ontologies: Alzheimer's Disease Ontology
  activity status: active
  contact:
    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
    url: https://creativecommons.org/licenses/by/4.0/
  ontology purl: http://purl.obolibrary.org/obo/ado.owl
  preferred prefix: ADO
  products:
    id: ado.owl
    ontology purl: http://purl.obolibrary.org/obo/ado.owl
  repository: https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO
  tracker: https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO/issues
ontologies: African Population Ontology
  activity status: active
  contact:
    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
    url: https://creativecommons.org/licenses/by/4.0/
  ontology purl: http://purl.obolibrary.org/obo/afpo.owl
  preferred prefix: AfPO
  products: AfPO (OWL edition)
    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
  products: AfPO (OBO 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
  products: AfPO (obographs JSON 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
  repository: https://github.com/h3abionet/afpo
  tags: ancestry
  tracker: https://github.com/h3abionet/afpo/issues
ontologies: Agronomy Ontology
  activity status: active
  contact:
    github: marieALaporte
    label: Marie-Angélique Laporte
    orcid: 0000-0002-8461-9745
  dependencies:
    id: bfo
  dependencies:
    id: envo
  dependencies:
    id: foodon
  dependencies:
    id: go
  dependencies:
    id: iao
  dependencies:
    id: ncbitaxon
  dependencies:
    id: obi
  dependencies:
    id: pato
  dependencies:
    id: peco
  dependencies:
    id: po
  dependencies:
    id: ro
  dependencies:
    id: to
  dependencies:
    id: uo
  dependencies:
    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
    url: https://creativecommons.org/licenses/by/4.0/
  ontology purl: http://purl.obolibrary.org/obo/agro.owl
  preferred prefix: AGRO
  products: AgrO
    description: Contains all AgrO terms and links to other relevant ontologies.
    id: agro.owl
    ontology purl: http://purl.obolibrary.org/obo/agro.owl
  publications: Data-driven Agricultural Research for Development: A Need for Data Harmonization Via Semantics.
    id: http://ceur-ws.org/Vol-1747/IT205_ICBO2016.pdf
  repository: https://github.com/AgriculturalSemantics/agro
  tags: agronomy
  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
  usages:
    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/
ontologies: Ontology for the Anatomy of the Insect SkeletoMuscular system (AISM)
  activity status: active
  contact:
    github: JCGiron
    label: Jennifer C. Girón
    orcid: 0000-0002-0851-6883
  dependencies:
    id: bfo
  dependencies:
    id: bspo
  dependencies:
    id: caro
  dependencies:
    id: pato
  dependencies:
    id: ro
  dependencies:
    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
    url: https://creativecommons.org/licenses/by/4.0/
  ontology purl: http://purl.obolibrary.org/obo/aism.owl
  preferred prefix: AISM
  products:
    id: aism.owl
    ontology purl: http://purl.obolibrary.org/obo/aism.owl
  products:
    id: aism.obo
    ontology purl: http://purl.obolibrary.org/obo/aism.obo
  products:
    id: aism.json
    ontology purl: http://purl.obolibrary.org/obo/aism.json
  repository: https://github.com/insect-morphology/aism
  tracker: https://github.com/insect-morphology/aism/issues
ontologies: The Amphioxus Development and Anatomy Ontology
  activity status: active
  contact:
    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
    url: http://creativecommons.org/licenses/by/3.0/
  ontology purl: http://purl.obolibrary.org/obo/amphx.owl
  preferred prefix: AMPHX
  products:
    id: amphx.owl
    ontology purl: http://purl.obolibrary.org/obo/amphx.owl
  products:
    id: amphx.obo
    ontology purl: http://purl.obolibrary.org/obo/amphx.obo
  repository: https://github.com/EBISPOT/amphx_ontology
  tracker: https://github.com/EBISPOT/amphx_ontology/issues
ontologies: Ascomycete phenotype ontology
  activity status: active
  contact:
    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
    url: https://creativecommons.org/licenses/by/4.0/
  ontology purl: http://purl.obolibrary.org/obo/apo.owl
  preferred prefix: APO
  products:
    id: apo.owl
    ontology purl: http://purl.obolibrary.org/obo/apo.owl
  products:
    id: apo.obo
    ontology purl: http://purl.obolibrary.org/obo/apo.obo
  publications: New mutant phenotype data curation system in the Saccharomyces Genome Database
  repository: https://github.com/obophenotype/ascomycete-phenotype-ontology
  tracker: https://github.com/obophenotype/ascomycete-phenotype-ontology/issues
ontologies: Apollo Structured Vocabulary
ontologies: Antibiotic Resistance Ontology
ontologies: Biological Collections Ontology
ontologies: Basic Formal Ontology
ontologies: Biomarker Ontology
ontologies: Biological Spatial Ontology
ontologies: BRENDA tissue / enzyme source
ontologies: Comparative Data Analysis Ontology
ontologies: Compositional Dietary Nutrition Ontology
ontologies: Chemical Entities of Biological Interest
ontologies: Chemical Information Ontology
ontologies: CHEBI Integrated Role Ontology
ontologies: Chemical Methods Ontology
ontologies: Coronavirus Infectious Disease Ontology
ontologies: Confidence Information Ontology
ontologies: Cell Ontology
ontologies: Collembola Anatomy Ontology
ontologies: Cell Line Ontology
ontologies: Clytia hemisphaerica Development and Anatomy Ontology
ontologies: Clinical measurement ontology
ontologies: Core Ontology for Biology and Biomedicine
ontologies: Coleoptera Anatomy Ontology (COLAO)
ontologies: Contributor Role Ontology
ontologies: Ctenophore Ontology
ontologies: CTO: Core Ontology of Clinical Trials
ontologies: Cardiovascular Disease Ontology
ontologies: Dictyostelium discoideum anatomy
ontologies: Dictyostelium discoideum phenotype ontology
ontologies: Drug-drug Interaction and Drug-drug Interaction Evidence Ontology
ontologies: Disease Drivers Ontology
ontologies: Human Disease Ontology
ontologies: Drosophila Phenotype Ontology
ontologies: The Drug Ontology
ontologies: Data Use Ontology
ontologies: The Echinoderm Anatomy and Development Ontology
ontologies: Evidence and Conclusion Ontology
ontologies: An ontology of core ecological entities
ontologies: Environmental conditions, treatments and exposures ontology
ontologies: Mouse Developmental Anatomy Ontology
ontologies: Environment Ontology
ontologies: Epilepsy Ontology
ontologies: Exercise Medicine Ontology
ontologies: Exposure ontology
ontologies: Fungal gross anatomy
ontologies: Biological Imaging Methods Ontology
ontologies: Drosophila gross anatomy
ontologies: FlyBase Controlled Vocabulary
ontologies: Drosophila development
ontologies: Food Interactions with Drugs Evidence Ontology
ontologies: Flora Phenotype Ontology
ontologies: Food-Biomarker Ontology
ontologies: Food Ontology
ontologies: FuTRES Ontology of Vertebrate Traits
ontologies: Fission Yeast Phenotype Ontology
ontologies: Plant Gall Ontology
ontologies: Gazetteer
ontologies: Genomics Cohorts Knowledge Ontology
ontologies: Genomic Epidemiology Ontology
ontologies: Genotype Ontology
ontologies: Geographical Entity Ontology
ontologies: Glycan Naming and Subsumption Ontology (GNOme)
ontologies: Gene Ontology
ontologies: Human Ancestry Ontology
ontologies: Hymenoptera Anatomy Ontology
ontologies: Homology Ontology
ontologies: Human Developmental Stages
ontologies: Health Surveillance Ontology
ontologies: Hypertension Ontology
ontologies: Information Artifact Ontology
ontologies: Integrative and Conjugative Element Ontology
ontologies: Informed Consent Ontology
ontologies: Infectious Disease Ontology
ontologies: Interaction Network Ontology
ontologies: clinical LABoratory Ontology

New mutant phenotype data curation system in the Saccharomyces Genome Database
id: https://www.ncbi.nlm.nih.gov/pubmed/20157474

id: NCBITaxon:4890
label: Ascomycota

Apollo Structured Vocabulary
activity status: active
contact:
  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
  url: https://creativecommons.org/licenses/by/4.0/
ontology purl: http://purl.obolibrary.org/obo/apollo_sv.owl
preferred prefix: APOLLO_SV
products:
  id: apollo_sv.owl
  ontology purl: http://purl.obolibrary.org/obo/apollo_sv.owl
publications: The Apollo Structured Vocabulary: an OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation
  id: https://doi.org/10.1186/s13326-016-0092-y
repository: https://github.com/ApolloDev/apollo-sv
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
  see also: https://midasnetwork.us/catalog/
  type: annotation
  user: https://midasnetwork.us/

Antibiotic Resistance Ontology
activity status: active
contact:
  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
  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
preferred prefix: ARO
products:
  id: aro.owl
  ontology purl: http://purl.obolibrary.org/obo/aro.owl
publications: CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database.
  id: https://www.ncbi.nlm.nih.gov/pubmed/31665441
repository: https://github.com/arpcard/aro
tracker: https://github.com/arpcard/aro/issues

Biological Collections Ontology
activity status: active
contact:
  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
  url: https://creativecommons.org/publicdomain/zero/1.0/
ontology purl: http://purl.obolibrary.org/obo/bco.owl
preferred prefix: BCO
products:
  id: bco.owl
  ontology purl: http://purl.obolibrary.org/obo/bco.owl
publications: Semantics in Support of Biodiversity Knowledge Discovery: An Introduction to the Biological Collections Ontology and Related Ontologies
  id: https://doi.org/10.1371/journal.pone.0089606
repository: https://github.com/BiodiversityOntologies/bco
tags: biodiversity collections
tracker: https://github.com/BiodiversityOntologies/bco/issues

Basic Formal Ontology
activity status: active
browsers: BioPortal Browser
  label: BioPortal
  url: http://bioportal.bioontology.org/ontologies/BFO
contact:
  github: phismith
  label: Barry Smith
  orcid: 0000-0003-1384-116X
depicted by: https://avatars2.githubusercontent.com/u/12972134
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
  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
preferred prefix: BFO
products:
  id: bfo.owl
  ontology purl: http://purl.obolibrary.org/obo/bfo.owl
products:
  id: bfo.obo
  ontology purl: http://purl.obolibrary.org/obo/bfo.obo
repository: https://github.com/BFO-ontology/BFO
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

Biomarker Ontology
activity status: active
browsers: BioPortal Ontology Browser
  label: BioPortal
  url: https://bioportal.bioontology.org/ontologies/BMONT
contact:
  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
  url: http://creativecommons.org/licenses/by/4.0/
ontology purl: http://purl.obolibrary.org/obo/bmont.owl
preferred prefix: 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
tracker: https://github.com/SCAI-BIO/BiomarkerOntology/issues

Biological Spatial Ontology
activity status: active
contact:
  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
  url: http://creativecommons.org/licenses/by/3.0/
ontology purl: http://purl.obolibrary.org/obo/bspo.owl
preferred prefix: BSPO
products:
  id: bspo.owl
  ontology purl: http://purl.obolibrary.org/obo/bspo.owl
products:
  id: bspo.obo
  ontology purl: http://purl.obolibrary.org/obo/bspo.obo
publications: Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology.
  id: https://www.ncbi.nlm.nih.gov/pubmed/25140222
repository: https://github.com/obophenotype/biological-spatial-ontology
tracker: https://github.com/obophenotype/biological-spatial-ontology/issues

BRENDA tissue / enzyme source
activity status: active
contact:
  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
  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
preferred prefix: BTO
products:
  id: bto.owl
  ontology purl: http://purl.obolibrary.org/obo/bto.owl
products:
  id: bto.obo
  ontology purl: http://purl.obolibrary.org/obo/bto.obo
products:
  id: bto.json
  ontology purl: http://purl.obolibrary.org/obo/bto.json
publications: The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources
  id: https://www.ncbi.nlm.nih.gov/pubmed/21030441
repository: https://github.com/BRENDA-Enzymes/BTO
tracker: https://github.com/BRENDA-Enzymes/BTO/issues

Comparative Data Analysis Ontology
activity status: active
contact:
  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
  url: https://creativecommons.org/publicdomain/zero/1.0/
ontology purl: http://purl.obolibrary.org/obo/cdao.owl
preferred prefix: CDAO
products:
  id: cdao.owl
  ontology purl: http://purl.obolibrary.org/obo/cdao.owl
publications: Initial Implementation of a Comparative Data Analysis Ontology
  id: https://doi.org/10.4137/EBO.S2320
repository: https://github.com/evoinfo/cdao
tracker: https://github.com/evoinfo/cdao/issues

Compositional Dietary Nutrition Ontology
activity status: active
contact:
  github: LilyAndres
  label: Liliana Andres Hernandez
  orcid: 0000-0002-7696-731X
dependencies:
  id: bfo
dependencies:
  id: chebi
dependencies:
  id: envo
dependencies:
  id: pato
dependencies:
  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
  url: https://creativecommons.org/licenses/by/3.0/
ontology purl: http://purl.obolibrary.org/obo/cdno.owl
preferred prefix: CDNO
products:
  id: cdno.owl
  name: Compositional Dietary Nutrition Ontology main release in OWL format
  ontology purl: http://purl.obolibrary.org/obo/cdno.owl
products:
  id: cdno.obo
  name: Compositional Dietary Nutrition Ontology additional release in OBO format
  ontology purl: http://purl.obolibrary.org/obo/cdno.obo
publications: Establishing a Common Nutritional Vocabulary - From Food Production to Diet
  id: https://doi.org/10.3389/fnut.2022.928837
repository: https://github.com/CompositionalDietaryNutritionOntology/cdno
tracker: https://github.com/CompositionalDietaryNutritionOntology/cdno/issues

Chemical Entities of Biological Interest
activity status: active
browsers: EBI CHEBI Browser
  label: CHEBI
  url: http://www.ebi.ac.uk/chebi/chebiOntology.do#graphView
contact:
  github: amalik01
  label: Adnan Malik
  orcid: 0000-0001-8123-5351
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
  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
preferred prefix: CHEBI
products:
  id: chebi.owl
  ontology purl: http://purl.obolibrary.org/obo/chebi.owl
products:
  id: chebi.obo
  ontology purl: http://purl.obolibrary.org/obo/chebi.obo
products:
  id: chebi.json
  ontology purl: http://purl.obolibrary.org/obo/chebi.json
products: chebi, compressed owl
  id: chebi.owl.gz
  ontology purl: http://purl.obolibrary.org/obo/chebi.owl.gz
products: chebi_lite, no syns or xrefs
  id: chebi/chebi_lite.obo
  ontology purl: http://purl.obolibrary.org/obo/chebi/chebi_lite.obo
products: chebi_core, no xrefs
  id: chebi/chebi_core.obo
  ontology purl: http://purl.obolibrary.org/obo/chebi/chebi_core.obo
publications: ChEBI: re-engineered for a sustainable future
  id: https://doi.org/10.1093/nar/gkaf1271
publications: ChEBI in 2016: Improved services and an expanding collection of metabolites.
  id: https://www.ncbi.nlm.nih.gov/pubmed/26467479
repository: https://github.com/ebi-chebi/ChEBI
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
  user: https://www.rhea-db.org/
usages:
  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
  user: http://zfin.org

Chemical Information Ontology
activity status: active
contact:
  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
  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
preferred prefix: CHEMINF
products:
  id: cheminf.owl
  ontology purl: http://purl.obolibrary.org/obo/cheminf.owl
publications: The chemical information ontology: provenance and disambiguation for chemical data on the biological semantic web
  id: https://www.ncbi.nlm.nih.gov/pubmed/21991315
repository: https://github.com/semanticchemistry/semanticchemistry
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/
usages:
  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/

CHEBI Integrated Role Ontology
activity status: active
contact:
  github: nicolevasilevsky
  label: Nicole Vasilevsky
  orcid: 0000-0001-5208-3432
dependencies:
  id: chebi
dependencies:
  id: go
dependencies:
  id: hp
dependencies:
  id: mp
dependencies:
  id: ncbitaxon
dependencies:
  id: pr
dependencies:
  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
  url: http://creativecommons.org/publicdomain/zero/1.0/
ontology purl: http://purl.obolibrary.org/obo/chiro.owl
preferred prefix: CHIRO
products:
  id: chiro.owl
  name: CHEBI Integrated Role Ontology main release in OWL format
  ontology purl: http://purl.obolibrary.org/obo/chiro.owl
products:
  id: chiro.obo
  name: CHEBI Integrated Role Ontology additional release in OBO format
  ontology purl: http://purl.obolibrary.org/obo/chiro.obo
publications: Extension of Roles in the ChEBI Ontology
  id: https://doi.org/10.26434/chemrxiv.12591221
repository: https://github.com/obophenotype/chiro
tracker: https://github.com/obophenotype/chiro/issues

Chemical Methods Ontology
activity status: active
contact:
  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
  url: http://creativecommons.org/licenses/by/4.0/
ontology purl: http://purl.obolibrary.org/obo/chmo.owl
preferred prefix: CHMO
products:
  id: chmo.owl
  ontology purl: http://purl.obolibrary.org/obo/chmo.owl
repository: https://github.com/rsc-ontologies/rsc-cmo
tracker: https://github.com/rsc-ontologies/rsc-cmo/issues

