ncbi.nlm.nih.gov/pubmed/31769834 title: 'The Sickle Cell Disease Ontology: enabling universal sickle cell-based knowledge representation.' repository: https://github.com/scdodev/scdo-ontology tags: - disease title: Sickle Cell Disease Ontology tracker: https://github.com/scdodev/scdo-ontology/issues - activity_status: orphaned contact: email: null label: chEBI description: An ontology of physico-chemical methods and properties. domain: chemistry and biochemistry homepage: http://www.ebi.ac.uk/chebi id: fix in_foundry: false layout: ontology_detail ontology_purl: http://purl.obolibrary.org/obo/fix.owl products: - id: fix.owl ontology_purl: http://purl.obolibrary.org/obo/fix.owl - id: fix.obo ontology_purl: http://purl.obolibrary.org/obo/fix.obo title: Physico-chemical methods and properties - activity_status: orphaned description: The Mathematical Modelling Ontology (MAMO) is a classification of the types of mathematical models used mostly in the life sciences, their variables, relationships and other relevant features. domain: simulation homepage: http://sourceforge.net/p/mamo-ontology/wiki/Home/ id: mamo layout: ontology_detail license: label: Artistic License 2.0 url: http://opensource.org/licenses/Artistic-2.0 ontology_purl: http://purl.obolibrary.org/obo/mamo.owl preferredPrefix: MAMO products: - id: mamo.owl ontology_purl: http://purl.obolibrary.org/obo/mamo.owl repository: http://sourceforge.net/p/mamo-ontology title: Mathematical modeling ontology tracker: http://sourceforge.net/p/mamo-ontology/tickets/ - activity_status: orphaned description: An ontology of physico-chemical processes, i.e. physico-chemical changes occurring in course of time. domain: chemistry and biochemistry id: rex layout: ontology_detail ontology_purl: http://purl.obolibrary.org/obo/rex.owl products: - id: rex.owl ontology_purl: http://purl.obolibrary.org/obo/rex.owl title: Physico-chemical process - activity_status: orphaned contact: email: cjmungall@lbl.gov label: Chris Mungall orcid: 0000-0002-6601-2165 description: Social Behavior in insects domain: biological systems homepage: https://github.com/obophenotype/sibo id: sibo layout: ontology_detail license: label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/3.0/ ontology_purl: http://purl.obolibrary.org/obo/sibo.owl preferredPrefix: SIBO products: - id: sibo.owl ontology_purl: http://purl.obolibrary.org/obo/sibo.owl - id: sibo.obo ontology_purl: http://purl.obolibrary.org/obo/sibo.obo repository: https://github.com/obophenotype/sibo tags: - behavior title: Social Insect Behavior Ontology tracker: https://github.com/obophenotype/sibo/issues - activity_status: orphaned contact: email: mauno.vihinen@med.lu.se github: maunov label: Mauno Vihinen orcid: 0000-0002-9614-7976 description: Variation Ontology, VariO, is an ontology for standardized, systematic description of effects, consequences and mechanisms of variations. domain: biological systems homepage: http://variationontology.org id: vario layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: https://creativecommons.org/licenses/by/4.0/ ontology_purl: http://purl.obolibrary.org/obo/vario.owl preferredPrefix: VariO products: - id: vario.owl ontology_purl: http://purl.obolibrary.org/obo/vario.owl title: VariO main release in OWL - id: vario.obo ontology_purl: http://purl.obolibrary.org/obo/vario.obo title: VariO in OBO format publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/24162187 title: Variation Ontology for annotation of variation effects and mechanisms - id: https://www.ncbi.nlm.nih.gov/pubmed/24533660 title: 'Variation ontology: annotator guide' - id: https://www.ncbi.nlm.nih.gov/pubmed/25616435 title: Types and effects of protein variations title: Variation Ontology tracker: http://variationontology.org/instructions.shtml - activity_status: inactive contact: email: jiezhen@med.umich.edu github: zhengj2007 label: Jie Zheng orcid: 0000-0002-2999-0103 depicted_by: https://raw.githubusercontent.com/EuPathDB/communitysite/master/assets/images/VEuPathDB-logo-s.png description: An ontology is developed to support Eukaryotic Pathogen, Host & Vector Genomics Resource (VEuPathDB; https://veupathdb.org). domain: organisms homepage: https://github.com/VEuPathDB-ontology/VEuPathDB-ontology id: eupath layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/4.0/ ontology_purl: http://purl.obolibrary.org/obo/eupath.owl preferredPrefix: EUPATH products: - id: eupath.owl ontology_purl: http://purl.obolibrary.org/obo/eupath.owl publications: - id: https://doi.org/10.5281/zenodo.6685957 title: Malaria study data integration and information retrieval based on OBO Foundry ontologies. repository: https://github.com/VEuPathDB-ontology/VEuPathDB-ontology tags: - functional genomics - population biology - clinical epidemiology - microbiomes title: VEuPathDB ontology tracker: https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues usages: - description: The VEuPathDB ontology is used in the VEuPathDB (Eukaryotic Pathogen, Vector & Host Informatics Resources) covers both functional genomics and population biology. type: annotation and query user: https://veupathdb.org - description: The VEuPathDB ontology is used in the clinical epidemiology resources. type: annotation and query user: https://clinepidb.org - description: The VEuPathDB ontology is used in the MicrobiomeDB, a systems biology platform for integrating, mining and analyzing microbiome experiments. type: annotation and query user: https://microbiomedb.org - activity_status: inactive contact: email: druzinsk@uic.edu github: RDruzinsky label: Robert Druzinsky orcid: 0000-0002-1572-1316 dependencies: - id: uberon description: The Mammalian Feeding Muscle Ontology is an antomy ontology for the muscles of the head and neck that participate in feeding, swallowing, and other oral-pharyngeal behaviors. domain: anatomy and development homepage: https://github.com/rdruzinsky/feedontology id: mfmo layout: ontology_detail license: label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/3.0/ ontology_purl: http://purl.obolibrary.org/obo/mfmo.owl preferredPrefix: MFMO products: - id: mfmo.owl ontology_purl: http://purl.obolibrary.org/obo/mfmo.owl repository: https://github.com/RDruzinsky/feedontology taxon: id: NCBITaxon:40674 label: Mammalian title: Mammalian Feeding Muscle Ontology tracker: https://github.com/RDruzinsky/feedontology/issues - activity_status: inactive contact: email: carrine.blank@umontana.edu github: carrineblank label: Carrine Blank orcid: 0000-0002-2100-6351 description: An ontology of prokaryotic phenotypic and metabolic characters domain: phenotype homepage: https://github.com/carrineblank/MicrO id: micro layout: ontology_detail license: label: CC BY 2.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: https://creativecommons.org/licenses/by/2.0/ ontology_purl: http://purl.obolibrary.org/obo/micro.owl preferredPrefix: MICRO products: - id: micro.owl ontology_purl: http://purl.obolibrary.org/obo/micro.owl repository: https://github.com/carrineblank/MicrO title: Ontology of Prokaryotic Phenotypic and Metabolic Characters tracker: https://github.com/carrineblank/MicrO/issues - activity_status: inactive contact: email: linikujp@gmail.com github: linikujp label: Asiyah Yu Lin orcid: 0000-0002-5379-5359 description: An application ontology to represent genetic susceptibility to a specific disease, adverse event, or a pathological process. domain: investigations homepage: https://github.com/linikujp/OGSF id: ogsf layout: ontology_detail license: label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: https://creativecommons.org/licenses/by/3.0/ ontology_purl: http://purl.obolibrary.org/obo/ogsf.owl preferredPrefix: OGSF products: - id: ogsf.owl ontology_purl: http://purl.obolibrary.org/obo/ogsf.owl repository: https://github.com/linikujp/OGSF title: Ontology of Genetic Susceptibility Factor tracker: https://github.com/linikujp/OGSF/issues - activity_status: inactive contact: email: frederic.bastian@unil.ch github: fbastian label: Frédéric Bastian orcid: 0000-0002-9415-5104 description: Life cycle stages for Medaka domain: anatomy and development homepage: https://github.com/obophenotype/developmental-stage-ontologies/wiki/OlatDv id: olatdv layout: ontology_detail license: label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/3.0/ ontology_purl: http://purl.obolibrary.org/obo/olatdv.owl page: https://github.com/obophenotype/developmental-stage-ontologies preferredPrefix: OlatDv products: - id: olatdv.obo ontology_purl: http://purl.obolibrary.org/obo/olatdv.obo - id: olatdv.owl ontology_purl: http://purl.obolibrary.org/obo/olatdv.owl repository: https://github.com/obophenotype/developmental-stage-ontologies title: Medaka Developmental Stages tracker: https://github.com/obophenotype/developmental-stage-ontologies/issues - activity_status: inactive contact: email: frederic.bastian@unil.ch github: fbastian label: Frédéric Bastian orcid: 0000-0002-9415-5104 description: Life cycle stages for Platynereis dumerilii domain: anatomy and development homepage: https://github.com/obophenotype/developmental-stage-ontologies/wiki/PdumDv id: pdumdv layout: ontology_detail license: label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/3.0/ ontology_purl: http://purl.obolibrary.org/obo/pdumdv.owl page: https://github.com/obophenotype/developmental-stage-ontologies preferredPrefix: PdumDv products: - id: pdumdv.owl ontology_purl: http://purl.obolibrary.org/obo/pdumdv.owl - id: pdumdv.obo ontology_purl: http://purl.obolibrary.org/obo/pdumdv.obo repository: https://github.com/obophenotype/developmental-stage-ontologies title: Platynereis Developmental Stages tracker: https://github.com/obophenotype/developmental-stage-ontologies/issues - activity_status: inactive contact: email: J.Bard@ed.ac.uk label: Jonathan Bard description: AEO is an ontology of anatomical structures that expands CARO, the Common Anatomy Reference Ontology domain: anatomy and development homepage: https://github.com/obophenotype/human-developmental-anatomy-ontology/ id: aeo layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: https://creativecommons.org/licenses/by/4.0/ ontology_purl: http://purl.obolibrary.org/obo/aeo.owl preferredPrefix: AEO products: - id: aeo.owl