Coronavirus Infectious Disease Ontology
activity status: active
contact:
  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
  url: http://creativecommons.org/licenses/by/4.0/
ontology purl: http://purl.obolibrary.org/obo/cido.owl
preferred prefix: CIDO
products:
  id: cido.owl
  ontology purl: http://purl.obolibrary.org/obo/cido.owl
publications: A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology
  id: https://www.ncbi.nlm.nih.gov/pubmed/36271389
repository: https://github.com/cido-ontology/cido
tracker: https://github.com/cido-ontology/cido/issues

Confidence Information Ontology
activity status: active
contact:
  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
  url: https://creativecommons.org/publicdomain/zero/1.0/
ontology purl: http://purl.obolibrary.org/obo/cio.owl
preferred prefix: CIO
products:
  id: cio.owl
  ontology purl: http://purl.obolibrary.org/obo/cio.owl
products:
  id: cio.obo
  ontology purl: http://purl.obolibrary.org/obo/cio.obo
publications: The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations
  id: https://www.ncbi.nlm.nih.gov/pubmed/25957950
repository: https://github.com/BgeeDB/confidence-information-ontology
tracker: https://github.com/BgeeDB/confidence-information-ontology

Cell Ontology
activity status: active
contact:
  github: dosumis
  label: David Osumi-Sutherland
  orcid: 0000-0002-7073-9172
dependencies:
  id: go
dependencies:
  id: ncbitaxon
dependencies:
  id: omo
dependencies:
  id: pato
dependencies:
  id: pr
dependencies:
  id: ro
dependencies:
  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
  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
preferred prefix: CL
products: Main CL OWL edition
  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
  uses: go
  uses: ncbitaxon
  uses: omo
  uses: pato
  uses: pr
  uses: ro
  uses: uberon
products: CL obo format edition
  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
products: CL OBOGraph-JSON 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
products: Basic CL
  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
products: Basic CL (OBO version)
  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
products: Basic CL (OBOGraph-JSON 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
products: CL base module
  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
products: CL base module (OBO version)
  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
products: CL base module (OBOGraph-JSON 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
publications: The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability.
  id: https://www.ncbi.nlm.nih.gov/pubmed/27377652
repository: https://github.com/obophenotype/cell-ontology
tags: cells
taxon:
  id: NCBITaxon:33208
  label: Metazoa
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
  examples:
    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
  publications: Brain Data Standards Ontology: A data-driven ontology of transcriptomically defined cell types in the primary motor cortex
    id: https://doi.org/10.1101/2021.10.10.463703
  type: annotation
  user: https://biccn.org/
usages:
  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
  publications: The human body at cellular resolution: the NIH Human Biomolecular Atlas Program.
    id: https://www.ncbi.nlm.nih.gov/pubmed/31597973
  type: annotation
  user: https://hubmapconsortium.org/
usages:
  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: CELLxGENE: a performant, scalable exploration platform for high dimensional sparse matrices
    id: https://doi.org/10.1101/2021.04.05.438318
  type: annotation
  user: https://cellxgene.cziscience.com/
usages:
  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
  publications: The Human Cell Atlas
    id: https://www.ncbi.nlm.nih.gov/pubmed/29206104
  type: annotation
  user: https://www.humancellatlas.org/
usages:
  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: Expression Atlas update: from tissues to single cells
    id: https://www.ncbi.nlm.nih.gov/pubmed/31665515
  type: annotation
  user: https://www.ebi.ac.uk/gxa/home
usages:
  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: Ontology application and use at the ENCODE DCC
    id: https://www.ncbi.nlm.nih.gov/pubmed/25776021
  see also: https://doi.org/10.25504/FAIRsharing.v0hbjs
  type: annotation
  user: https://www.encodeproject.org/
usages:
  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/

Collembola Anatomy Ontology
activity status: active
contact:
  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
  url: http://creativecommons.org/publicdomain/zero/1.0/
ontology purl: http://purl.obolibrary.org/obo/clao.owl
preferred prefix: CLAO
products:
  id: clao.owl
  ontology purl: http://purl.obolibrary.org/obo/clao.owl
products:
  id: clao.obo
  ontology purl: http://purl.obolibrary.org/obo/clao.obo
pull request added: 1337
repository: https://github.com/luis-gonzalez-m/Collembola
tracker: https://github.com/luis-gonzalez-m/Collembola/issues

Cell Line Ontology
activity status: active
contact:
  github: zhengj2007
  label: Jie Zheng
  orcid: 0000-0002-2999-0103
dependencies:
  id: cl
dependencies:
  id: doid
dependencies:
  id: ncbitaxon
dependencies:
  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
  url: http://creativecommons.org/licenses/by/3.0/
ontology purl: http://purl.obolibrary.org/obo/clo.owl
preferred prefix: CLO
products:
  id: clo.owl
  ontology purl: http://purl.obolibrary.org/obo/clo.owl
publications: CLO: The Cell Line Ontology
  id: https://www.ncbi.nlm.nih.gov/pubmed/25852852
repository: https://github.com/CLO-Ontology/CLO
tracker: https://github.com/CLO-Ontology/CLO/issues

Clytia hemisphaerica Development and Anatomy Ontology
activity status: active
contact:
  github: Leclere-L
  label: Lucas Leclere
  orcid: 0000-0002-7440-0467
dependencies:
  id: iao
dependencies:
  id: ro
dependencies:
  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
  url: http://creativecommons.org/licenses/by/3.0/
ontology purl: http://purl.obolibrary.org/obo/clyh.owl
preferred prefix: CLYH
products:
  id: clyh.owl
  ontology purl: http://purl.obolibrary.org/obo/clyh.owl
products:
  id: clyh.obo
  ontology purl: http://purl.obolibrary.org/obo/clyh.obo
pull request added: 1205
repository: https://github.com/EBISPOT/clyh_ontology
tracker: https://github.com/EBISPOT/clyh_ontology/issues

Clinical measurement ontology
activity status: active
browsers: RGD Ontology Browser
  label: RGD
  url: http://rgd.mcw.edu/rgdweb/ontology/view.html
contact:
  github: jrsjrs
  label: Jennifer Smith
  orcid: 0000-0002-6443-9376
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
  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/
preferred prefix: CMO
products:
  id: cmo.owl
  ontology purl: http://purl.obolibrary.org/obo/cmo.owl
products:
  id: cmo.obo
  ontology purl: http://purl.obolibrary.org/obo/cmo.obo
publications: Three ontologies to define phenotype measurement data.
  id: https://www.ncbi.nlm.nih.gov/pubmed/22654893
publications: The clinical measurement, measurement method and experimental condition ontologies: expansion, improvements and new applications.
  id: https://www.ncbi.nlm.nih.gov/pubmed/24103152
repository: https://github.com/rat-genome-database/CMO-Clinical-Measurement-Ontology
tags: clinical
tracker: https://github.com/rat-genome-database/CMO-Clinical-Measurement-Ontology/issues

Core Ontology for Biology and Biomedicine
activity status: active
contact:
  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
  url: https://creativecommons.org/publicdomain/zero/1.0/
ontology purl: http://purl.obolibrary.org/obo/cob.owl
preferred prefix: COB
products: COB
  description: Core Ontology for Biology and Biomedicine, main ontology
  id: cob.owl
  ontology purl: http://purl.obolibrary.org/obo/cob.owl
products: COB base module
  description: base module for COB
  id: cob/cob-base.owl
  ontology purl: http://purl.obolibrary.org/obo/cob/cob-base.owl
products: COB native 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
products: COB to external
  id: cob/cob-to-external.owl
  ontology purl: http://purl.obolibrary.org/obo/cob/cob-to-external.owl
  type: BridgeOntology
products: COB demo ontology (experimental)
  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
repository: https://github.com/OBOFoundry/COB
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
  examples:
    description: List of ontologies using the term 'organism' (See section entitled "Ontologies that use the Class")
    url: https://ontobee.org/ontology/COB
  user: (multiple)

Coleoptera Anatomy Ontology (COLAO)
activity status: active
contact:
  github: JCGiron
  label: Jennifer C. Giron
  orcid: 0000-0002-0851-6883
dependencies:
  id: aism
dependencies:
  id: bfo
dependencies:
  id: bspo
dependencies:
  id: caro
dependencies:
  id: pato
dependencies:
  id: ro
dependencies:
  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
  url: https://creativecommons.org/licenses/by/4.0/
ontology purl: http://purl.obolibrary.org/obo/colao.owl
preferred prefix: COLAO
products:
  id: colao.owl
  ontology purl: http://purl.obolibrary.org/obo/colao.owl
products:
  id: colao.obo
  ontology purl: http://purl.obolibrary.org/obo/colao.obo
repository: https://github.com/insect-morphology/colao
tags: insect anatomy
tracker: https://github.com/insect-morphology/colao/issues

Contributor Role Ontology
activity status: active
contact:
  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
  url: https://creativecommons.org/licenses/by/2.0/
ontology purl: http://purl.obolibrary.org/obo/cro.owl
preferred prefix: CRO
products: CRO
  id: cro.owl
  ontology purl: http://purl.obolibrary.org/obo/cro.owl
repository: https://github.com/data2health/contributor-role-ontology
tags: scholarly contribution roles
tracker: https://github.com/data2health/contributor-role-ontology/issues

Ctenophore Ontology
activity status: active
contact:
  github: cmungall
  label: Chris Mungall
  orcid: 0000-0002-6601-2165
dependencies:
  id: ro
dependencies:
  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
  url: http://creativecommons.org/licenses/by/3.0/
ontology purl: http://purl.obolibrary.org/obo/cteno.owl
preferred prefix: 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
tracker: https://github.com/obophenotype/ctenophore-ontology/issues

CTO: Core Ontology of Clinical Trials
activity status: active
contact:
  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
  url: http://creativecommons.org/licenses/by/4.0/
ontology purl: http://purl.obolibrary.org/obo/cto.owl
preferred prefix: CTO
products:
  id: cto.owl
  ontology purl: http://purl.obolibrary.org/obo/cto.owl
repository: https://github.com/ClinicalTrialOntology/CTO
tracker: https://github.com/ClinicalTrialOntology/CTO/issues

Cardiovascular Disease Ontology
activity status: active
contact:
  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
  url: https://creativecommons.org/licenses/by/4.0/
ontology purl: http://purl.obolibrary.org/obo/cvdo.owl
preferred prefix: CVDO
products:
  id: cvdo.owl
  ontology purl: http://purl.obolibrary.org/obo/cvdo.owl
repository: https://github.com/OpenLHS/CVDO
tracker: https://github.com/OpenLHS/CVDO/issues

Dictyostelium discoideum anatomy
activity status: active
contact:
  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
  url: https://creativecommons.org/publicdomain/zero/1.0/
ontology purl: http://purl.obolibrary.org/obo/ddanat.owl
preferred prefix: DDANAT
products:
  id: ddanat.owl
  ontology purl: http://purl.obolibrary.org/obo/ddanat.owl
products:
  id: ddanat.obo
  ontology purl: http://purl.obolibrary.org/obo/ddanat.obo
publications: An anatomy ontology to represent biological knowledge in Dictyostelium discoideum
  id: https://www.ncbi.nlm.nih.gov/pubmed/18366659
repository: https://github.com/dictyBase/migration-data
taxon:
  id: NCBITaxon:44689
  label: Dictyostelium discoideum
tracker: https://github.com/dictyBase/migration-data/issues
twitter: dictybase

Dictyostelium discoideum phenotype ontology
activity status: active
contact:
  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
  url: http://creativecommons.org/publicdomain/zero/1.0/
ontology purl: http://purl.obolibrary.org/obo/ddpheno.owl
preferred prefix: DDPHENO
products:
  id: ddpheno.owl
  ontology purl: http://purl.obolibrary.org/obo/ddpheno.owl
products:
  id: ddpheno.obo
  ontology purl: http://purl.obolibrary.org/obo/ddpheno.obo
publications: dictyBase and the Dicty Stock Center (version 2.0) - a progress report
  id: https://www.ncbi.nlm.nih.gov/pubmed/31840793
repository: https://github.com/obophenotype/dicty-phenotype-ontology
taxon:
  id: NCBITaxon:44689
  label: Dictyostelium discoideum
tracker: https://github.com/obophenotype/dicty-phenotype-ontology/issues
twitter: dictybase

Drug-drug Interaction and Drug-drug Interaction Evidence Ontology
activity status: active
contact:
  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
  url: https://creativecommons.org/licenses/by/4.0/
ontology purl: http://purl.obolibrary.org/obo/dideo.owl
preferred prefix: DIDEO
products:
  id: dideo.owl
  ontology purl: http://purl.obolibrary.org/obo/dideo.owl
repository: https://github.com/DIDEO/DIDEO
tracker: https://github.com/DIDEO/DIDEO/issues

Disease Drivers Ontology
activity status: active
browsers: DO Browser
  label: DO
  url: https://disease-ontology.org/
contact:
  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
  url: https://creativecommons.org/publicdomain/zero/1.0/
ontology purl: http://purl.obolibrary.org/obo/disdriv.owl
preferred prefix: 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
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/
  user: https://disease-ontology.org/

Human Disease Ontology
activity status: active
browsers: DO Browser
  label: DO
  url: https://disease-ontology.org/do
contact:
  github: lschriml
  label: Lynn Schriml
  orcid: 0000-0001-8910-9851
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
  url: https://creativecommons.org/publicdomain/zero/1.0/
ontology purl: http://purl.obolibrary.org/obo/doid.owl
preferred prefix: DOID
products: Disease Ontology, OWL format. This file contains DO's is_a asserted hierarchy plus equivalent axioms to other OBO Foundry ontologies.
  id: doid.owl
  ontology purl: http://purl.obolibrary.org/obo/doid.owl
products: Disease Ontology, OBO format. This file omits the equivalent axioms.
  id: doid.obo
  ontology purl: http://purl.obolibrary.org/obo/doid.obo
publications: 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/25348409
publications: The Human Disease Ontology 2022 update
  id: https://www.ncbi.nlm.nih.gov/pubmed/34755882
repository: https://github.com/DiseaseOntology/HumanDiseaseOntology
tags: disease
taxon:
  id: NCBITaxon:9606
  label: Homo sapiens
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
  examples:
    description: The landing page for Coronavirus Infectious Disease
    url: https://www.alliancegenome.org/disease/DOID:0080599
  user: https://www.alliancegenome.org
usages:
  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
usages:
  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

Drosophila Phenotype Ontology
activity status: active
browsers: FlyBase Browser
  label: FB
  url: http://flybase.org/.bin/cvreport.html
contact:
  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
  url: http://creativecommons.org/licenses/by/4.0/
ontology purl: http://purl.obolibrary.org/obo/dpo.owl
preferred prefix: FBcv
products:
  id: dpo.owl
  ontology purl: http://purl.obolibrary.org/obo/dpo.owl
products:
  id: dpo.obo
  ontology purl: http://purl.obolibrary.org/obo/dpo.obo
products:
  id: dpo.json
  ontology purl: http://purl.obolibrary.org/obo/dpo.json
publications: The Drosophila phenotype ontology.
  id: https://www.ncbi.nlm.nih.gov/pubmed/24138933
repository: https://github.com/FlyBase/drosophila-phenotype-ontology
taxon:
  id: NCBITaxon:7227
  label: Drosophila
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
  user: http://flybase.org

The Drug Ontology
activity status: active
contact:
  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
  url: http://creativecommons.org/licenses/by/3.0/
ontology purl: http://purl.obolibrary.org/obo/dron.owl
preferred prefix: DRON
products:
  id: dron.owl
  ontology purl: http://purl.obolibrary.org/obo/dron.owl
publications: Therapeutic indications and other use-case-driven updates in the drug ontology: anti-malarials, anti-hypertensives, opioid analgesics, and a large term request
  id: https://doi.org/10.1186/s13326-017-0121-5
repository: https://github.com/ufbmi/dron
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

Data Use Ontology
activity status: active
contact:
  github: mcourtot
  label: Melanie Courtot
  orcid: 0000-0002-9551-6370
dependencies:
  id: bfo
dependencies:
  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
  url: http://creativecommons.org/licenses/by/4.0/
ontology purl: http://purl.obolibrary.org/obo/duo.owl
preferred prefix: DUO
products:
  id: duo.owl
  ontology purl: http://purl.obolibrary.org/obo/duo.owl
repository: https://github.com/EBISPOT/DUO
tracker: https://github.com/EBISPOT/DUO/issues

The Echinoderm Anatomy and Development Ontology
activity status: active
contact:
  github: ettensohn
  label: Charles Ettensohn
  orcid: 0000-0002-3625-0955
dependencies:
  id: cl
dependencies:
  id: ro
dependencies:
  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
  url: http://creativecommons.org/licenses/by/3.0/
ontology purl: http://purl.obolibrary.org/obo/ecao.owl
preferred prefix: ECAO
products:
  id: ecao.owl
  ontology purl: http://purl.obolibrary.org/obo/ecao.owl
products:
  id: ecao.obo
  ontology purl: http://purl.obolibrary.org/obo/ecao.obo
repository: https://github.com/echinoderm-ontology/ecao_ontology
tracker: https://github.com/echinoderm-ontology/ecao_ontology/issues

Evidence and Conclusion Ontology
activity status: active
browsers: ECO Browser
  label: ECO
  url: https://www.evidenceontology.org/browse
contact:
  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: NSF ABI-1458400
  id: https://www.nsf.gov/awardsearch/showAward
homepage: https://www.evidenceontology.org
id: eco
layout: ontology_detail
license:
  label: CC0 1.0
  url: https://creativecommons.org/publicdomain/zero/1.0/
ontology purl: http://purl.obolibrary.org/obo/eco.owl
preferred prefix: ECO
products:
  id: eco.owl
  ontology purl: http://purl.obolibrary.org/obo/eco.owl
products:
  id: eco.obo
  ontology purl: http://purl.obolibrary.org/obo/eco.obo
publications: ECO: the Evidence and Conclusion Ontology, an update for 2022.
  id: https://www.ncbi.nlm.nih.gov/pubmed/34986598
  preferred: true
publications: ECO, the Evidence & Conclusion Ontology: community standard for evidence information.
  id: https://www.ncbi.nlm.nih.gov/pubmed/30407590
publications: Standardized description of scientific evidence using the Evidence Ontology (ECO)
  id: https://www.ncbi.nlm.nih.gov/pubmed/25052702
repository: https://github.com/evidenceontology/evidenceontology
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
usages:
  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: The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species
    id: https://www.ncbi.nlm.nih.gov/pubmed/27899636
  type: annotation
  user: https://monarchinitiative.org/

An ontology of core ecological entities
activity status: active
contact:
  github: pbuttigieg
  label: Pier Luigi Buttigieg
  orcid: 0000-0002-4366-3088
dependencies:
  id: bfo
dependencies:
  id: chebi
dependencies:
  id: envo
dependencies:
  id: go
dependencies:
  id: iao
dependencies:
  id: pato
dependencies:
  id: pco
dependencies:
  id: po
dependencies:
  id: ro
dependencies:
  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
  url: http://creativecommons.org/licenses/by/3.0/
ontology purl: http://purl.obolibrary.org/obo/ecocore.owl
preferred prefix: ECOCORE
products:
  id: ecocore.owl
  ontology purl: http://purl.obolibrary.org/obo/ecocore.owl
products:
  id: ecocore.obo
  ontology purl: http://purl.obolibrary.org/obo/ecocore.obo
repository: https://github.com/EcologicalSemantics/ecocore
tags: ecological functions
tags: ecological interactions
tracker: https://github.com/EcologicalSemantics/ecocore/issues

Environmental conditions, treatments and exposures ontology
activity status: active
contact:
  github: diatomsRcool
  label: Anne Thessen
  orcid: 0000-0002-2908-3327
dependencies:
  id: chebi
dependencies:
  id: envo
dependencies:
  id: exo
dependencies:
  id: go
dependencies:
  id: iao
dependencies:
  id: maxo
dependencies:
  id: nbo
dependencies:
  id: ncbitaxon
dependencies:
  id: ncit
dependencies:
  id: pato
dependencies:
  id: ro
dependencies:
  id: uberon
dependencies:
  id: xco
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
  url: https://creativecommons.org/publicdomain/zero/1.0/
ontology purl: http://purl.obolibrary.org/obo/ecto.owl
preferred prefix: 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
products:
  id: ecto.obo
  name: Environmental conditions, treatments and exposures ontology additional release in OBO format
  ontology purl: http://purl.obolibrary.org/obo/ecto.obo
products:
  id: ecto.json
  name: Environmental conditions, treatments and exposures ontology additional release in OBOJSon format
  ontology purl: http://purl.obolibrary.org/obo/ecto.json
products:
  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
products:
  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
products:
  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
tracker: https://github.com/EnvironmentOntology/environmental-exposure-ontology/issues

Mouse Developmental Anatomy Ontology
activity status: active
contact:
  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
  url: https://creativecommons.org/licenses/by/4.0/
ontology purl: http://purl.obolibrary.org/obo/emapa.owl
preferred prefix: EMAPA
products:
  id: emapa.owl
  ontology purl: http://purl.obolibrary.org/obo/emapa.owl
products:
  id: emapa.obo
  ontology purl: http://purl.obolibrary.org/obo/emapa.obo
publications: An internet-accessible database of mouse developmental anatomy based on a systematic nomenclature
  id: https://www.ncbi.nlm.nih.gov/pubmed/9651497
publications: EMAP/EMAPA ontology of mouse developmental anatomy: 2013 update
  id: https://www.ncbi.nlm.nih.gov/pubmed/23972281
publications: Mouse Anatomy Ontologies: Enhancements and Tools for Exploring and Integrating Biomedical Data
  id: https://www.ncbi.nlm.nih.gov/pubmed/26208972
publications: Textual Anatomics: the Mouse Developmental Anatomy Ontology and the Gene Expression Database for Mouse Development (GXD)
  id: https://doi.org/10.1016/B978-0-12-800043-4.00023-3
repository: https://github.com/obophenotype/developmental-mouse-anatomy-ontology
taxon:
  id: NCBITaxon:10088
  label: Mus
tracker: https://github.com/obophenotype/developmental-mouse-anatomy-ontology/issues
usages:
  description: GXD
  see also: https://doi.org/10.25504/FAIRsharing.q9neh8
  user: http://www.informatics.jax.org/expression.shtml

Environment Ontology
activity status: active
contact:
  github: pbuttigieg
  label: Pier Luigi Buttigieg
  orcid: 0000-0002-4366-3088
dependencies:
  id: chebi
dependencies:
  id: foodon
dependencies:
  id: go
dependencies:
  id: ncbitaxon
dependencies:
  id: pco
dependencies:
  id: po
dependencies:
  id: ro
dependencies:
  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
  url: http://creativecommons.org/publicdomain/zero/1.0/
ontology purl: http://purl.obolibrary.org/obo/envo.owl
page: https://github.com/EnvironmentOntology/envo
preferred prefix: ENVO
products: main ENVO OWL release
  id: envo.owl
  ontology purl: http://purl.obolibrary.org/obo/envo.owl
products: ENVO in obographs JSON format
  id: envo.json
  ontology purl: http://purl.obolibrary.org/obo/envo.json
products: ENVO in OBO Format. May be lossy
  id: envo.obo
  ontology purl: http://purl.obolibrary.org/obo/envo.obo
products: OBO-Basic edition of ENVO
  id: envo/subsets/envo-basic.obo
  ontology purl: http://purl.obolibrary.org/obo/envo/subsets/envo-basic.obo
products: Earth Microbiome Project subset
  id: envo/subsets/envoEmpo.owl
  ontology purl: http://purl.obolibrary.org/obo/envo/subsets/envoEmpo.owl
products: GSC Lite subset of ENVO
  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
publications: The environment ontology: contextualising biological and biomedical entities
  id: https://doi.org/10.1186/2041-1480-4-43
  preferred: true
publications: The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation
  id: https://doi.org/10.1186/s13326-016-0097-6
repository: https://github.com/EnvironmentOntology/envo
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
usages:
  description: describing stomach contents
  type: data-annotation
  user: http://globalbioticinteractions.org
usages:
  description: annotating datasets in data repositories
  see also: http://blogs.nature.com/scientificdata/2015/12/17/isa-explorer/
  type: dataset-description
  user: http://www.nature.com/sdata/
usages:
  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/
usages:
  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/
usages:
  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/

Epilepsy Ontology
activity status: active
contact:
  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
  url: http://creativecommons.org/licenses/by/4.0/
ontology purl: http://purl.obolibrary.org/obo/epio.owl
preferred prefix: EPIO
products:
  id: epio.owl
  ontology purl: http://purl.obolibrary.org/obo/epio.owl
products:
  id: EPIO_merged.owl
  ontology purl: http://purl.obolibrary.org/obo/EPIO_merged.owl
repository: https://github.com/SCAI-BIO/EpilepsyOntology
tags: disease
tracker: https://github.com/SCAI-BIO/EpilepsyOntology/issues

Exercise Medicine Ontology
activity status: active
contact:
  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
  url: https://creativecommons.org/licenses/by/4.0/
ontology purl: http://purl.obolibrary.org/obo/exmo.owl
preferred prefix: EXMO
products:
  id: exmo.owl
  ontology purl: http://purl.obolibrary.org/obo/exmo.owl
publications: Core reference ontology for individualized exercise prescription
  id: https://www.ncbi.nlm.nih.gov/pubmed/39695140
repository: https://github.com/Exercise-Medicine-Ontology/EXMO
tracker: https://github.com/Exercise-Medicine-Ontology/EXMO/issues

Exposure ontology
activity status: active
contact:
  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
  url: https://creativecommons.org/licenses/by/4.0/
ontology purl: http://purl.obolibrary.org/obo/exo.owl
preferred prefix: ExO
products:
  id: exo.owl
  ontology purl: http://purl.obolibrary.org/obo/exo.owl
products:
  id: exo.obo
  ontology purl: http://purl.obolibrary.org/obo/exo.obo
repository: https://github.com/CTDbase/exposure-ontology
tracker: https://github.com/CTDbase/exposure-ontology/issues

Fungal gross anatomy
activity status: active
contact:
  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
  url: http://creativecommons.org/publicdomain/zero/1.0/
ontology purl: http://purl.obolibrary.org/obo/fao.owl
preferred prefix: FAO
products:
  id: fao.owl
  ontology purl: http://purl.obolibrary.org/obo/fao.owl
products:
  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
tracker: https://github.com/obophenotype/fungal-anatomy-ontology/issues

Biological Imaging Methods Ontology
activity status: active
browsers: BioPortal Browser
  label: BioPortal
  url: https://bioportal.bioontology.org/ontologies/FBbi
contact:
  github: gouttegd
  label: Damien Goutte-Gattat
  orcid: 0000-0002-6095-8718
dependencies:
  id: iao
dependencies:
  id: omo
dependencies:
  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
  url: https://creativecommons.org/licenses/by/4.0/
ontology purl: http://purl.obolibrary.org/obo/fbbi.owl
preferred prefix: FBbi
products:
  id: fbbi.owl
  ontology purl: http://purl.obolibrary.org/obo/fbbi.owl
products:
  id: fbbi.obo
  ontology purl: http://purl.obolibrary.org/obo/fbbi.obo
products:
  id: fbbi/fbbi-base.owl
  ontology purl: http://purl.obolibrary.org/obo/fbbi/fbbi-base.owl
products:
  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
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
  user: https://flybase.org
usages:
  description: Virtual Fly Brain uses FBbi to annotate images.
  user: https://virtualflybrain.org
usages:
  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

Drosophila gross anatomy
activity status: active
browsers: FlyBase Browser
  label: FB
  url: http://flybase.org/.bin/cvreport.html
browsers: Virtual Fly Brain
  label: VFB
  url: http://www.virtualflybrain.org/site/stacks/index.htm
browsers: BioPortal Browser
  label: BioPortal
  url: http://bioportal.bioontology.org/ontologies/FB-BT
contact:
  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
  url: http://creativecommons.org/licenses/by/4.0/
ontology purl: http://purl.obolibrary.org/obo/fbbt.owl
preferred prefix: FBbt
products:
  id: fbbt.owl
  ontology purl: http://purl.obolibrary.org/obo/fbbt.owl
products:
  id: fbbt.obo
  ontology purl: http://purl.obolibrary.org/obo/fbbt.obo
products:
  id: fbbt.json
  ontology purl: http://purl.obolibrary.org/obo/fbbt.json
products:
  id: fbbt/fbbt-simple.owl
  ontology purl: http://purl.obolibrary.org/obo/fbbt/fbbt-simple.owl
products:
  id: fbbt/fbbt-simple.obo
  ontology purl: http://purl.obolibrary.org/obo/fbbt/fbbt-simple.obo
publications: The Drosophila anatomy ontology
  id: https://www.ncbi.nlm.nih.gov/pubmed/24139062
  preferred: true
publications: A strategy for building neuroanatomy ontologies
  id: https://www.ncbi.nlm.nih.gov/pubmed/22402613
publications: The Virtual Fly Brain Browser and Query Interface
  id: https://www.ncbi.nlm.nih.gov/pubmed/22180411
publications: FlyBase: anatomical data, images and queries
  id: https://www.ncbi.nlm.nih.gov/pubmed/16381917
repository: https://github.com/FlyBase/drosophila-anatomy-developmental-ontology
tags: Drosophilid anatomy
taxon:
  id: NCBITaxon:7227
  label: Drosophila
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
  examples:
    description: genes expressed in ring neuron R2 in VFB
    url: http://www.virtualflybrain.org/do/gene_list.html
  user: http://www.virtualflybrain.org/
usages:
  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
  user: http://flybase.org

FlyBase Controlled Vocabulary
activity status: active
browsers: FlyBase Browser
  label: FB
  url: http://flybase.org/.bin/cvreport.html
contact:
  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
  url: http://creativecommons.org/licenses/by/4.0/
ontology purl: http://purl.obolibrary.org/obo/fbcv.owl
preferred prefix: FBcv
products:
  id: fbcv.owl
  ontology purl: http://purl.obolibrary.org/obo/fbcv.owl
products:
  id: fbcv.obo
  ontology purl: http://purl.obolibrary.org/obo/fbcv.obo
products:
  id: fbcv.json
  ontology purl: http://purl.obolibrary.org/obo/fbcv.json
repository: https://github.com/FlyBase/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
  user: http://flybase.org

Drosophila development
activity status: active
browsers: FlyBase Browser
  label: FB
  url: http://flybase.org/.bin/cvreport.html
contact:
  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
  url: http://creativecommons.org/licenses/by/4.0/
ontology purl: http://purl.obolibrary.org/obo/fbdv.owl
preferred prefix: FBdv
products:
  id: fbdv.owl
  ontology purl: http://purl.obolibrary.org/obo/fbdv.owl
products:
  id: fbdv.obo
  ontology purl: http://purl.obolibrary.org/obo/fbdv.obo
products:
  id: fbdv.json
  ontology purl: http://purl.obolibrary.org/obo/fbdv.json
products:
  id: fbdv/fbdv-simple.owl
  ontology purl: http://purl.obolibrary.org/obo/fbdv/fbdv-simple.owl
products:
  id: fbdv/fbdv-simple.obo
  ontology purl: http://purl.obolibrary.org/obo/fbdv/fbdv-simple.obo
repository: https://github.com/FlyBase/drosophila-developmental-ontology
taxon:
  id: NCBITaxon:7227
  label: Drosophila
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

Food Interactions with Drugs Evidence Ontology
activity status: active
contact:
  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
  url: https://creativecommons.org/publicdomain/zero/1.0/
ontology purl: http://purl.obolibrary.org/obo/fideo.owl
preferred prefix: FIDEO
products:
  id: fideo.owl
  ontology purl: http://purl.obolibrary.org/obo/fideo.owl
repository: https://gitub.u-bordeaux.fr/erias/fideo
tracker: https://gitub.u-bordeaux.fr/erias/fideo/issues

Flora Phenotype Ontology
activity status: active
contact:
  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
  url: https://creativecommons.org/publicdomain/zero/1.0/
ontology purl: http://purl.obolibrary.org/obo/flopo.owl
preferred prefix: FLOPO
products:
  id: flopo.owl
  ontology purl: http://purl.obolibrary.org/obo/flopo.owl
publications: The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants
  id: https://www.ncbi.nlm.nih.gov/pubmed/27842607
repository: https://github.com/flora-phenotype-ontology/flopoontology
taxon:
  id: NCBITaxon:33090
  label: Viridiplantae
tracker: https://github.com/flora-phenotype-ontology/flopoontology/issues

Food-Biomarker Ontology
activity status: active
contact:
  github: pcastellanoescuder
  label: Pol Castellano Escuder
  orcid: 0000-0001-6466-877X
dependencies:
  id: chebi
dependencies:
  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
  url: http://creativecommons.org/licenses/by/3.0/
ontology purl: http://purl.obolibrary.org/obo/fobi.owl
preferred prefix: FOBI
products: FOBI is an ontology to represent food intake data and associate it with metabolomic data
  format: owl-rdf/xml
  id: fobi.owl
  ontology purl: http://purl.obolibrary.org/obo/fobi.owl
publications: FOBI: an ontology to represent food intake data and associate it with metabolomic data
  id: https://www.ncbi.nlm.nih.gov/pubmed/32556148
publications: The fobitools framework: the first steps towards food enrichment analysis
  id: https://www.ncbi.nlm.nih.gov/pubmed/34601570
repository: https://github.com/pcastellanoescuder/FoodBiomarkerOntology
tracker: https://github.com/pcastellanoescuder/FoodBiomarkerOntology/issues

Food Ontology
activity status: active
contact:
  github: ddooley
  label: Damion Dooley
  orcid: 0000-0002-8844-9165
dependencies:
  id: bfo
dependencies:
  id: chebi
dependencies:
  id: envo
dependencies:
  id: eo
dependencies:
  id: ncbitaxon
dependencies:
  id: obi
dependencies:
  id: ro
dependencies:
  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
  url: http://creativecommons.org/licenses/by/4.0/
ontology purl: http://purl.obolibrary.org/obo/foodon.owl
preferred prefix: FOODON
products: FoodOn ontology with import file references and over 9,000 food products
  format: owl-rdf/xml
  id: foodon.owl
  ontology purl: http://purl.obolibrary.org/obo/foodon.owl
products: FoodOn core ontology (currently the same as foodon.owl)
  format: owl-rdf/xml
  id: foodon_core.owl
  ontology purl: http://purl.obolibrary.org/obo/foodon_core.owl
publications: FoodOn: a harmonized food ontology to increase global food traceability, quality control and data integration
  id: https://www.ncbi.nlm.nih.gov/pubmed/31304272
repository: https://github.com/FoodOntology/foodon
tags: food
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/
usages:
  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
usages:
  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