ontology_purl: http://purl.obolibrary.org/obo/aeo.owl repository: https://github.com/obophenotype/human-developmental-anatomy-ontology title: Anatomical Entity Ontology tracker: https://github.com/obophenotype/human-developmental-anatomy-ontology/issues - activity_status: inactive contact: email: cjmungall@lbl.gov github: cmungall label: Chris Mungall orcid: 0000-0002-6601-2165 description: An anatomical and developmental ontology for cephalopods domain: anatomy and development homepage: https://github.com/obophenotype/cephalopod-ontology id: ceph layout: ontology_detail license: label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/3.0/ ontology_purl: http://purl.obolibrary.org/obo/ceph.owl products: - id: ceph.owl ontology_purl: http://purl.obolibrary.org/obo/ceph.owl title: main version - id: ceph.obo ontology_purl: http://purl.obolibrary.org/obo/ceph.obo title: oboformat edition repository: https://github.com/obophenotype/cephalopod-ontology taxon: id: NCBITaxon:6605 label: Cephalopod title: Cephalopod Ontology tracker: https://github.com/obophenotype/cephalopod-ontology/issues - activity_status: inactive contact: email: J.Bard@ed.ac.uk label: Jonathan Bard dependencies: - id: aeo - id: caro - id: cl description: A structured controlled vocabulary of stage-specific anatomical structures of the developing human. domain: anatomy and development homepage: https://github.com/obophenotype/human-developmental-anatomy-ontology id: ehdaa2 layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: https://creativecommons.org/licenses/by/4.0/ ontology_purl: http://purl.obolibrary.org/obo/ehdaa2.owl products: - id: ehdaa2.owl ontology_purl: http://purl.obolibrary.org/obo/ehdaa2.owl - id: ehdaa2.obo ontology_purl: http://purl.obolibrary.org/obo/ehdaa2.obo publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/22973865 title: A new ontology (structured hierarchy) of human developmental anatomy for the first 7 weeks (Carnegie stages 1-20). repository: https://github.com/obophenotype/human-developmental-anatomy-ontology taxon: id: NCBITaxon:9606 label: Homo sapiens title: Human developmental anatomy, abstract tracker: https://github.com/obophenotype/human-developmental-anatomy-ontology/issues - activity_status: inactive contact: email: mejino@u.washington.edu label: Onard Mejino description: This is currently a slimmed down version of FMA domain: anatomy and development homepage: http://si.washington.edu/projects/fma id: fma layout: ontology_detail license: label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: https://creativecommons.org/licenses/by/3.0/ ontology_purl: http://purl.obolibrary.org/obo/fma.owl page: http://en.wikipedia.org/wiki/Foundational_Model_of_Anatomy preferredPrefix: FMA products: - id: fma.owl ontology_purl: http://purl.obolibrary.org/obo/fma.owl publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/18688289 title: Translating the Foundational Model of Anatomy into OWL - id: https://www.ncbi.nlm.nih.gov/pubmed/18360535 title: 'The foundational model of anatomy in OWL: Experience and perspectives' - id: https://www.ncbi.nlm.nih.gov/pubmed/16779026 title: 'Challenges in converting frame-based ontology into OWL: the Foundational Model of Anatomy case-study' repository: https://bitbucket.org/uwsig/fma taxon: id: NCBITaxon:9606 label: Homo sapiens title: Foundational Model of Anatomy Ontology (subset) tracker: https://bitbucket.org/uwsig/fma/issues - activity_status: inactive contact: email: topalis@imbb.forth.gr label: Pantelis Topalis description: An application ontology to cover all aspects of malaria as well as the intervention attempts to control it. domain: health homepage: https://www.vectorbase.org/ontology-browser id: idomal layout: ontology_detail license: label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png url: https://creativecommons.org/publicdomain/zero/1.0/ ontology_purl: http://purl.obolibrary.org/obo/idomal.owl products: - id: idomal.owl ontology_purl: http://purl.obolibrary.org/obo/idomal.owl - id: idomal.obo ontology_purl: http://purl.obolibrary.org/obo/idomal.obo repository: https://github.com/VEuPathDB-ontology/IDOMAL title: Malaria Ontology - activity_status: inactive contact: email: louis@imbb.forth.gr label: Christos (Kitsos) Louis description: Application ontology for entities related to insecticide resistance in mosquitos domain: environment id: miro layout: ontology_detail ontology_purl: http://purl.obolibrary.org/obo/miro.owl products: - id: miro.owl ontology_purl: http://purl.obolibrary.org/obo/miro.owl - id: miro.obo ontology_purl: http://purl.obolibrary.org/obo/miro.obo repository: https://github.com/VEuPathDB-ontology/MIRO taxon: id: NCBITaxon:44484 label: Anopheles title: Mosquito insecticide resistance - activity_status: inactive browsers: - label: RNAO title: RNA Ontology jOWL Browser url: http://bgsu-rna.github.io/rnao/ contact: email: BatchelorC@rsc.org label: Colin Batchelor orcid: 0000-0001-5985-7429 description: Controlled vocabulary pertaining to RNA function and based on RNA sequences, secondary and three-dimensional structures. domain: chemistry and biochemistry homepage: https://github.com/bgsu-rna/rnao id: rnao layout: ontology_detail license: label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png url: https://creativecommons.org/publicdomain/zero/1.0/ ontology_purl: http://purl.obolibrary.org/obo/rnao.owl products: - id: rnao.owl ontology_purl: http://purl.obolibrary.org/obo/rnao.owl - id: rnao.obo ontology_purl: http://purl.obolibrary.org/obo/rnao.obo repository: https://github.com/BGSU-RNA/rnao tags: - molecular structure title: RNA ontology tracker: https://github.com/BGSU-RNA/rnao/issues - activity_status: inactive contact: email: dsonensh@odu.edu label: Daniel Sonenshine description: 'The anatomy of the Tick, Families: Ixodidae, Argassidae' domain: anatomy and development homepage: https://www.vectorbase.org/ontology-browser id: tads layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: https://creativecommons.org/licenses/by/4.0/ ontology_purl: http://purl.obolibrary.org/obo/tads.owl products: - id: tads.owl ontology_purl: http://purl.obolibrary.org/obo/tads.owl - id: tads.obo ontology_purl: http://purl.obolibrary.org/obo/tads.obo repository: https://github.com/VEuPathDB-ontology/TADS taxon: id: NCBITaxon:6939 label: Ixodidae title: Tick Anatomy Ontology - activity_status: inactive contact: email: topalis@imbb.forth.gr label: Pantelis Topalis description: A structured controlled vocabulary of the anatomy of mosquitoes. domain: anatomy and development homepage: https://www.vectorbase.org/ontology-browser id: tgma layout: ontology_detail license: label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png url: https://creativecommons.org/publicdomain/zero/1.0/ ontology_purl: http://purl.obolibrary.org/obo/tgma.owl products: - id: tgma.owl ontology_purl: http://purl.obolibrary.org/obo/tgma.owl - id: tgma.obo ontology_purl: http://purl.obolibrary.org/obo/tgma.obo repository: https://github.com/VEuPathDB-ontology/TGMA taxon: id: NCBITaxon:44484 label: Anopheles title: Mosquito gross anatomy ontology - activity_status: inactive contact: email: Anne.Morgat@sib.swiss github: amorgat label: Anne Morgat orcid: 0000-0002-1216-2969 dependencies: - id: ro description: A manually curated resource for the representation and annotation of metabolic pathways domain: biological systems homepage: https://github.com/geneontology/unipathway id: upa layout: ontology_detail license: label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/3.0/ ontology_purl: http://purl.obolibrary.org/obo/upa.owl products: - id: upa.owl ontology_purl: http://purl.obolibrary.org/obo/upa.owl - id: upa.obo ontology_purl: http://purl.obolibrary.org/obo/upa.obo publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/22102589 title: 'UniPathway: a resource for the exploration and annotation of metabolic pathways' repository: https://github.com/geneontology/unipathway tags: - pathways title: Unipathway tracker: https://github.com/geneontology/unipathway/issues - activity_status: inactive contact: email: david.c.blackburn@gmail.com label: David Blackburn orcid: 0000-0002-1810-9886 domain: anatomy and development homepage: http://github.com/seger/aao id: aao is_obsolete: true layout: ontology_detail replaced_by: uberon taxon: id: NCBITaxon:8292 label: Amphibia title: Amphibian gross anatomy - activity_status: inactive contact: email: adw_geeks@umich.edu label: Animal Diversity Web technical staff domain: organisms homepage: http://www.animaldiversity.org id: adw is_obsolete: true layout: ontology_detail title: Animal natural history and life history - activity_status: inactive contact: email: mcourtot@gmail.com label: Melanie Courtot orcid: 0000-0002-9551-6370 description: The Adverse Event Reporting Ontology (AERO) is an ontology aimed at supporting clinicians at the time of data entry, increasing quality and accuracy of reported adverse events domain: health homepage: http://purl.obolibrary.org/obo/aero id: aero is_obsolete: true layout: ontology_detail license: label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/3.0/ products: - id: aero.owl ontology_purl: http://purl.obolibrary.org/obo/aero.owl title: Adverse Event Reporting Ontology - activity_status: inactive contact: email: david.c.blackburn@gmail.com label: David Blackburn orcid: 0000-0002-1810-9886 domain: organisms homepage: http://www.amphibanat.org id: ato is_obsolete: true layout: ontology_detail taxon: id: NCBITaxon:8292 label: Amphibia title: Amphibian taxonomy - activity_status: inactive contact: email: jiezheng@pennmedicine.upenn.edu github: zhengj2007 label: Jie Zheng orcid: 0000-0002-2999-0103 description: An application ontology built for beta cell genomics studies. domain: anatomy and development homepage: https://github.com/obi-bcgo/bcgo id: bcgo in_foundry: false is_obsolete: true layout: ontology_detail license: label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/3.0/ products: - id: bcgo.owl ontology_purl: http://purl.obolibrary.org/obo/bcgo.owl repository: https://github.com/obi-bcgo/bcgo title: Beta Cell Genomics Ontology tracker: https://github.com/obi-bcgo/bcgo/issues - activity_status: inactive contact: email: henrich@embl.de github: ThorstenHen