FuTRES Ontology of Vertebrate Traits
activity status: active
contact:
  github: megbalk
  label: Meghan Balk
  orcid: 0000-0003-2699-3066
dependencies:
  id: bco
dependencies:
  id: bfo
dependencies:
  id: bspo
dependencies:
  id: iao
dependencies:
  id: oba
dependencies:
  id: pato
dependencies:
  id: ro
dependencies:
  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
  url: https://creativecommons.org/publicdomain/zero/1.0/
ontology purl: http://purl.obolibrary.org/obo/fovt.owl
preferred prefix: 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
products:
  id: fovt.obo
  name: FuTRES Ontology of Vertebrate Traits additional release in OBO format
  ontology purl: http://purl.obolibrary.org/obo/fovt.obo
products:
  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
products:
  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
tracker: https://github.com/futres/fovt/issues

Fission Yeast Phenotype Ontology
activity status: active
contact:
  github: ValWood
  label: Val Wood
  orcid: 0000-0001-6330-7526
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
  url: http://creativecommons.org/licenses/by/4.0/
ontology purl: http://purl.obolibrary.org/obo/fypo.owl
preferred prefix: FYPO
products:
  id: fypo.owl
  ontology purl: http://purl.obolibrary.org/obo/fypo.owl
products:
  id: fypo.obo
  ontology purl: http://purl.obolibrary.org/obo/fypo.obo
publications: FYPO: The Fission Yeast Phenotype Ontology.
  id: https://www.ncbi.nlm.nih.gov/pubmed/23658422
repository: https://github.com/pombase/fypo
taxon:
  id: NCBITaxon:4896
  label: S. pombe
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

Plant Gall Ontology
activity status: active
contact:
  github: adeans
  label: Andy Deans
  orcid: 0000-0002-2119-4663
dependencies:
  id: caro
dependencies:
  id: flopo
dependencies:
  id: ncbitaxon
dependencies:
  id: obi
dependencies:
  id: pato
dependencies:
  id: po
dependencies:
  id: poro
dependencies:
  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
  url: https://creativecommons.org/publicdomain/zero/1.0/
ontology purl: http://purl.obolibrary.org/obo/gallont.owl
preferred prefix: GALLONT
products:
  id: gallont.owl
  ontology purl: http://purl.obolibrary.org/obo/gallont.owl
products:
  id: gallont.json
  ontology purl: http://purl.obolibrary.org/obo/gallont.json
products:
  id: gallont.obo
  ontology purl: http://purl.obolibrary.org/obo/gallont.obo
repository: https://github.com/adeans/gallont
tracker: https://github.com/adeans/gallont/issues

Gazetteer
activity status: active
contact:
  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
  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
preferred prefix: GAZ
products:
  id: gaz.owl
  ontology purl: http://purl.obolibrary.org/obo/gaz.owl
products:
  id: gaz.obo
  ontology purl: http://purl.obolibrary.org/obo/gaz.obo
products: GAZ countries
  description: A country specific subset of the GAZ.
  id: gaz/gaz-countries.owl
  ontology purl: http://purl.obolibrary.org/obo/gaz/gaz-countries.owl
repository: https://github.com/EnvironmentOntology/gaz
tracker: https://github.com/EnvironmentOntology/gaz/issues

Genomics Cohorts Knowledge Ontology
activity status: active
contact:
  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
  url: https://creativecommons.org/licenses/by/4.0/
ontology purl: http://purl.obolibrary.org/obo/gecko.owl
preferred prefix: GECKO
products:
  id: gecko.owl
  ontology purl: http://purl.obolibrary.org/obo/gecko.owl
repository: https://github.com/IHCC-cohorts/GECKO
tags: cohort studies
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/

Genomic Epidemiology Ontology
activity status: active
contact:
  github: ddooley
  label: Damion Dooley
  orcid: 0000-0002-8844-9165
dependencies:
  id: chebi
dependencies:
  id: ncbitaxon
dependencies:
  id: po
dependencies:
  id: ro
dependencies:
  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
  url: http://creativecommons.org/licenses/by/3.0/
ontology purl: http://purl.obolibrary.org/obo/genepio.owl
page: https://github.com/GenEpiO/genepio
preferred prefix: 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
tracker: https://github.com/GenEpiO/genepio/issues/

Genotype Ontology
activity status: active
contact:
  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
  url: https://creativecommons.org/licenses/by/4.0/
ontology purl: http://purl.obolibrary.org/obo/geno.owl
preferred prefix: GENO
products: GENO
  id: geno.owl
  ontology purl: http://purl.obolibrary.org/obo/geno.owl
repository: https://github.com/monarch-initiative/GENO-ontology
tags: genotype-to-phenotype associations
tracker: https://github.com/monarch-initiative/GENO-ontology/issues

Geographical Entity Ontology
activity status: active
contact:
  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
  url: https://creativecommons.org/licenses/by/4.0/
ontology purl: http://purl.obolibrary.org/obo/geo.owl
preferred prefix: GEO
products:
  id: geo.owl
  ontology purl: http://purl.obolibrary.org/obo/geo.owl
repository: https://github.com/ufbmi/geographical-entity-ontology
tracker: https://github.com/ufbmi/geographical-entity-ontology/issues

Glycan Naming and Subsumption Ontology (GNOme)
activity status: active
browsers: GNOme Glycan Structure Browser
  label: Structure Browser
  url: https://gnome.glyomics.org/StructureBrowser.html
browsers: GNOme Glycan Composition Browser
  label: Composition Browser
  url: https://gnome.glyomics.org/CompositionBrowser.html
contact:
  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
  url: https://creativecommons.org/licenses/by/4.0/
ontology purl: http://purl.obolibrary.org/obo/gno.owl
preferred prefix: GNO
products:
  description: Glycan Naming and Subsumption Ontology, OWL format (primary)
  id: gno.owl
  ontology purl: http://purl.obolibrary.org/obo/gno.owl
products:
  description: Glycan Naming and Subsumption Ontology, OBO format (automated conversion from OWL)
  id: gno.obo
  ontology purl: http://purl.obolibrary.org/obo/gno.obo
products:
  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: GNOme - Glycan Naming and Subsumption Ontology
  id: https://doi.org/10.5281/zenodo.6678278
repository: https://github.com/glygen-glycan-data/GNOme
tags: glycan structure
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/
usages:
  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/
usages:
  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

Gene Ontology
activity status: active
browsers: Gene Ontology AmiGO 2 Browser
  label: AmiGO
  url: http://amigo.geneontology.org/amigo/term/GO:0008150#display-lineage-tab
contact:
  github: suzialeksander
  label: Suzi Aleksander
  orcid: 0000-0001-6787-2901
dependencies:
  id: cl
  subset: go/extensions/cl_import.owl
dependencies: GO bridge to NIFSTD
  connects:
    id: nifstd
  connects:
    id: go
  description: Bridging axioms between nifstd and go
  id: go/extensions/go-bridge-to-nifstd.owl
  publications: The Gene Ontology (GO) Cellular Component Ontology: integration with SAO (Subcellular Anatomy Ontology) and other recent developments.
    id: http://www.ncbi.nlm.nih.gov/pubmed/24093723
  type: BridgeOntology
dependencies:
  id: ncbitaxon
  subset: go/extensions/ncbitaxon_import.owl
dependencies:
  id: ro
  subset: go/extensions/ro_import.owl
dependencies:
  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
  url: https://creativecommons.org/licenses/by/4.0/
ontology purl: http://purl.obolibrary.org/obo/go.owl
preferred prefix: GO
products: GO (OWL edition)
  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
products: GO (OBO Format 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
products: GO (JSON 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/
products: GO-Plus
  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
products: GO Base Module
  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
products: GO-Plus
  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/
products: GO-Basic, Filtered, for use with legacy tools
  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
products: GO-Basic, Filtered, for use with legacy tools (JSON)
  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
products: GO Taxon Groupings
  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
products: 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.owl
  ontology purl: http://purl.obolibrary.org/obo/go/snapshot/go.owl
  page: http://geneontology.org/page/download-ontology
products: GO (OBO Format 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
publications: Gene ontology: tool for the unification of biology. The Gene Ontology Consortium
  id: https://www.ncbi.nlm.nih.gov/pubmed/10802651
publications: The Gene Ontology resource: enriching a GOld mine
  id: https://www.ncbi.nlm.nih.gov/pubmed/33290552
repository: https://github.com/geneontology/go-ontology
tags: biology
taxon:
  id: NCBITaxon:1
  label: All life
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
usages:
  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
usages:
  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
usages:
  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
  examples:
    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
usages:
  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

Human Ancestry Ontology
activity status: active
contact:
  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
  url: https://creativecommons.org/licenses/by/4.0/
ontology purl: http://purl.obolibrary.org/obo/hancestro.owl
preferred prefix: HANCESTRO
products: HANCESTRO
  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
products: HANCESTRO Base
  description: Base version of HANCESTRO
  id: hancestro-base.owl
  ontology purl: http://purl.obolibrary.org/obo/hancestro-base.owl
publications: A standardized framework for representation of ancestry data in genomics studies, with application to the NHGRI-EBI GWAS Catalog
  id: https://www.ncbi.nlm.nih.gov/pubmed/29448949
repository: https://github.com/EBISPOT/hancestro
tags: ancestry
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
  user: http://www.ebi.ac.uk/efo
usages:
  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
  user: https://genepio.org/
usages:
  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
  user: http://foodon.org

Hymenoptera Anatomy Ontology
activity status: active
contact:
  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
  url: https://creativecommons.org/publicdomain/zero/1.0/
ontology purl: http://purl.obolibrary.org/obo/hao.owl
preferred prefix: HAO
products:
  id: hao.owl
  ontology purl: http://purl.obolibrary.org/obo/hao.owl
products:
  id: hao.obo
  ontology purl: http://purl.obolibrary.org/obo/hao.obo
products:
  id: hao/depictions.owl
  ontology purl: http://purl.obolibrary.org/obo/hao/depictions.owl
publications: A gross anatomy ontology for hymenoptera
  id: https://www.ncbi.nlm.nih.gov/pubmed/21209921
repository: https://github.com/hymao/hao
taxon:
  id: NCBITaxon:7399
  label: Hymenoptera
tracker: https://github.com/hymao/hao/issues

Homology Ontology
activity status: active
contact:
  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
  url: https://creativecommons.org/publicdomain/zero/1.0/
ontology purl: http://purl.obolibrary.org/obo/hom.owl
preferred prefix: HOM
products:
  id: hom.owl
  ontology purl: http://purl.obolibrary.org/obo/hom.owl
publications: An ontology to clarify homology-related concepts
  id: https://doi.org/10.1016/j.tig.2009.12.012
repository: https://github.com/BgeeDB/homology-ontology
tracker: https://github.com/BgeeDB/homology-ontology/issues

Human Developmental Stages
activity status: active
contact:
  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
  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
preferred prefix: HsapDv
products:
  id: hsapdv.owl
  ontology purl: http://purl.obolibrary.org/obo/hsapdv.owl
products:
  id: hsapdv.obo
  ontology purl: http://purl.obolibrary.org/obo/hsapdv.obo
repository: https://github.com/obophenotype/developmental-stage-ontologies
tracker: https://github.com/obophenotype/developmental-stage-ontologies/issues

Health Surveillance Ontology
activity status: active
contact:
  github: nandadorea
  label: Fernanda Dorea
  orcid: 0000-0001-8638-8525
dependencies:
  id: bfo
dependencies:
  id: ncbitaxon
dependencies:
  id: obi
dependencies:
  id: ro
dependencies:
  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
  url: http://creativecommons.org/licenses/by/3.0/
ontology purl: http://purl.obolibrary.org/obo/hso.owl
page: https://github.com/SVA-SE/HSO
preferred prefix: 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
tracker: https://github.com/SVA-SE/HSO/issues/

Hypertension Ontology
activity status: active
contact:
  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
  url: http://creativecommons.org/licenses/by/4.0/
ontology purl: http://purl.obolibrary.org/obo/htn.owl
preferred prefix: HTN
products: HTN
  id: htn.owl
  ontology purl: http://purl.obolibrary.org/obo/htn.owl
repository: https://github.com/aellenhicks/htn_owl
tracker: https://github.com/aellenhicks/htn_owl/issues

Information Artifact Ontology
activity status: active
contact:
  github: zhengj2007
  label: Jie Zheng
  orcid: 0000-0002-2999-0103
depicted by: https://avatars0.githubusercontent.com/u/13591168
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
  url: http://creativecommons.org/licenses/by/4.0/
ontology purl: http://purl.obolibrary.org/obo/iao.owl
preferred prefix: IAO
products:
  id: iao.owl
  ontology purl: http://purl.obolibrary.org/obo/iao.owl
products: IAO ontology metadata
  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
products: IAO dev
  id: iao/dev/iao.owl
  ontology purl: http://purl.obolibrary.org/obo/iao/dev/iao.owl
products: ontology of document acts
  contact:
    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
repository: https://github.com/information-artifact-ontology/IAO
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

Integrative and Conjugative Element Ontology
activity status: active
contact:
  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
  url: http://creativecommons.org/licenses/by/4.0/
ontology purl: http://purl.obolibrary.org/obo/iceo.owl
preferred prefix: ICEO
products:
  id: iceo.owl
  ontology purl: http://purl.obolibrary.org/obo/iceo.owl
publications: ICEO, a biological ontology for representing and analyzing bacterial integrative and conjugative elements
  id: https://www.ncbi.nlm.nih.gov/pubmed/35058462
repository: https://github.com/ontoice/ICEO
tracker: https://github.com/ontoice/ICEO/issues

Informed Consent Ontology
activity status: active
contact:
  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
  url: http://creativecommons.org/licenses/by/4.0/
ontology purl: http://purl.obolibrary.org/obo/ico.owl
preferred prefix: ICO
products:
  id: ico.owl
  ontology purl: http://purl.obolibrary.org/obo/ico.owl
repository: https://github.com/ICO-ontology/ICO
tags: informed consent
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

Infectious Disease Ontology
activity status: active
contact:
  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
  url: https://creativecommons.org/licenses/by/3.0/
ontology purl: http://purl.obolibrary.org/obo/ido.owl
preferred prefix: IDO
products:
  id: ido.owl
  ontology purl: http://purl.obolibrary.org/obo/ido.owl
publications: The Infectious Disease Ontology in the age of COVID-19
  id: https://www.ncbi.nlm.nih.gov/pubmed/34275487
repository: https://github.com/infectious-disease-ontology/infectious-disease-ontology
taxon:
  id: NCBITaxon:9606
  label: Homo sapiens
tracker: https://github.com/infectious-disease-ontology/infectious-disease-ontology/issues

Interaction Network Ontology
activity status: active
contact:
  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
  url: http://creativecommons.org/licenses/by/3.0/
ontology purl: http://purl.obolibrary.org/obo/ino.owl
preferred prefix: INO
products:
  id: ino.owl
  ontology purl: http://purl.obolibrary.org/obo/ino.owl
publications: Development and application of an Interaction Network Ontology for literature mining of vaccine-associated gene-gene interactions
  id: https://doi.org/10.1186/2041-1480-6-2
repository: https://github.com/INO-ontology/ino
tracker: https://github.com/INO-ontology/ino/issues

clinical LABoratory Ontology
activity status: active
contact:
  github: pfabry
  label: Paul Fabry
  orcid: 0000-0002-3336-2476
dependencies:
  id: iao
dependencies:
  id: obi
dependencies:
  id: ogms
dependencies:
  id: omiabis
dependencies:
  id: omrse
dependencies:
  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
  url: https://creativecommons.org/licenses/by/4.0/
ontology purl: http://purl.obolibrary.org/obo/labo.owl
preferred prefix: LABO
products:
  id: labo.owl
  ontology purl: http://purl.obolibrary.org/obo/labo.owl
publications: LABO: An Ontology for Laboratory Test Prescription and Reporting
  id: https://doi.org/10.5281/zenodo.6522019
repository: https://github.com/OpenLHS/LABO
tags: clinical documentation
taxon:
  id: NCBITaxon:9606
  label: Homo sapiens
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/

Lepidoptera Anatomy Ontology
activity status: active
contact:
  github: luis-gonzalez-m
  label: Luis A. Gonzalez-Montana
  orcid: 0000-0002-9136-9932
dependencies:
  id: aism
dependencies:
  id: bfo
dependencies:
  id: bspo
dependencies:
  id: caro
dependencies:
  id: pato
dependencies:
  id: ro
dependencies:
  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
  url: https://creativecommons.org/licenses/by/4.0/
ontology purl: http://purl.obolibrary.org/obo/lepao.owl
preferred prefix: LEPAO
products:
  id: lepao.owl
  ontology purl: http://purl.obolibrary.org/obo/lepao.owl
products:
  id: lepao.obo
  ontology purl: http://purl.obolibrary.org/obo/lepao.obo
repository: https://github.com/insect-morphology/lepao
tags: insect anatomy
tracker: https://github.com/insect-morphology/lepao/issues

Mouse adult gross anatomy
activity status: active
contact:
  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
  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
preferred prefix: MA
products:
  id: ma.owl
  ontology purl: http://purl.obolibrary.org/obo/ma.owl
products:
  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
tracker: https://github.com/obophenotype/adult-mouse-anatomy-ontology/issues
usages:
  description: GXD
  see also: https://doi.org/10.25504/FAIRsharing.q9neh8
  user: http://www.informatics.jax.org/expression.shtml

Medical Action Ontology
activity status: active
contact:
  github: LCCarmody
  label: Leigh Carmody
  orcid: 0000-0001-7941-2961
dependencies:
  id: chebi
dependencies:
  id: foodon
dependencies:
  id: go
dependencies:
  id: hp
dependencies:
  id: iao
dependencies:
  id: nbo
dependencies:
  id: obi
dependencies:
  id: ro
dependencies:
  id: uberon
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
  url: http://creativecommons.org/licenses/by/4.0/
ontology purl: http://purl.obolibrary.org/obo/maxo.owl
preferred prefix: MAXO
products:
  id: maxo.owl
  name: Medical Action Ontology main release in OWL format
  ontology purl: http://purl.obolibrary.org/obo/maxo.owl
products:
  id: maxo.obo
  name: Medical Action Ontology additional release in OBO format
  ontology purl: http://purl.obolibrary.org/obo/maxo.obo
products:
  id: maxo.json
  name: Medical Action Ontology additional release in OBOJSon format
  ontology purl: http://purl.obolibrary.org/obo/maxo.json
products:
  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
products:
  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
products:
  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
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/

Microbial Conditions Ontology
activity status: active
contact:
  github: citmejia
  label: Citlalli Mejía-Almonte
  orcid: 0000-0002-0142-5591
dependencies:
  id: bfo
dependencies:
  id: chebi
dependencies:
  id: cl
dependencies:
  id: clo
dependencies:
  id: micro
dependencies:
  id: ncbitaxon
dependencies:
  id: ncit
dependencies:
  id: obi
dependencies:
  id: omit
dependencies:
  id: omp
dependencies:
  id: pato
dependencies:
  id: peco
dependencies:
  id: uberon
dependencies:
  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
  url: http://creativecommons.org/licenses/by/3.0/
ontology purl: http://purl.obolibrary.org/obo/mco.owl
preferred prefix: MCO
products:
  id: mco.owl
  ontology purl: http://purl.obolibrary.org/obo/mco.owl
products:
  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
tracker: https://github.com/microbial-conditions-ontology/microbial-conditions-ontology/issues

Model Card Report Ontology
activity status: active
contact:
  github: ProfTuan
  label: Tuan Amith
  orcid: 0000-0003-4333-1857
dependencies:
  id: iao
dependencies:
  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
  url: https://creativecommons.org/licenses/by/4.0/
ontology purl: http://purl.obolibrary.org/obo/mcro.owl
preferred prefix: MCRO
products:
  id: mcro.owl
  ontology purl: http://purl.obolibrary.org/obo/mcro.owl
publications: Toward a standard formal semantic representation of the model card report
  id: https://doi.org/10.1186/s12859-022-04797-6
repository: https://github.com/UTHealth-Ontology/MCRO
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: Application of an ontology for model cards to generate computable artifacts for linking machine learning information from biomedical research
    id: https://doi.org/10.1145/3543873.3587601
  user: https://github.com/UTHealth-Ontology/MCRO-Software

Mental Functioning Ontology
activity status: active
contact:
  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
  url: http://creativecommons.org/licenses/by/3.0/
ontology purl: http://purl.obolibrary.org/obo/mf.owl
preferred prefix: MF
products:
  id: mf.owl
  ontology purl: http://purl.obolibrary.org/obo/mf.owl
repository: https://github.com/jannahastings/mental-functioning-ontology
tracker: https://github.com/jannahastings/mental-functioning-ontology/issues

Emotion Ontology
activity status: active
contact:
  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
  url: http://creativecommons.org/licenses/by/3.0/
ontology purl: http://purl.obolibrary.org/obo/mfoem.owl
preferred prefix: MFOEM
products:
  id: mfoem.owl
  ontology purl: http://purl.obolibrary.org/obo/mfoem.owl
repository: https://github.com/jannahastings/emotion-ontology
tracker: https://github.com/jannahastings/emotion-ontology/issues

Mental Disease Ontology
activity status: active
contact:
  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
  url: http://creativecommons.org/licenses/by/3.0/
ontology purl: http://purl.obolibrary.org/obo/mfomd.owl
preferred prefix: MFOMD
products:
  id: mfomd.owl
  ontology purl: http://purl.obolibrary.org/obo/mfomd.owl
repository: https://github.com/jannahastings/mental-functioning-ontology
tracker: https://github.com/jannahastings/mental-functioning-ontology/issues

Molecular Interactions Controlled Vocabulary
activity status: active
contact:
  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
  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
preferred prefix: MI
products:
  id: mi.owl
  ontology purl: http://purl.obolibrary.org/obo/mi.owl
products:
  id: mi.obo
  ontology purl: http://purl.obolibrary.org/obo/mi.obo
repository: https://github.com/HUPO-PSI/psi-mi-CV
tracker: https://github.com/HUPO-PSI/psi-mi-CV/issues

MIAPA Ontology
activity status: active
contact:
  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
  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
preferred prefix: MIAPA
products:
  id: miapa.owl
  ontology purl: http://purl.obolibrary.org/obo/miapa.owl
publications: Taking the First Steps towards a Standard for Reporting on Phylogenies: Minimum Information about a Phylogenetic Analysis (MIAPA)
  id: https://doi.org/10.1089/omi.2006.10.231
repository: https://github.com/evoinfo/miapa
tracker: https://github.com/evoinfo/miapa/issues

Measurement method ontology
activity status: active
browsers: RGD Ontology Browser
  label: RGD
  url: http://rgd.mcw.edu/rgdweb/ontology/view.html
contact:
  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
id: mmo
layout: ontology_detail
license:
  label: CC0 1.0
  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/
preferred prefix: MMO
products:
  id: mmo.owl
  ontology purl: http://purl.obolibrary.org/obo/mmo.owl
products:
  id: mmo.obo
  ontology purl: http://purl.obolibrary.org/obo/mmo.obo
publications: Three ontologies to define phenotype measurement data.
  id: https://www.ncbi.nlm.nih.gov/pubmed/22654893
publications: The clinical measurement, measurement method and experimental condition ontologies: expansion, improvements and new applications.
  id: https://www.ncbi.nlm.nih.gov/pubmed/24103152
repository: https://github.com/rat-genome-database/MMO-Measurement-Method-Ontology
tags: clinical
tracker: https://github.com/rat-genome-database/MMO-Measurement-Method-Ontology/issues

Mouse Developmental Stages
activity status: active
contact:
  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
  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
preferred prefix: MmusDv
products:
  id: mmusdv.owl
  ontology purl: http://purl.obolibrary.org/obo/mmusdv.owl
products:
  id: mmusdv.obo
  ontology purl: http://purl.obolibrary.org/obo/mmusdv.obo
repository: https://github.com/obophenotype/developmental-stage-ontologies
tracker: https://github.com/obophenotype/developmental-stage-ontologies/issues

Protein modification
activity status: active
contact:
  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
  url: https://creativecommons.org/licenses/by/4.0/
ontology purl: http://purl.obolibrary.org/obo/mod.owl
preferred prefix: MOD
products: PSI-MOD.owl
  description: PSI-MOD Ontology, OWL format
  id: mod.owl
  ontology purl: http://purl.obolibrary.org/obo/mod.owl
products: PSI-MOD.obo
  description: PSI-MOD Ontology, OBO format
  id: mod.obo
  ontology purl: http://purl.obolibrary.org/obo/mod.obo
publications: The PSI-MOD community standard for representation of protein modification data
  id: https://www.ncbi.nlm.nih.gov/pubmed/18688235
repository: https://github.com/HUPO-PSI/psi-mod-CV
tags: proteins
tracker: https://github.com/HUPO-PSI/psi-mod-CV/issues

Mondo Disease Ontology
activity status: active
browsers: Monarch Initiative Disease Browser
  label: Monarch
  url: https://monarchinitiative.org/disease/MONDO:0019609
contact:
  github: sabrinatoro
  label: Sabrina Toro
  orcid: 0000-0002-4142-7153
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
  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
preferred prefix: MONDO
products: Mondo OWL edition
  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
products: Mondo OBO Format 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
products: Mondo JSON 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
products: Mondo Base Release
  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
products: Mondo Simple 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
publications: Mondo: Integrating Disease Terminology Across Communities
  id: https://doi.org/10.1093/genetics/iyaf215
publications: Mondo: Unifying diseases for the world, by the world
  id: https://www.medrxiv.org/content/10.1101/2022.04.13.22273750
repository: https://github.com/monarch-initiative/mondo
tags: disease
taxon:
  id: NCBITaxon:33208
  label: Metazoa
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: The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species
    id: https://www.ncbi.nlm.nih.gov/pubmed/27899636
  type: annotation
  user: https://monarchinitiative.org/
usages:
  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/
usages:
  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/
usages:
  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/
usages:
  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/

Molecular Process Ontology
activity status: active
contact:
  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
  url: https://creativecommons.org/licenses/by/4.0/
ontology purl: http://purl.obolibrary.org/obo/mop.owl
preferred prefix: MOP
products: Molecular Process Ontology
  id: mop.owl
  ontology purl: http://purl.obolibrary.org/obo/mop.owl
repository: https://github.com/rsc-ontologies/rxno
tracker: https://github.com/rsc-ontologies/rxno/issues

Mammalian Phenotype Ontology
activity status: active
browsers: MGI MP Browser
  label: MGI
  url: https://www.informatics.jax.org/vocab/mp_ontology/
browsers: RGD MP Browser
  label: RGD
  url: https://rgd.mcw.edu/rgdweb/ontology/view.html
browsers: Monarch Phenotype Page
  label: Monarch
  url: http://monarchinitiative.org/phenotype/MP:0000001
contact:
  github: sbello
  label: Sue Bello
  orcid: 0000-0003-4606-0597
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
  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
preferred prefix: MP
products: MP (OWL edition)
  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
products: MP (OBO 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
products: MP (obographs JSON 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
products: MP Base Module
  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
publications: Expanding and refining the Mammalian Phenotype Ontology to enhance disease model discovery
  id: https://www.ncbi.nlm.nih.gov/pubmed/40963406
publications: The Mammalian Phenotype Ontology as a unifying standard for experimental and high-throughput phenotyping data
  id: https://www.ncbi.nlm.nih.gov/pubmed/22961259
publications: Expanding the mammalian phenotype ontology to support automated exchange of high throughput mouse phenotyping data generated by large-scale mouse knockout screens
  id: https://www.ncbi.nlm.nih.gov/pubmed/25825651
repository: https://github.com/mgijax/mammalian-phenotype-ontology
taxon:
  id: NCBITaxon:40674
  label: Mammalia
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
usages:
  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
  user: https://rgd.mcw.edu/rgdweb/ontology/view.html
usages:
  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/

Mouse pathology ontology
activity status: active
contact:
  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
  url: http://creativecommons.org/licenses/by/3.0/
ontology purl: http://purl.obolibrary.org/obo/mpath.owl
preferred prefix: 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
tracker: https://github.com/PaulNSchofield/mpath/issues

Minimum PDDI Information Ontology
activity status: active
contact:
  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
  url: http://creativecommons.org/licenses/by/4.0/
ontology purl: http://purl.obolibrary.org/obo/mpio.owl
preferred prefix: MPIO
products:
  id: mpio.owl
  ontology purl: http://purl.obolibrary.org/obo/mpio.owl
repository: https://github.com/MPIO-Developers/MPIO
tracker: https://github.com/MPIO-Developers/MPIO/issues

MHC Restriction Ontology
activity status: active
contact:
  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
  url: https://creativecommons.org/licenses/by/3.0/
ontology purl: http://purl.obolibrary.org/obo/mro.owl
preferred prefix: MRO
products:
  id: mro.owl
  ontology purl: http://purl.obolibrary.org/obo/mro.owl
repository: https://github.com/IEDB/MRO
tags: Major Histocompatibility Complex
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: An ontology for major histocompatibility restriction
    id: https://www.ncbi.nlm.nih.gov/pubmed/26759709
  type: annotation
  user: https://www.iedb.org/

Mass spectrometry ontology
activity status: active
contact:
  github: mobiusklein
  label: Joshua Klein
  orcid: 0000-0003-1279-6838
dependencies:
  id: pato
dependencies:
  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
  url: https://creativecommons.org/licenses/by/3.0/
ontology purl: http://purl.obolibrary.org/obo/ms.owl
page: http://www.psidev.info/groups/controlled-vocabularies
preferred prefix: MS
products:
  id: ms.obo
  ontology purl: http://purl.obolibrary.org/obo/ms.obo
products:
  id: ms.owl
  ontology purl: http://purl.obolibrary.org/obo/ms.owl
publications: The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary.
  id: https://www.ncbi.nlm.nih.gov/pubmed/23482073
repository: https://github.com/HUPO-PSI/psi-ms-CV
tags: MS experiments
tracker: https://github.com/HUPO-PSI/psi-ms-CV/issues

Neuro Behavior Ontology
activity status: active
browsers: BioPortal Ontology Browser
  label: BioPortal
  url: https://bioportal.bioontology.org/ontologies/NBO
contact:
  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
  url: http://creativecommons.org/licenses/by/3.0/
ontology purl: http://purl.obolibrary.org/obo/nbo.owl
preferred prefix: NBO
products:
  id: nbo.owl
  ontology purl: http://purl.obolibrary.org/obo/nbo.owl
publications: Analyzing gene expression data in mice with the Neuro Behavior Ontology
  id: https://www.ncbi.nlm.nih.gov/pubmed/24177753
repository: https://github.com/obo-behavior/behavior-ontology
tags: behavior
tracker: https://github.com/obo-behavior/behavior-ontology/issues

NCBI organismal classification
activity status: active
browsers: NCBI Taxonomy Browser
  label: NCBI
  url: http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi
contact:
  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
  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
preferred prefix: NCBITaxon
products: Main release
  id: ncbitaxon.owl
  ontology purl: http://purl.obolibrary.org/obo/ncbitaxon.owl
products: OBO Format version of Main release
  id: ncbitaxon.obo
  ontology purl: http://purl.obolibrary.org/obo/ncbitaxon.obo
products: OBOGraphs JSON version of Main release
  id: ncbitaxon.json
  ontology purl: http://purl.obolibrary.org/obo/ncbitaxon.json
products: taxslim
  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
products: taxslim disjointness axioms
  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
repository: https://github.com/obophenotype/ncbitaxon
tags: taxonomy
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

NCI Thesaurus OBO Edition
activity status: active
contact:
  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
  url: https://creativecommons.org/licenses/by/4.0/
ontology purl: http://purl.obolibrary.org/obo/ncit.owl
preferred prefix: NCIT
products: NCIt OBO Edition OWL format
  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
products: NCIt OBO Edition OBO format
  id: ncit.obo
  ontology purl: http://purl.obolibrary.org/obo/ncit.obo
repository: https://github.com/ncit-obo-org/ncit-obo-edition
tracker: https://github.com/ncit-obo-org/ncit-obo-edition/issues

Non-Coding RNA Ontology
activity status: active
contact:
  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
  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
preferred prefix: NCRO
products: NCRO development version
  id: ncro/dev/ncro.owl
  ontology purl: http://purl.obolibrary.org/obo/ncro/dev/ncro.owl
repository: https://github.com/OmniSearch/ncro
tracker: https://github.com/OmniSearch/ncro/issues

Next Generation Biobanking Ontology
activity status: active
contact:
  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
  url: https://creativecommons.org/licenses/by/4.0/
ontology purl: http://purl.obolibrary.org/obo/ngbo.owl
preferred prefix: NGBO
products:
  id: ngbo.owl
  ontology purl: http://purl.obolibrary.org/obo/ngbo.owl
pull request added: 2214
repository: https://github.com/Dalalghamdi/NGBO
tracker: https://github.com/Dalalghamdi/NGBO/issues

NOMEN - A nomenclatural ontology for biological names
activity status: active
contact:
  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: NSF ABI-1356381
  id: https://www.nsf.gov/awardsearch/showAward
homepage: https://github.com/SpeciesFileGroup/nomen
id: nomen
layout: ontology_detail
license:
  label: CC0 1.0
  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
preferred prefix: NOMEN
products: NOMEN
  description: core ontology
  id: nomen.owl
  is canonical: true
  ontology purl: http://purl.obolibrary.org/obo/nomen.owl
  type: owl:Ontology
repository: https://github.com/SpeciesFileGroup/nomen
tags: biological nomenclature
tracker: https://github.com/SpeciesFileGroup/nomen/issues
usages:
  description: TaxonWorks is an integrated web-based workbench for taxonomists and biodiversity scientists.
  see also: https://github.com/SpeciesFileGroup/taxonworks
  type: application
  user: https://taxonworks.org

Ontology of Adverse Events
activity status: active
contact:
  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
  url: http://creativecommons.org/licenses/by/3.0/
ontology purl: http://purl.obolibrary.org/obo/oae.owl
preferred prefix: OAE
products:
  id: oae.owl
  ontology purl: http://purl.obolibrary.org/obo/oae.owl
repository: https://github.com/OAE-ontology/OAE
tags: adverse events
tracker: https://github.com/OAE-ontology/OAE/issues

Ontology of Arthropod Circulatory Systems
activity status: active
contact:
  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
  url: http://creativecommons.org/licenses/by/3.0/
ontology purl: http://purl.obolibrary.org/obo/oarcs.owl
preferred prefix: OARCS
products:
  id: oarcs.owl
  ontology purl: http://purl.obolibrary.org/obo/oarcs.owl
repository: https://github.com/aszool/oarcs
tracker: https://github.com/aszool/oarcs/issues