label: Thorsten Henrich orcid: 0000-0002-1548-3290 domain: anatomy and development homepage: http://4dx.embl.de/4DXpress id: bila is_obsolete: true layout: ontology_detail products: - id: bila.owl ontology_purl: http://purl.obolibrary.org/obo/bila.owl replaced_by: uberon taxon: id: NCBITaxon:33213 label: Bilateria title: Bilateria anatomy - activity_status: inactive contact: email: vlee@ebi.ac.uk label: Vivian Lee domain: chemistry and biochemistry homepage: http://www.ebi.ac.uk/Rebholz-srv/GRO/GRO.html id: bootstrep is_obsolete: true layout: ontology_detail replaced_by: molecular_function title: Gene Regulation Ontology - activity_status: inactive contact: email: haendel@ohsu.edu github: mellybelly label: Melissa Haendel orcid: 0000-0001-9114-8737 description: An upper level ontology to facilitate interoperability between existing anatomy ontologies for different species domain: anatomy and development homepage: https://github.com/obophenotype/caro/ id: caro is_obsolete: true layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: https://creativecommons.org/licenses/by/4.0/ preferredPrefix: CARO products: - id: caro.owl ontology_purl: http://purl.obolibrary.org/obo/caro.owl repository: https://github.com/obophenotype/caro title: Common Anatomy Reference Ontology tracker: https://github.com/obophenotype/caro/issues - activity_status: inactive contact: email: engelsta@ohsu.edu label: Mark Engelstad orcid: 0000-0001-5889-4463 domain: health homepage: https://code.google.com/p/craniomaxillofacial-ontology/ id: cmf is_obsolete: true layout: ontology_detail title: CranioMaxilloFacial ontology - activity_status: inactive contact: email: Lindsay.Cowell@utsouthwestern.edu label: Lindsay Cowell orcid: 0000-0003-1617-8244 domain: anatomy and development homepage: http://www.dukeontologygroup.org/Projects.html id: dc_cl is_obsolete: true layout: ontology_detail replaced_by: cl taxon: id: all label: null title: Dendritic cell - activity_status: inactive contact: email: maria.herrero@kcl.ac.uk label: Maria Herrero description: A formal represention for drug-drug interactions knowledge. domain: health homepage: http://labda.inf.uc3m.es/doku.php?id=es:labda_dinto id: dinto is_obsolete: true layout: ontology_detail license: label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: https://creativecommons.org/licenses/by/3.0/ products: - id: dinto.owl ontology_purl: http://purl.obolibrary.org/obo/dinto.owl publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/26147071 title: 'DINTO: Using OWL Ontologies and SWRL Rules to Infer Drug–Drug Interactions and Their Mechanisms.' repository: https://github.com/labda/DINTO title: The Drug-Drug Interactions Ontology tracker: https://github.com/labda/DINTO/issues - activity_status: inactive contact: email: J.Bard@ed.ac.uk label: Jonathan Bard domain: anatomy and development homepage: http://genex.hgu.mrc.ac.uk/ id: ehda is_obsolete: true layout: ontology_detail replaced_by: ehdaa2 taxon: id: NCBITaxon:9606 label: Homo sapiens title: Human developmental anatomy, timed version - activity_status: inactive contact: email: J.Bard@ed.ac.uk label: Jonathan Bard domain: anatomy and development homepage: null id: ehdaa is_obsolete: true layout: ontology_detail replaced_by: ehdaa2 taxon: id: NCBITaxon:9606 label: Homo sapiens title: Human developmental anatomy, abstract version - activity_status: inactive contact: email: Terry.Hayamizu@jax.org github: tfhayamizu label: Terry Hayamizu orcid: 0000-0002-0956-8634 description: A structured controlled vocabulary of stage-specific anatomical structures of the mouse (Mus). domain: anatomy and development homepage: http://emouseatlas.org id: emap is_obsolete: true layout: ontology_detail page: https://www.emouseatlas.org/emap/about/what_is_emap.html products: - id: emap.owl ontology_purl: http://purl.obolibrary.org/obo/emap.owl replaced_by: emapa taxon: id: NCBITaxon:10088 label: Mus title: Mouse gross anatomy and development, timed - activity_status: inactive contact: email: jaiswalp@science.oregonstate.edu github: jaiswalp label: Pankaj Jaiswal orcid: 0000-0002-1005-8383 depicted_by: http://planteome.org/sites/default/files/garland_logo.PNG description: A structured, controlled vocabulary which describes the treatments, growing conditions, and/or study types used in plant biology experiments. domain: environment homepage: http://planteome.org/ id: eo is_obsolete: true layout: ontology_detail license: label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: https://creativecommons.org/licenses/by/4.0/ page: http://browser.planteome.org/amigo/term/EO:0007359 products: - id: eo.owl ontology_purl: http://purl.obolibrary.org/obo/eo.owl - id: eo.obo ontology_purl: http://purl.obolibrary.org/obo/eo.obo publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/22847540 title: Ontologies as integrative tools for plant science. replaced_by: peco repository: https://github.com/Planteome/plant-environment-ontology title: Plant Environment Ontology tracker: https://github.com/Planteome/plant-environment-ontology/issues usages: - description: Planteome uses EO to describe traits for genes