Ontology of Biological Attributes
activity status: active
contact:
  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
  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
preferred prefix: OBA
products:
  id: oba.owl
  ontology purl: http://purl.obolibrary.org/obo/oba.owl
products:
  id: oba.obo
  ontology purl: http://purl.obolibrary.org/obo/oba.obo
products:
  id: oba/subsets/oba-basic.obo
  ontology purl: http://purl.obolibrary.org/obo/oba/subsets/oba-basic.obo
publications: The Ontology of Biological Attributes (OBA) - computational traits for the life sciences
  id: https://doi.org/10.1007/s00335-023-09992-1
repository: https://github.com/obophenotype/bio-attribute-ontology
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: The NHGRI-EBI GWAS Catalog: standards for reusability, sustainability and diversity
    id: https://doi.org/10.1093/nar/gkae1070
  type: annotation
  user: https://www.ebi.ac.uk/gwas/
usages:
  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: The next-generation Open Targets Platform: reimagined, redesigned, rebuilt
    id: https://doi.org/10.1093/nar/gkac1046
  type: Database
  user: https://platform.opentargets.org
usages:
  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
  publications: TraitBank: Practical semantics for organism attribute data
    id: https://doi.org/10.3233/SW-150190
  type: Database
  user: https://eol.org/traitbank
usages:
  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: A solution to the challenges of interdisciplinary aggregation and use of specimen-level trait data
    id: https://doi.org/10.1016/j.isci.2022.105101
  type: annotation
  user: https://futres.org/

Ontology of Biological and Clinical Statistics
activity status: active
contact:
  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
  url: http://creativecommons.org/licenses/by/4.0/
ontology purl: http://purl.obolibrary.org/obo/obcs.owl
preferred prefix: OBCS
products:
  id: obcs.owl
  ontology purl: http://purl.obolibrary.org/obo/obcs.owl
repository: https://github.com/obcs/obcs
tags: 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

Ontology for Biomedical Investigations
activity status: active
browsers: BioPortal Browser
  label: BioPortal
  url: http://bioportal.bioontology.org/ontologies/OBI
contact:
  github: bpeters42
  label: Bjoern Peters
  orcid: 0000-0002-8457-6693
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
  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
preferred prefix: OBI
products: OBI
  description: The full version of OBI in OWL format
  id: obi.owl
  ontology purl: http://purl.obolibrary.org/obo/obi.owl
products: OBI in OBO
  description: The OBO-format version of OBI
  id: obi.obo
  ontology purl: http://purl.obolibrary.org/obo/obi.obo
products: OBI Core
  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
products: OBI Base module
  description: Base module for OBI
  id: obi/obi-base.owl
  ontology purl: http://purl.obolibrary.org/obo/obi/obi-base.owl
publications: The Ontology for Biomedical Investigations
  id: https://www.ncbi.nlm.nih.gov/pubmed/27128319
repository: https://github.com/obi-ontology/obi
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
usages:
  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/
  user: https://www.encodeproject.org/
usages:
  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
usages:
  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/
usages:
  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#all
  user: http://www.neuinfo.org

Ontology for Biobanking
activity status: active
contact:
  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
  url: http://creativecommons.org/licenses/by/4.0/
ontology purl: http://purl.obolibrary.org/obo/obib.owl
preferred prefix: OBIB
products:
  id: obib.owl
  ontology purl: http://purl.obolibrary.org/obo/obib.owl
repository: https://github.com/biobanking/biobanking
tags: biobanking
tags: specimens
tags: bio-repository
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
usages:
  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
usages:
  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

Occupation Ontology
activity status: active
browsers: BioPortal Ontology Browser
  label: BioPortal
  url: https://bioportal.bioontology.org/ontologies/OCCO
contact:
  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
  url: https://creativecommons.org/licenses/by/4.0/
ontology purl: http://purl.obolibrary.org/obo/occo.owl
preferred prefix: OCCO
products:
  id: occo.owl
  ontology purl: http://purl.obolibrary.org/obo/occo.owl
repository: https://github.com/Occupation-Ontology/OccO
tracker: https://github.com/Occupation-Ontology/OccO/issues

The Ontology of Genes and Genomes
activity status: active
contact:
  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
  url: http://creativecommons.org/licenses/by/3.0/
ontology purl: http://purl.obolibrary.org/obo/ogg.owl
preferred prefix: OGG
products:
  id: ogg.owl
  ontology purl: http://purl.obolibrary.org/obo/ogg.owl
repository: https://bitbucket.org/hegroup/ogg
tracker: https://bitbucket.org/hegroup/ogg/issues/

Ontology for General Medical Science
activity status: active
contact:
  github: BAevermann
  label: Brian Aevermann
  orcid: 0000-0003-1346-1327
depicted by: https://avatars2.githubusercontent.com/u/12973154
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
  url: http://creativecommons.org/licenses/by/4.0/
ontology purl: http://purl.obolibrary.org/obo/ogms.owl
preferred prefix: OGMS
products:
  id: ogms.owl
  ontology purl: http://purl.obolibrary.org/obo/ogms.owl
publications: Toward an ontological treatment of disease and diagnosis
  id: https://www.ncbi.nlm.nih.gov/pubmed/21347182
  preferred: true
publications: Biomarkers in the Ontology for General Medical Science
  id: https://www.ncbi.nlm.nih.gov/pubmed/25991121
repository: https://github.com/OGMS/ogms
tags: medicine
taxon:
  id: NCBITaxon:9606
  label: Homo sapiens
tracker: https://github.com/OGMS/ogms/issues

Oral Health and Disease Ontology
activity status: active
contact:
  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
  url: http://creativecommons.org/licenses/by/4.0/
ontology purl: http://purl.obolibrary.org/obo/ohd.owl
preferred prefix: OHD
products: Oral Health and Disease Ontology
  id: ohd.owl
  ontology purl: http://purl.obolibrary.org/obo/ohd.owl
publications: Structuring, reuse and analysis of electronic dental data using the Oral Health and Disease Ontology
  id: https://www.ncbi.nlm.nih.gov/pubmed/32819435
repository: https://github.com/oral-health-and-disease-ontologies/ohd-ontology
tracker: https://github.com/oral-health-and-disease-ontologies/ohd-ontology/issues

Ontology of Host-Microbiome Interactions
activity status: active
contact:
  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
  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
preferred prefix: OHMI
products:
  id: ohmi.owl
  ontology purl: http://purl.obolibrary.org/obo/ohmi.owl
repository: https://github.com/ohmi-ontology/ohmi
tracker: https://github.com/ohmi-ontology/ohmi/issues

Ontology of Host Pathogen Interactions
activity status: active
contact:
  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
  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
preferred prefix: OHPI
products:
  id: ohpi.owl
  ontology purl: http://purl.obolibrary.org/obo/ohpi.owl
publications: Victors: a web-based knowledge base of virulence factors in human and animal pathogens
  id: https://www.ncbi.nlm.nih.gov/pubmed/30365026
repository: https://github.com/OHPI/ohpi
tracker: https://github.com/OHPI/ohpi/issues

Ontology for MIRNA Target
activity status: active
contact:
  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
  url: https://creativecommons.org/licenses/by/3.0/
ontology purl: http://purl.obolibrary.org/obo/omit.owl
page: http://omit.cis.usouthal.edu/
preferred prefix: OMIT
products:
  id: omit.owl
  ontology purl: http://purl.obolibrary.org/obo/omit.owl
repository: https://github.com/OmniSearch/omit
tracker: https://github.com/OmniSearch/omit/issues

OBO Metadata Ontology
activity status: active
contact:
  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
  url: https://creativecommons.org/publicdomain/zero/1.0/
ontology purl: http://purl.obolibrary.org/obo/omo.owl
preferred prefix: 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
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

Ontology of Microbial Phenotypes
activity status: active
contact:
  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
  url: http://creativecommons.org/licenses/by/3.0/
ontology purl: http://purl.obolibrary.org/obo/omp.owl
preferred prefix: OMP
products:
  id: omp.owl
  ontology purl: http://purl.obolibrary.org/obo/omp.owl
products:
  id: omp.obo
  ontology purl: http://purl.obolibrary.org/obo/omp.obo
publications: An ontology for microbial phenotypes
  id: https://doi.org/10.1186/s12866-014-0294-3
repository: https://github.com/microbialphenotypes/OMP-ontology
tracker: https://github.com/microbialphenotypes/OMP-ontology/issues

Ontology for Modeling and Representation of Social Entities
activity status: active
contact:
  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
  url: https://creativecommons.org/licenses/by/4.0/
ontology purl: http://purl.obolibrary.org/obo/omrse.owl
preferred prefix: OMRSE
products:
  id: omrse.owl
  ontology purl: http://purl.obolibrary.org/obo/omrse.owl
publications: The ontology of medically related social entities: recent developments
  id: https://www.ncbi.nlm.nih.gov/pubmed/27406187
repository: https://github.com/mcwdsi/OMRSE
tags: social
tags: behavior
taxon:
  id: NCBITaxon:9606
  label: Homo sapiens
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
usages:
  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: Development of an Intervention Setting Ontology for behaviour change: Specifying where interventions take place
    id: https://doi.org/10.12688/wellcomeopenres.15904.1
  type: owl:Ontology
  user: https://www.humanbehaviourchange.org

Ontology for Nutritional Epidemiology
activity status: active
contact:
  github: cyang0128
  label: Chen Yang
  orcid: 0000-0001-9202-5309
dependencies:
  id: foodon
dependencies:
  id: obi
dependencies:
  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
  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
preferred prefix: 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
tags: observational studies
tags: dietary surveys
tracker: https://github.com/cyang0128/Nutritional-epidemiologic-ontologies/issues

Ontology for Nutritional Studies
activity status: active
contact:
  github: FrancescoVit
  label: Francesco Vitali
  orcid: 0000-0001-9125-4337
dependencies:
  id: bfo
dependencies:
  id: chebi
dependencies:
  id: envo
dependencies:
  id: foodon
dependencies:
  id: ncbitaxon
dependencies:
  id: obi
dependencies:
  id: ro
dependencies:
  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
  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
preferred prefix: ONS
products: ONS latest release
  id: ons.owl
  ontology purl: http://purl.obolibrary.org/obo/ons.owl
publications: ONS: an ontology for a standardized description of interventions and observational studies in nutrition
  id: https://www.ncbi.nlm.nih.gov/pubmed/29736190
repository: https://github.com/enpadasi/Ontology-for-Nutritional-Studies
tags: nutrition, nutritional studies, nutrition professionals
tracker: https://github.com/enpadasi/Ontology-for-Nutritional-Studies/issues

OntoAvida: ontology for Avida digital evolution platform
activity status: active
browsers: Ontoavida HTML Browser
  label: Human-readable (HTML)
  url: https://owl.fortunalab.org/ontoavida/
contact:
  github: miguelfortuna
  label: Miguel A. Fortuna
  orcid: 0000-0002-8374-1941
dependencies:
  id: fbcv
dependencies:
  id: gsso
dependencies:
  id: ncit
dependencies:
  id: ro
dependencies:
  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
  url: https://creativecommons.org/licenses/by/4.0/
ontology purl: http://purl.obolibrary.org/obo/ontoavida.owl
preferred prefix: ONTOAVIDA
products: OWL
  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
products: OBO
  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
publications: Ontology for the Avida digital evolution platform
  id: https://doi.org/10.1038/s41597-023-02514-3
repository: https://gitlab.com/fortunalab/ontoavida
tags: digital evolution
tags: artificial life
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

Obstetric and Neonatal Ontology
activity status: active
browsers: BioPortal Browser
  label: BioPortal
  url: https://bioportal.bioontology.org/ontologies/ONTONEO
browsers: OntoBee Browser
  label: OntoBee
  url: https://ontobee.org/ontology/ONTONEO
contact:
  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
  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
preferred prefix: ONTONEO
products: ONTONEO
  description: The full version of ONTONEO in OWL format
  id: ontoneo.owl
  ontology purl: http://purl.obolibrary.org/obo/ontoneo.owl
publications: OntONeo: The Obstetric and Neonatal Ontology
  id: https://doi.org/10.5281/zenodo.17429771
publications: Formal Ontologies in Knowledge Organization within the Obstetric and Neonatal Domain
  id: https://doi.org/10.5281/zenodo.17508651
repository: https://github.com/ontoneo-project/Ontoneo
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/
usages:
  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

Ontology of Organizational Structures of Trauma centers and Trauma systems
activity status: active
contact:
  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
  url: http://creativecommons.org/licenses/by/4.0/
ontology purl: http://purl.obolibrary.org/obo/oostt.owl
preferred prefix: OOSTT
products:
  id: oostt.owl
  ontology purl: http://purl.obolibrary.org/obo/oostt.owl
repository: https://github.com/OOSTT/OOSTT
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/
usages:
  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
usages:
  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

Ontology for Parasite LifeCycle
activity status: active
contact:
  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
  url: https://creativecommons.org/licenses/by/4.0/
ontology purl: http://purl.obolibrary.org/obo/opl.owl
preferred prefix: 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
tags: parasite organism
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
usages:
  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

Ontology of Precision Medicine and Investigation
activity status: active
contact:
  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
  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
preferred prefix: OPMI
products:
  id: opmi.owl
  ontology purl: http://purl.obolibrary.org/obo/opmi.owl
repository: https://github.com/OPMI/opmi
tracker: https://github.com/OPMI/opmi/issues

Ontology of RNA Sequencing
activity status: active
contact:
  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
  url: http://creativecommons.org/licenses/by/4.0/
ontology purl: http://purl.obolibrary.org/obo/ornaseq.owl
preferred prefix: ORNASEQ
products:
  id: ornaseq.owl
  ontology purl: http://purl.obolibrary.org/obo/ornaseq.owl
repository: https://github.com/safisher/ornaseq
tracker: https://github.com/safisher/ornaseq/issues

Ontology of Vaccine Adverse Events
activity status: active
contact:
  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
  url: http://creativecommons.org/licenses/by/3.0/
ontology purl: http://purl.obolibrary.org/obo/ovae.owl
preferred prefix: OVAE
products:
  id: ovae.owl
  ontology purl: http://purl.obolibrary.org/obo/ovae.owl
repository: https://github.com/OVAE-Ontology/ovae
tracker: https://github.com/OVAE-Ontology/ovae/issues

Phenotype And Trait Ontology
activity status: active
browsers: BioPortal Ontology Browser
  label: BioPortal
  url: https://bioportal.bioontology.org/ontologies/PATO
contact:
  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
  url: http://creativecommons.org/licenses/by/3.0/
ontology purl: http://purl.obolibrary.org/obo/pato.owl
preferred prefix: PATO
products:
  id: pato.owl
  ontology purl: http://purl.obolibrary.org/obo/pato.owl
products:
  id: pato.obo
  ontology purl: http://purl.obolibrary.org/obo/pato.obo
products:
  id: pato.json
  ontology purl: http://purl.obolibrary.org/obo/pato.json
products:
  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: The anatomy of phenotype ontologies: principles, properties and applications
  id: https://www.ncbi.nlm.nih.gov/pubmed/28387809
publications: Using ontologies to describe mouse phenotypes
  id: https://www.ncbi.nlm.nih.gov/pubmed/15642100
repository: https://github.com/pato-ontology/pato
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
  publications: Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources
    id: https://www.ncbi.nlm.nih.gov/pubmed/30476213
  type: annotation
  user: https://hpo.jax.org/app/

Physiologically-Based Pharmacokinetic Ontology
activity status: active
browsers: BioPortal Ontology Browser
  label: BioPortal
  url: https://bioportal.bioontology.org/ontologies/pbpko
contact:
  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
  url: http://creativecommons.org/licenses/by/3.0/
ontology purl: http://purl.obolibrary.org/obo/pbpko.owl
preferred prefix: PBPKO
products:
  id: pbpko.owl
  ontology purl: http://purl.obolibrary.org/obo/pbpko.owl
products:
  id: pbpko.obo
  ontology purl: http://purl.obolibrary.org/obo/pbpko.obo
products:
  id: pbpko.json
  ontology purl: http://purl.obolibrary.org/obo/pbpko.json
repository: https://github.com/InSilicoVida-Research-Lab/pbpko
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

Provisional Cell Ontology
activity status: active
contact:
  github: dosumis
  label: David Osumi-Sutherland
  orcid: 0000-0002-7073-9172
dependencies:
  id: bfo
dependencies:
  id: chebi
dependencies:
  id: cl
dependencies:
  id: go
dependencies:
  id: nbo
dependencies:
  id: ncbitaxon
dependencies:
  id: omo
dependencies:
  id: pato
dependencies:
  id: pr
dependencies:
  id: ro
dependencies:
  id: so
dependencies:
  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
  url: http://creativecommons.org/licenses/by/4.0/
ontology purl: http://purl.obolibrary.org/obo/pcl.owl
preferred prefix: PCL
products:
  id: pcl.owl
  ontology purl: http://purl.obolibrary.org/obo/pcl.owl
products:
  id: pcl.obo
  ontology purl: http://purl.obolibrary.org/obo/pcl.obo
products:
  id: pcl.json
  ontology purl: http://purl.obolibrary.org/obo/pcl.json
products:
  id: pcl-base.owl
  ontology purl: http://purl.obolibrary.org/obo/pcl-base.owl
products:
  id: pcl-base.obo
  ontology purl: http://purl.obolibrary.org/obo/pcl-base.obo
products:
  id: pcl-base.json
  ontology purl: http://purl.obolibrary.org/obo/pcl-base.json
products:
  id: pcl-full.owl
  ontology purl: http://purl.obolibrary.org/obo/pcl-full.owl
products:
  id: pcl-full.obo
  ontology purl: http://purl.obolibrary.org/obo/pcl-full.obo
products:
  id: pcl-full.json
  ontology purl: http://purl.obolibrary.org/obo/pcl-full.json
products:
  id: pcl-simple.owl
  ontology purl: http://purl.obolibrary.org/obo/pcl-simple.owl
products:
  id: pcl-simple.obo
  ontology purl: http://purl.obolibrary.org/obo/pcl-simple.obo
products:
  id: pcl-simple.json
  ontology purl: http://purl.obolibrary.org/obo/pcl-simple.json
repository: https://github.com/obophenotype/provisional_cell_ontology
tracker: https://github.com/obophenotype/provisional_cell_ontology/issues

Population and Community Ontology
activity status: active
contact:
  github: ramonawalls
  label: Ramona Walls
  orcid: 0000-0001-8815-0078
dependencies:
  id: bfo
dependencies:
  id: caro
dependencies:
  id: envo
dependencies:
  id: go
dependencies:
  id: iao
dependencies:
  id: ncbitaxon
dependencies:
  id: pato
dependencies:
  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
  url: http://creativecommons.org/publicdomain/zero/1.0/
ontology purl: http://purl.obolibrary.org/obo/pco.owl
preferred prefix: PCO
products:
  id: pco.owl
  ontology purl: http://purl.obolibrary.org/obo/pco.owl
repository: https://github.com/PopulationAndCommunityOntology/pco
tags: collections of organisms
tracker: https://github.com/PopulationAndCommunityOntology/pco/issues

The Prescription of Drugs Ontology
activity status: active
contact:
  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
  url: https://creativecommons.org/licenses/by/4.0/
ontology purl: http://purl.obolibrary.org/obo/pdro.owl
preferred prefix: PDRO
products:
  id: pdro.owl
  ontology purl: http://purl.obolibrary.org/obo/pdro.owl
publications: The Prescription of Drug Ontology 2.0 (PDRO): More Than the Sum of Its Parts
  id: https://www.ncbi.nlm.nih.gov/pubmed/34831777
repository: https://github.com/OpenLHS/PDRO
tags: clinical documentation
tracker: https://github.com/OpenLHS/PDRO/issues

Plant Experimental Conditions Ontology
activity status: active
contact:
  github: jaiswalp
  label: Pankaj Jaiswal
  orcid: 0000-0002-1005-8383
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
  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
preferred prefix: PECO
products:
  id: peco.owl
  ontology purl: http://purl.obolibrary.org/obo/peco.owl
products:
  id: peco.obo
  ontology purl: http://purl.obolibrary.org/obo/peco.obo
publications: The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics.
  id: https://www.ncbi.nlm.nih.gov/pubmed/29186578
repository: https://github.com/Planteome/plant-experimental-conditions-ontology
tags: experimental conditions
tracker: https://github.com/Planteome/plant-experimental-conditions-ontology/issues

Pathogen Host Interaction Phenotype Ontology
activity status: active
contact:
  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
  url: http://creativecommons.org/licenses/by/3.0/
ontology purl: http://purl.obolibrary.org/obo/phipo.owl
preferred prefix: PHIPO
products:
  id: phipo.owl
  ontology purl: http://purl.obolibrary.org/obo/phipo.owl
products:
  id: phipo.obo
  ontology purl: http://purl.obolibrary.org/obo/phipo.obo
publications: PHI-base in 2022: a multi-species phenotype database for Pathogen-Host Interactions
  id: https://www.ncbi.nlm.nih.gov/pubmed/34788826
repository: https://github.com/PHI-base/phipo
tracker: https://github.com/PHI-base/phipo/issues

planaria-ontology
activity status: active
contact:
  github: srobb1
  label: Sofia Robb
  orcid: 0000-0002-3528-5267
dependencies:
  id: ro
dependencies:
  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
  url: http://creativecommons.org/licenses/by/3.0/
ontology purl: http://purl.obolibrary.org/obo/plana.owl
preferred prefix: PLANA
products:
  id: plana.owl
  ontology purl: http://purl.obolibrary.org/obo/plana.owl
products:
  id: plana.obo
  ontology purl: http://purl.obolibrary.org/obo/plana.obo
publications: Planarian Anatomy Ontology: a resource to connect data within and across experimental platforms
  id: https://www.ncbi.nlm.nih.gov/pubmed/34318308
repository: https://github.com/obophenotype/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/

Planarian Phenotype Ontology
activity status: active
contact:
  github: srobb1
  label: Sofia Robb
  orcid: 0000-0002-3528-5267
dependencies:
  id: go
dependencies:
  id: pato
dependencies:
  id: plana
dependencies:
  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
  url: http://creativecommons.org/licenses/by/3.0/
ontology purl: http://purl.obolibrary.org/obo/planp.owl
preferred prefix: PLANP
products:
  id: planp.owl
  ontology purl: http://purl.obolibrary.org/obo/planp.owl
products:
  id: planp.obo
  ontology purl: http://purl.obolibrary.org/obo/planp.obo
repository: https://github.com/obophenotype/planarian-phenotype-ontology
tracker: https://github.com/obophenotype/planarian-phenotype-ontology/issues

Plant Ontology
activity status: active
browsers: Planteome browser
  label: Planteome
  url: http://browser.planteome.org/amigo
contact:
  github: jaiswalp
  label: Pankaj Jaiswal
  orcid: 0000-0002-1005-8383
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
  url: https://creativecommons.org/licenses/by/4.0/
ontology purl: http://purl.obolibrary.org/obo/po.owl
page: https://github.com/Planteome/plant-ontology
preferred prefix: PO
products:
  id: po.owl
  ontology purl: http://purl.obolibrary.org/obo/po.owl
products:
  id: po.obo
  ontology purl: http://purl.obolibrary.org/obo/po.obo
publications: The plant ontology as a tool for comparative plant anatomy and genomic analyses.
  id: https://www.ncbi.nlm.nih.gov/pubmed/23220694
publications: The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics.
  id: https://www.ncbi.nlm.nih.gov/pubmed/29186578
repository: https://github.com/Planteome/plant-ontology
taxon:
  id: NCBITaxon:33090
  label: Viridiplantae
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/
usages:
  description: Maize CELL genomics DB uses PO to annotate images
  examples:
    description: LhG4 Promoter Drivers
    url: http://maize.jcvi.org/cellgenomics/geneDB_list.php
  user: http://maize.jcvi.org/
usages:
  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/
usages:
  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
  user: http://gramene.org/

Porifera Ontology
activity status: active
contact:
  github: bobthacker
  label: Bob Thacker
  orcid: 0000-0002-9654-0073
dependencies:
  id: ro
dependencies:
  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
  url: http://creativecommons.org/licenses/by/3.0/
ontology purl: http://purl.obolibrary.org/obo/poro.owl
preferred prefix: PORO
products:
  id: poro.owl
  ontology purl: http://purl.obolibrary.org/obo/poro.owl
products:
  id: poro.obo
  ontology purl: http://purl.obolibrary.org/obo/poro.obo
publications: The Porifera Ontology (PORO): enhancing sponge systematics with an anatomy ontology
  id: https://www.ncbi.nlm.nih.gov/pubmed/25276334
repository: https://github.com/obophenotype/porifera-ontology
taxon:
  id: NCBITaxon:6040
  label: Porifera
tracker: https://github.com/obophenotype/porifera-ontology/issues

Plant Phenology Ontology
activity status: active
contact:
  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
  url: http://creativecommons.org/licenses/by/3.0/
ontology purl: http://purl.obolibrary.org/obo/ppo.owl
preferred prefix: 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
tracker: https://github.com/PlantPhenoOntology/PPO/issues

PRotein Ontology (PRO)
activity status: active
browsers: BioPortal Browser
  label: BioPortal
  url: http://bioportal.bioontology.org/ontologies/PR
browsers: PRO Home
  label: PRO
  url: http://proconsortium.org
contact:
  github: nataled
  label: Darren Natale
  orcid: 0000-0001-5809-9523
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
  url: http://creativecommons.org/licenses/by/4.0/
ontology purl: http://purl.obolibrary.org/obo/pr.owl
preferred prefix: PR
products: pro_reasoned.owl
  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
products: pro_reasoned.obo
  description: PRO after reasoning has been applied, OBO format.
  id: pr.obo
  ontology purl: http://purl.obolibrary.org/obo/pr.obo
products: pro_nonreasoned.owl
  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
products: pro_nonreasoned.obo
  description: PRO without reasoning applied, OBO format.
  id: pr-asserted.obo
  ontology purl: http://purl.obolibrary.org/obo/pr-asserted.obo
publications: Protein Ontology (PRO): enhancing and scaling up the representation of protein entities
  id: https://www.ncbi.nlm.nih.gov/pubmed/27899649
repository: https://github.com/PROconsortium/PRoteinOntology
tags: proteins
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
usages:
  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

Process Chemistry Ontology
activity status: active
contact:
  github: schaferw
  label: Wes Schafer
  orcid: 0000-0002-8786-1756
dependencies:
  id: chebi
dependencies:
  id: cheminf
dependencies:
  id: obi
dependencies:
  id: pato
dependencies:
  id: ro
dependencies:
  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
  url: https://creativecommons.org/licenses/by/4.0/
ontology purl: http://purl.obolibrary.org/obo/proco.owl
preferred prefix: PROCO
products:
  id: proco.owl
  ontology purl: http://purl.obolibrary.org/obo/proco.owl
repository: https://github.com/proco-ontology/PROCO
tracker: https://github.com/proco-ontology/PROCO/issues

Performance Summary Display Ontology
activity status: active
contact:
  github: zachll
  label: Zach Landis-Lewis
  orcid: 0000-0002-9117-9338
dependencies:
  id: bfo
dependencies:
  id: iao
dependencies:
  id: ro
dependencies:
  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
  url: http://creativecommons.org/licenses/by/3.0/
ontology purl: http://purl.obolibrary.org/obo/psdo.owl
preferred prefix: PSDO
products:
  id: psdo.owl
  ontology purl: http://purl.obolibrary.org/obo/psdo.owl
repository: https://github.com/Display-Lab/psdo
tags: learning systems
tracker: https://github.com/Display-Lab/psdo/issues

Plant Stress Ontology
activity status: active
contact:
  github: cooperl09
  label: Laurel Cooper
  orcid: 0000-0002-6379-8932
dependencies:
  id: ro
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
  url: http://creativecommons.org/licenses/by/4.0/
ontology purl: http://purl.obolibrary.org/obo/pso.owl
preferred prefix: PSO
products:
  id: pso.owl
  ontology purl: http://purl.obolibrary.org/obo/pso.owl
products:
  id: pso.obo
  ontology purl: http://purl.obolibrary.org/obo/pso.obo
publications: The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics.
  id: https://www.ncbi.nlm.nih.gov/pubmed/29186578
repository: https://github.com/Planteome/plant-stress-ontology
tags: plant disease
tags: abiotic stress
tracker: https://github.com/Planteome/plant-stress-ontology/issues

Pathway ontology
activity status: active
browsers: RGD Ontology Browser
  label: RGD
  url: http://rgd.mcw.edu/rgdweb/ontology/view.html
contact:
  github: gthayman
  label: G. Thomas Hayman
  orcid: 0000-0002-9553-7227
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
  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/
preferred prefix: PW
products:
  id: pw.owl
  ontology purl: http://purl.obolibrary.org/obo/pw.owl
products:
  id: pw.obo
  ontology purl: http://purl.obolibrary.org/obo/pw.obo
publications: The Rat Genome Database pathway portal.
  id: https://www.ncbi.nlm.nih.gov/pubmed/21478484
publications: The pathway ontology - updates and applications.
  id: https://www.ncbi.nlm.nih.gov/pubmed/24499703
repository: https://github.com/rat-genome-database/PW-Pathway-Ontology
tags: biological process
tracker: https://github.com/rat-genome-database/PW-Pathway-Ontology/issues

Radiation Biology Ontology
activity status: active
contact:
  github: DanBerrios
  label: Daniel C. Berrios
  orcid: 0000-0003-4312-9552
dependencies:
  id: bfo
dependencies:
  id: chmo
dependencies:
  id: envo
dependencies:
  id: obi
dependencies:
  id: pato
dependencies:
  id: ro
dependencies:
  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
  url: http://creativecommons.org/licenses/by/3.0/
ontology purl: http://purl.obolibrary.org/obo/rbo.owl
preferred prefix: RBO
products:
  id: rbo.owl
  name: Radiation Biology Ontology main release in OWL format
  ontology purl: http://purl.obolibrary.org/obo/rbo.owl
products:
  id: rbo.obo
  name: Radiation Biology Ontology additional release in OBO format
  ontology purl: http://purl.obolibrary.org/obo/rbo.obo
products:
  id: rbo.json
  name: Radiation Biology Ontology additional release in OBOJSon format
  ontology purl: http://purl.obolibrary.org/obo/rbo.json
products:
  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
products:
  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
products:
  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
tracker: https://github.com/Radiobiology-Informatics-Consortium/RBO/issues

Relation Ontology
activity status: active
contact:
  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
  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
preferred prefix: RO
products: Relation Ontology
  description: Canonical edition
  id: ro.owl
  ontology purl: http://purl.obolibrary.org/obo/ro.owl
products: Relation Ontology in obo format
  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
products: Relation Ontology in obojson format
  id: ro.json
  ontology purl: http://purl.obolibrary.org/obo/ro.json
products: RO Core relations
  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
products: RO base ontology
  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
products: Interaction relations
  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
products: Ecology subset
  id: ro/subsets/ro-eco.owl
  ontology purl: http://purl.obolibrary.org/obo/ro/subsets/ro-eco.owl
products: Neuroscience 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
repository: https://github.com/oborel/obo-relations
tags: relations
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: A method for increasing expressivity of Gene Ontology annotations using a compositional approach
    id: https://www.ncbi.nlm.nih.gov/pubmed/24885854
  type: annotation
  user: http://geneontology.org

Rat Strain Ontology
activity status: active
browsers: RGD Ontology Browser
  label: RGD
  url: http://rgd.mcw.edu/rgdweb/ontology/view.html
contact:
  github: shurjenw
  label: Shur-Jen Wang
  orcid: 0000-0001-5256-8683
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
  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/
preferred prefix: RS
products:
  id: rs.owl
  ontology purl: http://purl.obolibrary.org/obo/rs.owl
products:
  id: rs.obo
  ontology purl: http://purl.obolibrary.org/obo/rs.obo
publications: Rat Strain Ontology: structured controlled vocabulary designed to facilitate access to strain data at RGD.
  id: https://www.ncbi.nlm.nih.gov/pubmed/24267899
repository: https://github.com/rat-genome-database/RS-Rat-Strain-Ontology
taxon:
  id: NCBITaxon:10114
  label: Rattus
tracker: https://github.com/rat-genome-database/RS-Rat-Strain-Ontology/issues

Name Reaction Ontology
activity status: active
contact:
  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
  url: https://creativecommons.org/licenses/by/4.0/
ontology purl: http://purl.obolibrary.org/obo/rxno.owl
preferred prefix: RXNO
products: Name Reaction Ontology
  id: rxno.owl
  ontology purl: http://purl.obolibrary.org/obo/rxno.owl
repository: https://github.com/rsc-ontologies/rxno
tracker: https://github.com/rsc-ontologies/rxno/issues

Scientific Evidence and Provenance Information Ontology
activity status: active
contact:
  github: mbrush
  label: Matthew Brush
  orcid: 0000-0002-1048-5019
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
  url: https://creativecommons.org/licenses/by/3.0/
ontology purl: http://purl.obolibrary.org/obo/sepio.owl
preferred prefix: SEPIO
products: SEPIO
  id: sepio.owl
  ontology purl: http://purl.obolibrary.org/obo/sepio.owl
repository: https://github.com/monarch-initiative/SEPIO-ontology
tags: scientific claims
tags: evidence
tracker: https://github.com/monarch-initiative/SEPIO-ontology/issues

Space Life Sciences Ontology
activity status: active
browsers: BioPortal Ontology Browser
  label: BioPortal
  url: https://bioportal.bioontology.org/ontologies/SLSO
contact:
  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
  url: http://creativecommons.org/licenses/by/3.0/
ontology purl: http://purl.obolibrary.org/obo/slso.owl
preferred prefix: SLSO
products:
  id: slso.owl
  ontology purl: http://purl.obolibrary.org/obo/slso.owl
products:
  id: slso.obo
  ontology purl: http://purl.obolibrary.org/obo/slso.obo
products:
  id: slso.json
  ontology purl: http://purl.obolibrary.org/obo/slso.json
products:
  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
tracker: https://github.com/nasa/LSDAO/issues

Sequence types and features ontology
activity status: active
contact:
  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
  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
preferred prefix: SO
products: Main SO OWL release
  id: so.owl
  ontology purl: http://purl.obolibrary.org/obo/so.owl
products: Main SO release in OBO Format
  id: so.obo
  ontology purl: http://purl.obolibrary.org/obo/so.obo
products: 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.owl
  ontology purl: http://purl.obolibrary.org/obo/so/subsets/SOFA.owl
products: Sequence Ontology Feature Annotation (SOFA) subset (OBO Format)
  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
publications: The Sequence Ontology: a tool for the unification of genome annotations.
  id: https://www.ncbi.nlm.nih.gov/pubmed/15892872
publications: Evolution of the Sequence Ontology terms and relationships.
  id: https://www.ncbi.nlm.nih.gov/pubmed/20226267
repository: https://github.com/The-Sequence-Ontology/SO-Ontologies
tags: biological sequence
tracker: https://github.com/The-Sequence-Ontology/SO-Ontologies/issues