and germplasm examples: - description: Genes and proteins annotated to cold temperature regiment url: http://browser.planteome.org/amigo/term/EO:0007174 user: http://planteome.org/ - description: Gramene uses EO for the annotation of plant genes and QTLs examples: - description: Gramene annotations to cold temperature regiment url: http://archive.gramene.org/db/ontology/search?id=EO:0007174 user: http://gramene.org/ - activity_status: inactive description: An ontology designed to support the semantic annotation of epidemiology resources domain: health homepage: https://code.google.com/p/epidemiology-ontology/ id: epo in_foundry: false is_obsolete: true layout: ontology_detail products: - id: epo.owl ontology_purl: http://purl.obolibrary.org/obo/epo.owl title: Epidemiology Ontology - activity_status: inactive contact: email: Marc_Ciriello@hms.harvard.edu label: Marc Ciriello description: An ontology of research resources such as instruments. protocols, reagents, animal models and biospecimens. domain: information homepage: https://open.med.harvard.edu/wiki/display/eaglei/Ontology id: ero is_obsolete: true layout: ontology_detail license: label: CC BY 2.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: https://creativecommons.org/licenses/by/2.0/ products: - id: ero.owl ontology_purl: http://purl.obolibrary.org/obo/ero.owl tags: - resources title: eagle-i resource ontology - activity_status: inactive contact: email: evoc@sanbi.ac.za label: eVOC mailing list domain: anatomy and development id: ev is_obsolete: true layout: ontology_detail title: eVOC (Expressed Sequence Annotation for Humans) - activity_status: inactive contact: email: cp390@cam.ac.uk github: Clare72 label: Clare Pilgrim orcid: 0000-0002-1373-1705 description: The taxonomy of the family Drosophilidae (largely after Baechli) and of other taxa referred to in FlyBase. domain: organisms homepage: http://www.flybase.org/ id: fbsp is_obsolete: true layout: ontology_detail products: - id: fbsp.owl ontology_purl: http://purl.obolibrary.org/obo/fbsp.owl tags: - taxonomy taxon: id: NCBITaxon:7227 label: Drosophila title: Fly taxonomy - activity_status: inactive contact: email: burkesquires@gmail.com label: Burke Squires domain: health homepage: http://purl.obolibrary.org/obo/flu/ id: flu in_foundry: false is_obsolete: true layout: ontology_detail products: - id: flu.owl ontology_purl: http://purl.obolibrary.org/obo/flu.owl title: Influenza Ontology tracker: http://purl.obolibrary.org/obo/flu/tracker - activity_status: inactive contact: email: po-discuss@plantontology.org label: Plant Ontology Administrators domain: anatomy and development homepage: http://www.gramene.org/plant_ontology/ id: gro is_obsolete: true layout: ontology_detail title: Cereal Plant Gross Anatomy - activity_status: inactive contact: email: peteremidford@yahoo.com label: Peter Midford orcid: 0000-0001-6512-3296 domain: organisms homepage: http://www.mesquiteproject.org/ontology/Habronattus/index.html id: habronattus is_obsolete: true layout: ontology_detail title: Habronattus courtship - activity_status: inactive domain: chemistry and biochemistry homepage: http://www.inoh.org id: iev is_obsolete: true layout: ontology_detail title: Event (INOH pathway ontology) - activity_status: inactive contact: email: curator@inoh.org label: INOH curators domain: chemistry and biochemistry homepage: http://www.inoh.org id: imr is_obsolete: true layout: ontology_detail title: Molecule role (INOH Protein name/family name ontology) - activity_status: inactive contact: email: interhelp@ebi.ac.uk label: InterPro Help domain: chemistry and biochemistry homepage: http://www.ebi.ac.uk/interpro/index.html id: ipr is_obsolete: true layout: ontology_detail title: Protein Domains - activity_status: inactive contact: email: bakerc@unb.ca label: Christopher Baker orcid: 0000-0003-4004-6479 description: An ontology representation of the LIPIDMAPS nomenclature classification. domain: chemistry and biochemistry id: lipro in_foundry: false is_obsolete: true layout: ontology_detail tags: - lipids title: Lipid Ontology - activity_status: inactive contact: email: peteremidford@yahoo.com label: Peter Midford orcid: 0000-0001-6512-3296 domain: organisms homepage: http://www.mesquiteproject.org/ontology/Loggerhead/index.html id: loggerhead is_obsolete: true layout: ontology_detail title: Loggerhead nesting - activity_status: inactive contact: email: julie@igbmc.u-strasbg.fr label: Julie Thompson domain: chemistry and biochemistry homepage: http://www-igbmc.u-strasbg.fr/BioInfo/MAO/mao.html id: mao is_obsolete: true layout: ontology_detail title: Multiple alignment - activity_status: inactive contact: email: j.bard@ed.ac.uk label: Jonathan Bard domain: anatomy and development homepage: null id: mat is_obsolete: true layout: ontology_detail title: Minimal anatomical terminology - activity_status: inactive contact: email: henrich@embl.de github: ThorstenHen label: Thorsten Henrich orcid: 0000-0002-1548-3290 description: A structured controlled vocabulary of the anatomy and development of the Japanese medaka fish, Oryzias latipes. domain: anatomy and development id: mfo is_obsolete: true layout: ontology_detail products: - id: mfo.owl ontology_purl: http://purl.obolibrary.org/obo/mfo.owl replaced_by: olatdv taxon: id: NCBITaxon:8089 label: Oryzias title: Medaka fish anatomy and development - activity_status: inactive contact: email: topalis@imbb.forth.gr label: Pantelis Topalis description: An application ontology for use with miRNA databases. domain: chemistry and biochemistry homepage: http://code.google.com/p/mirna-ontology/ id: mirnao is_obsolete: true layout: ontology_detail license: label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png url: https://creativecommons.org/publicdomain/zero/1.0/ products: - id: mirnao.owl ontology_purl: http://purl.obolibrary.org/obo/mirnao.owl title: microRNA Ontology - activity_status: inactive contact: email: stoeckrt@pcbi.upenn.edu label: Chris Stoeckert orcid: 0000-0002-5714-991X description: A standardized description of a microarray experiment in support of MAGE v.1. domain: investigations homepage: http://mged.sourceforge.net/ontologies/MGEDontology.php id: mo is_obsolete: true layout: ontology_detail page: http://mged.sourceforge.net/software/downloads.php products: - id: mo.owl ontology_purl: http://purl.obolibrary.org/obo/mo.owl replaced_by: obi title: Microarray experimental conditions - activity_status: inactive contact: email: smtifahim@gmail.com label: Fahim Imam orcid: 0000-0003-4752-543X description: Neuronal cell types domain: anatomy and development homepage: http://neuinfo.org/ id: nif_cell is_obsolete: true layout: ontology_detail replaced_by: cl title: NIF Cell - activity_status: inactive contact: email: smtifahim@gmail.com label: Fahim Imam orcid: 0000-0003-4752-543X domain: health homepage: http://neuinfo.org/ id: nif_dysfunction is_obsolete: true layout: ontology_detail replaced_by: doid title: NIF Dysfunction - activity_status: inactive contact: email: smtifahim@gmail.com label: Fahim Imam orcid: 0000-0003-4752-543X domain: anatomy and development homepage: http://neuinfo.org/ id: nif_grossanatomy is_obsolete: true layout: ontology_detail replaced_by: uberon title: NIF Gross Anatomy - activity_status: inactive contact: email: schober@imbi.uni-freiburg.de label: Schober Daniel description: Descriptors relevant to the experimental conditions of the Nuclear Magnetic Resonance (NMR) component in a metabolomics investigation. domain: investigations homepage: http://msi-ontology.sourceforge.net/ id: nmr is_obsolete: true layout: ontology_detail page: http://msi-ontology.sourceforge.net/ontology/NMR.owlDocument.doc products: - id: nmr.owl ontology_purl: http://purl.obolibrary.org/obo/nmr.owl title: NMR-instrument specific component of metabolomics investigations - activity_status: inactive contact: email: cjmungall@lbl.gov label: Chris Mungall orcid: 0000-0002-6601-2165 domain: upper homepage: http://www.obofoundry.org/ro id: obo_rel is_obsolete: true layout: ontology_detail replaced_by: ro title: OBO relationship types (legacy) - activity_status: inactive contact: email: linikujp@gmail.com github: linikujp label: Asiyah Yu Lin orcid: 0000-0002-5379-5359 description: An ontology that formalizes the genomic element by defining an upper class genetic interval domain: chemistry and biochemistry homepage: https://code.google.com/p/ontology-for-genetic-interval/ id: ogi is_obsolete: true layout: ontology_detail products: - id: ogi.owl ontology_purl: http://purl.obolibrary.org/obo/ogi.owl replaced_by: ogsf title: Ontology for genetic interval tracker: https://code.google.com/p/ontology-for-genetic-interval/issues/list - activity_status: inactive contact: email: mbrochhausen@gmail.com label: Mathias Brochhausen orcid: 0000-0003-1834-3856 description: An ontological version of MIABIS (Minimum Information About BIobank data Sharing) domain: health homepage: https://github.com/OMIABIS/omiabis-dev id: omiabis is_obsolete: true layout: ontology_detail license: label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png url: http://creativecommons.org/licenses/by/3.0/ products: - id: omiabis.owl ontology_purl: http://purl.obolibrary.org/obo/omiabis.owl repository: https://github.com/OMIABIS/omiabis-dev title: Ontologized MIABIS tracker: https://github.com/OMIABIS/omiabis-dev/issues - activity_status: inactive contact: email: jaiswalp@science.oregonstate.edu github: jaiswalp label: Pankaj Jaiswal orcid: 0000-0002-1005-8383 domain: anatomy and development homepage: http://www.plantontology.org id: pao is_obsolete: true layout: ontology_detail taxon: id: NCBITaxon:33090 label: Viridiplantae title: Plant Anatomy Ontology - activity_status: inactive contact: email: henrich@embl.de github: ThorstenHen label: Thorsten Henrich orcid: 0000-0002-1548-3290 domain: anatomy and development homepage: http://4dx.embl.de/platy id: pd_st is_obsolete: true layout: ontology_detail replaced_by: pdumdv taxon: id: NCBITaxon:6358 label: Platynereis title: Platynereis stage ontology - activity_status: inactive contact: email: po-discuss@plantontology.org label: Plant Ontology Administrators domain: anatomy and development homepage: http://www.plantontology.org id: pgdso is_obsolete: true layout: ontology_detail taxon: id: NCBITaxon:33090 label: Viridiplantae title: Plant Growth and Development Stage - activity_status: inactive contact: email: mb4@sanger.ac.uk label: Matt Berriman domain: anatomy and development homepage: http://www.sanger.ac.uk/Users/mb4/PLO/ id: plo is_obsolete: true layout: ontology_detail title: Plasmodium life cycle - activity_status: inactive contact: email: satya30@uga.edu label: Satya S. Sahoo domain: chemistry and biochemistry homepage: http://lsdis.cs.uga.edu/projects/glycomics/propreo/ id: propreo is_obsolete: true layout: ontology_detail title: Proteomics data and process provenance - activity_status: inactive contact: email: john.garavelli@ebi.ac.uk label: John Garavelli orcid: 0000-0002-4131-735X description: For the description of covalent bonds in proteins. domain: chemistry and biochemistry homepage: http://www.ebi.ac.uk/RESID/ id: resid is_obsolete: true layout: ontology_detail tags: - proteins title: Protein covalent bond - activity_status: inactive contact: email: slarson@ncmir.ucsd.edu label: Stephen Larson domain: anatomy and development homepage: http://ccdb.ucsd.edu/CCDBWebSite/sao.html id: sao is_obsolete: true layout: ontology_detail replaced_by: go taxon: id: NCBITaxon:9606 label: Homo sapiens title: Subcellular anatomy ontology - activity_status: inactive contact: email: psidev-gps-dev@lists.sourceforge.net label: SEP developers via the PSI and MSI mailing lists description: A structured controlled vocabulary for the annotation of sample processing and separation techniques in scientific experiments. domain: investigations homepage: http://psidev.info/index.php?q=node/312 id: sep is_obsolete: true layout: ontology_detail page: http://psidev.info/index.php?q=node/312 products: - id: sep.owl ontology_purl: http://purl.obolibrary.org/obo/sep.owl tags: - provenance title: Sample processing and separation techniques - activity_status: inactive contact: email: Adrien.Coulet@loria.fr label: Adrien Coulet domain: chemistry and biochemistry homepage: http://www.loria.fr/~coulet/sopharm2.0_description.php id: sopharm is_obsolete: true layout: ontology_detail taxon: id: NCBITaxon:9606 label: Homo sapiens title: Suggested Ontology for Pharmacogenomics - activity_status: inactive contact: email: pierre.sprumont@unifr.ch label: Pierre Sprumont domain: anatomy and development homepage: null id: tahe is_obsolete: true layout: ontology_detail taxon: id: NCBITaxon:9606 label: Homo sapiens title: Terminology of Anatomy of Human Embryology - activity_status: inactive contact: email: pierre.sprumont@unifr.ch label: Pierre Sprumont domain: health homepage: null id: tahh is_obsolete: true layout: ontology_detail taxon: id: NCBITaxon:9606 label: Homo sapiens title: Terminology of Anatomy of Human Histology - activity_status: inactive contact: email: wasila.dahdul@usd.edu label: Wasila Dahdul orcid: 0000-0003-3162-7490 description: Multispecies fish anatomy ontology. Originally seeded from ZFA, but intended to cover terms relevant to other taxa domain: anatomy and development homepage: http://wiki.phenoscape.org/wiki/Teleost_Anatomy_Ontology id: tao is_obsolete: true layout: ontology_detail license: label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png url: http://creativecommons.org/publicdomain/zero/1.0/ products: - id: tao.owl ontology_purl: http://purl.obolibrary.org/obo/tao.owl publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/20547776 title: 'The teleost anatomy ontology: anatomical representation for the genomics age' replaced_by: uberon taxon: id: NCBITaxon:32443 label: Teleostei title: Teleost Anatomy Ontology - activity_status: inactive depicted_by: http://bgee.org/img/logo/bgee13_logo.png domain: anatomy and development id: vhog is_obsolete: true layout: ontology_detail products: - id: vhog.owl ontology_purl: http://purl.obolibrary.org/obo/vhog.owl replaced_by: uberon title: Vertebrate Homologous Ontology Group Ontology - activity_status: inactive contact: email: wasila.dahdul@usd.edu label: Wasila Dahdul orcid: 0000-0003-3162-7490 description: Vertebrate skeletal anatomy ontology. domain: anatomy and development homepage: https://www.nescent.org/phenoscape/Main_Page id: vsao is_obsolete: true layout: ontology_detail page: https://www.phenoscape.org/wiki/Skeletal_Anatomy_Jamboree products: - id: vsao.owl ontology_purl: http://purl.obolibrary.org/obo/vsao.owl replaced_by: uberon taxon: id: NCBITaxon:7742 label: Vertebrata title: Vertebrate Skeletal Anatomy Ontology- - activity_status: inactive contact: email: cherry@genome.stanford.edu label: Mike Cherry orcid: 0000-0001-9163-5180 domain: phenotype homepage: http://www.yeastgenome.org/ id: ypo is_obsolete: true layout: ontology_detail replaced_by: apo taxon: id: NCBITaxon:4932 label: Saccharomyces cerevisiae title: Yeast phenotypes - activity_status: inactive contact: email: Leszek@missouri.edu label: Leszek Vincent orcid: 0000-0002-9316-2919 domain: anatomy and development homepage: http://www.maizemap.org/ id: zea is_obsolete: true layout: ontology_detail taxon: id: NCBITaxon:4575 label: Zea title: Maize gross anatomy