Spider Ontology
activity status: active
contact:
  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
  url: https://creativecommons.org/licenses/by/3.0/
ontology purl: http://purl.obolibrary.org/obo/spd.owl
preferred prefix: SPD
products:
  id: spd.owl
  ontology purl: http://purl.obolibrary.org/obo/spd.owl
publications: The Spider Anatomy Ontology (SPD)—A Versatile Tool to Link Anatomy with Cross-Disciplinary Data
  id: https://doi.org/10.3390/d11100202
repository: https://github.com/obophenotype/spider-ontology
taxon:
  id: NCBITaxon:6893
  label: spiders
tracker: https://github.com/obophenotype/spider-ontology/issues

The Statistical Methods Ontology
activity status: active
contact:
  github: proccaserra
  label: Philippe Rocca-Serra
  orcid: 0000-0001-9853-5668
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
  url: http://creativecommons.org/licenses/by/3.0/
ontology purl: http://purl.obolibrary.org/obo/stato.owl
preferred prefix: STATO
products:
  id: stato.owl
  ontology purl: http://purl.obolibrary.org/obo/stato.owl
publications: Experiment design driven FAIRification of omics data matrices, an exemplar
  id: https://www.ncbi.nlm.nih.gov/pubmed/31831744
publications: Semantic concept schema of the linear mixed model of experimental observations
  id: https://www.ncbi.nlm.nih.gov/pubmed/32109232
repository: https://github.com/ISA-tools/stato
tags: statistics
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: struct: an R/Bioconductor-based framework for standardized metabolomics data analysis and beyond
    id: https://www.ncbi.nlm.nih.gov/pubmed/33325493
  type: annotation
  user: https://bioconductor.org/packages/release/bioc/html/struct.html
usages:
  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: Making science computable: Developing code systems for statistics, study design, and risk of bias
    id: https://www.ncbi.nlm.nih.gov/pubmed/33486066
  type: annotation
  user: https://fevir.net/resources/CodeSystem/27270#STATO:0000039
usages:
  description: OBCS
  publications: The Ontology of Biological and Clinical Statistics (OBCS) for standardized and reproducible statistical analysis
    id: https://www.ncbi.nlm.nih.gov/pubmed/27627881
  type: annotation
  user: https://github.com/obcs/obcs

Software ontology
activity status: active
contact:
  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
  url: https://creativecommons.org/licenses/by/4.0/
ontology purl: http://purl.obolibrary.org/obo/swo.owl
preferred prefix: SWO
products:
  id: swo.owl
  ontology purl: http://purl.obolibrary.org/obo/swo.owl
products:
  id: swo.json
  ontology purl: http://purl.obolibrary.org/obo/swo.json
publications: The Software Ontology (SWO): a resource for reproducibility in biomedical data analysis, curation and digital preservation
  id: https://www.ncbi.nlm.nih.gov/pubmed/25068035
repository: https://github.com/allysonlister/swo
tags: software
tracker: https://github.com/allysonlister/swo/issues

Symptom Ontology
activity status: active
contact:
  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
  url: https://creativecommons.org/publicdomain/zero/1.0/
ontology purl: http://purl.obolibrary.org/obo/symp.owl
preferred prefix: SYMP
products:
  id: symp.owl
  ontology purl: http://purl.obolibrary.org/obo/symp.owl
products:
  id: symp.obo
  ontology purl: http://purl.obolibrary.org/obo/symp.obo
publications: GeMInA, Genomic Metadata for Infectious Agents, a geospatial surveillance pathogen database
  id: https://www.ncbi.nlm.nih.gov/pubmed/19850722
publications: The Human Disease Ontology 2022 update
  id: https://www.ncbi.nlm.nih.gov/pubmed/34755882
repository: https://github.com/DiseaseOntology/SymptomOntology
tags: disease
taxon:
  id: NCBITaxon:9606
  label: Homo sapiens
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/
  user: https://disease-ontology.org/

terms4FAIRskills
activity status: active
contact:
  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
  url: https://creativecommons.org/licenses/by/4.0/
ontology purl: http://purl.obolibrary.org/obo/t4fs.owl
preferred prefix: T4FS
products:
  id: t4fs.owl
  ontology purl: http://purl.obolibrary.org/obo/t4fs.owl
products:
  id: t4fs.obo
  ontology purl: http://purl.obolibrary.org/obo/t4fs.obo
products:
  id: t4fs.json
  ontology purl: http://purl.obolibrary.org/obo/t4fs.json
products: 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.owl
  ontology purl: http://purl.obolibrary.org/obo/t4fs-community.owl
products: 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.obo
  ontology purl: http://purl.obolibrary.org/obo/t4fs-community.obo
products: 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.
  id: t4fs-community.json
  ontology purl: http://purl.obolibrary.org/obo/t4fs-community.json
publications: EOSC Co-creation funded project 074: Delivery of a proof of concept for terms4FAIRskills: Technical report
  id: https://doi.org/10.5281/zenodo.4705219
pull request added: 2140
repository: https://github.com/terms4fairskills/FAIRterminology
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/
usages:
  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
usages:
  description: FAIRsFAIR Competence Centre (project wp6) will provide a platform for training materials resulting from project training activities, annot
  user: https://www.fairsfair.eu/

Taxonomic rank vocabulary
activity status: active
contact:
  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
  url: http://creativecommons.org/publicdomain/zero/1.0/
ontology purl: http://purl.obolibrary.org/obo/taxrank.owl
preferred prefix: TAXRANK
products:
  id: taxrank.owl
  ontology purl: http://purl.obolibrary.org/obo/taxrank.owl
products:
  id: taxrank.obo
  ontology purl: http://purl.obolibrary.org/obo/taxrank.obo
publications: The vertebrate taxonomy ontology: a framework for reasoning across model organism and species phenotypes
  id: https://doi.org/10.1186/2041-1480-4-34
repository: https://github.com/phenoscape/taxrank
tags: taxonomy
tracker: https://github.com/phenoscape/taxrank/issues

Plant Trait Ontology
activity status: active
browsers: Planteome browser
  label: Planteome
  url: http://browser.planteome.org/amigo/term/TO:0000387#display-lineage-tab
contact:
  github: jaiswalp
  label: Pankaj Jaiswal
  orcid: 0000-0002-1005-8383
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
  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
preferred prefix: TO
products:
  id: to.owl
  ontology purl: http://purl.obolibrary.org/obo/to.owl
products:
  id: to.obo
  ontology purl: http://purl.obolibrary.org/obo/to.obo
publications: The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics.
  id: https://www.ncbi.nlm.nih.gov/pubmed/29186578
repository: https://github.com/Planteome/plant-trait-ontology
taxon:
  id: NCBITaxon:33090
  label: Viridiplantae
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/
usages:
  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
  user: http://gramene.org/

Pathogen Transmission Ontology
activity status: active
contact:
  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
  url: https://creativecommons.org/publicdomain/zero/1.0/
ontology purl: http://purl.obolibrary.org/obo/trans.owl
preferred prefix: TRANS
products:
  id: trans.owl
  ontology purl: http://purl.obolibrary.org/obo/trans.owl
products:
  id: trans.obo
  ontology purl: http://purl.obolibrary.org/obo/trans.obo
publications: GeMInA, Genomic Metadata for Infectious Agents, a geospatial surveillance pathogen database
  id: https://www.ncbi.nlm.nih.gov/pubmed/19850722
publications: The Human Disease Ontology 2022 update
  id: https://www.ncbi.nlm.nih.gov/pubmed/34755882
repository: https://github.com/DiseaseOntology/PathogenTransmissionOntology
tags: disease
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/
  user: https://disease-ontology.org/

Teleost taxonomy ontology
activity status: active
contact:
  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
  url: http://creativecommons.org/publicdomain/zero/1.0/
ontology purl: http://purl.obolibrary.org/obo/tto.owl
preferred prefix: TTO
products:
  id: tto.obo
  ontology purl: http://purl.obolibrary.org/obo/tto.obo
products:
  id: tto.owl
  ontology purl: http://purl.obolibrary.org/obo/tto.owl
publications: The Teleost Taxonomy Ontology
  id: https://doi.org/10.1038/npre.2010.4629.1
repository: https://github.com/phenoscape/teleost-taxonomy-ontology
tags: taxonomy
taxon:
  id: NCBITaxon:32443
  label: Teleostei
tracker: https://github.com/phenoscape/teleost-taxonomy-ontology/issues

Toxic Process Ontology
activity status: active
browsers: BioPortal Browser
  label: BioPortal
  url: http://bioportal.bioontology.org/ontologies/TXPO
browsers: TOXPILOT
  label: TOXPILOT
  url: https://toxpilot.nibiohn.go.jp/
contact:
  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
  url: https://creativecommons.org/licenses/by/3.0/
ontology purl: http://purl.obolibrary.org/obo/txpo.owl
preferred prefix: TXPO
products:
  id: txpo.owl
  ontology purl: http://purl.obolibrary.org/obo/txpo.owl
publications: Ontological approach to the knowledge systematization of a toxic process and toxic course representation framework for early drug risk management
  id: https://www.ncbi.nlm.nih.gov/pubmed/32883995
repository: https://github.com/txpo-ontology/TXPO
tags: toxicity
tracker: https://github.com/txpo-ontology/TXPO/issues

Uberon multi-species anatomy ontology
activity status: active
browsers: Gene Ontology AmiGO 2 Browser
  label: RGD
  url: http://rgd.mcw.edu/rgdweb/ontology/view.html
browsers: Gene Ontology AmiGO 2 Browser
  label: AmiGO (SUBSET)
  url: http://amigo.geneontology.org/amigo/term/UBERON:0001062#display-lineage-tab
browsers: Bgee gene expression queries
  label: Bgee (gene expression)
  url: http://bgee.org/
browsers: FANTOM5 Data Portal
  label: FANTOM5
  url: http://fantom.gsc.riken.jp/5/sstar/UBERON:0001890
browsers: INCF KnowledgeSpace Portal
  label: KnowledgeSpace
  url: https://knowledge-space.org/index.php/pages/view/UBERON:0000061
contact:
  github: cmungall
  label: Chris Mungall
  orcid: 0000-0002-6601-2165
dependencies:
  id: bfo
dependencies:
  id: bspo
dependencies:
  id: chebi
dependencies:
  id: cl
dependencies:
  id: envo
dependencies:
  id: go
dependencies:
  id: nbo
dependencies:
  id: ncbitaxon
dependencies:
  id: omo
dependencies:
  id: pato
dependencies:
  id: pr
dependencies:
  id: ro
description: An integrated cross-species anatomy ontology covering animals and bridging multiple species-specific ontologies
domain: anatomy and development
funded by: NIH R24-OD011883
  id: https://taggs.hhs.gov/Detail/AwardDetail
funded by: NIH R01-HG004838
  id: https://grantome.com/grant/NIH/R01-HG004838
funded by: NIH P41-HG002273
  id: https://taggs.hhs.gov/Detail/AwardDetail
funded by: NSF DEB-0956049
  id: https://www.nsf.gov/awardsearch/showAward
homepage: http://uberon.org
id: uberon
layout: ontology_detail
license:
  label: CC BY 3.0
  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
preferred prefix: UBERON
products: Uberon
  description: core ontology
  id: uberon.owl
  is canonical: true
  ontology purl: http://purl.obolibrary.org/obo/uberon.owl
  type: owl:Ontology
products: Uberon base 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
products: Uberon basic
  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
  type: obo-basic-ontology
products: Uberon collected metazoan 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
  type: MergedOntology
products: Uberon composite metazoan ontology
  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
  type: MergedOntology
products: Uberon composite vertebrate ontology
  id: uberon/composite-vertebrate.owl
  mireots from: zfa
  mireots from: xao
  mireots from: fbbt
  mireots from: wbbt
  mireots from: ma
  mireots from: fma
  mireots from: emapa
  mireots from: ehdaa2
  ontology purl: http://purl.obolibrary.org/obo/uberon/composite-vertebrate.owl
  page: https://obophenotype.github.io/uberon/combined_multispecies/
  taxon: Vertebrata
  type: MergedOntology
publications: Uberon, an integrative multi-species anatomy ontology
  id: https://www.ncbi.nlm.nih.gov/pubmed/22293552
publications: Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon
  id: https://www.ncbi.nlm.nih.gov/pubmed/25009735
repository: https://github.com/obophenotype/uberon
taxon:
  id: NCBITaxon:33208
  label: Metazoa
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/
  see also: https://doi.org/10.25504/FAIRsharing.x6d6sx
  type: annotation
  user: http://bgee.org/
usages:
  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: Ontology application and use at the ENCODE DCC
    id: https://www.ncbi.nlm.nih.gov/pubmed/25776021
  see also: https://doi.org/10.25504/FAIRsharing.v0hbjs
  type: annotation
  user: https://www.encodeproject.org/
usages:
  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/
usages:
  description: Querying expression and phenotype data
  type: query
  user: https://monarchinitiative.org/
usages:
  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/
usages:
  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
usages:
  description: Searchable collection of neuroscience data and ontology for neuroscience
  type: Database
  user: https://neuinfo.org/
usages:
  description: cooperative data platform to be used by diverse communities in making data more FAIR.
  type: Database
  user: https://scicrunch.org/
usages:
  description: SCPortalen
  publications: SCPortalen: human and mouse single-cell centric database
    id: https://www.ncbi.nlm.nih.gov/pubmed/29045713
  type: Database
  user: http://single-cell.clst.riken.jp/
usages:
  description: ChEMBL uses Uberon to describe organ/tissue information in assays
  publications: ChEMBL: towards direct deposition of bioassay data
    id: https://www.ncbi.nlm.nih.gov/pubmed/30398643
  type: Database
  user: https://www.ebi.ac.uk/chembl/

Units of measurement ontology
activity status: active
contact:
  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
  url: http://creativecommons.org/licenses/by/3.0/
ontology purl: http://purl.obolibrary.org/obo/uo.owl
preferred prefix: UO
products:
  id: uo.owl
  ontology purl: http://purl.obolibrary.org/obo/uo.owl
products:
  id: uo.obo
  ontology purl: http://purl.obolibrary.org/obo/uo.obo
products:
  id: uo.json
  ontology purl: http://purl.obolibrary.org/obo/uo.json
publications: The Units Ontology: a tool for integrating units of measurement in science
  id: https://www.ncbi.nlm.nih.gov/pubmed/23060432
repository: https://github.com/bio-ontology-research-group/unit-ontology
tracker: https://github.com/bio-ontology-research-group/unit-ontology/issues

Unified Phenotype Ontology (uPheno)
activity status: active
contact:
  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
  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
preferred prefix: UPHENO
products: uPheno 1 (inactive)
  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
products: uPheno MP-HP equivalence axioms
  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
products: uPheno 2
  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
publications: The Unified Phenotype Ontology (uPheno): A framework for cross-species integrative phenomics
  id: https://doi.org/10.1101/2024.09.18.613276
publications: Phenotype Ontologies Traversing All The Organisms (POTATO) workshop aims to reconcile logical definitions across species
  id: https://zenodo.org/record/2382757
publications: Phenotype Ontologies Traversing All The Organisms (POTATO) workshop: 2nd edition
  id: https://zenodo.org/record/3352149
repository: https://github.com/obophenotype/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: The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species
    id: https://www.ncbi.nlm.nih.gov/pubmed/27899636
  type: analysis
  user: https://monarchinitiative.org/

Vertebrate Breed Ontology
activity status: active
contact:
  github: sabrinatoro
  label: Sabrina Toro
  orcid: 0000-0002-4142-7153
dependencies:
  id: ncbitaxon
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
  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
preferred prefix: VBO
products:
  id: vbo.owl
  name: Vertebrate Breed Ontology main release in OWL format
  ontology purl: http://purl.obolibrary.org/obo/vbo.owl
products:
  id: vbo.obo
  name: Vertebrate Breed Ontology additional release in OBO format
  ontology purl: http://purl.obolibrary.org/obo/vbo.obo
products:
  id: vbo.json
  name: Vertebrate Breed Ontology additional release in OBOJSon format
  ontology purl: http://purl.obolibrary.org/obo/vbo.json
products:
  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
products:
  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
products:
  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: The Vertebrate Breed Ontology: Toward Effective Breed Data Standardization
  id: https://doi.org/10.1111/jvim.70133
repository: https://github.com/monarch-initiative/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/
usages:
  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

Vaccine Ontology
activity status: active
contact:
  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
  url: http://creativecommons.org/licenses/by/4.0/
ontology purl: http://purl.obolibrary.org/obo/vo.owl
preferred prefix: VO
products:
  id: vo.owl
  ontology purl: http://purl.obolibrary.org/obo/vo.owl
publications: Ontology representation and analysis of vaccine formulation and administration and their effects on vaccine immune responses
  id: https://www.ncbi.nlm.nih.gov/pubmed/23256535
publications: Mining of vaccine-associated IFN-γ gene interaction networks using the Vaccine Ontology
  id: https://www.ncbi.nlm.nih.gov/pubmed/21624163
repository: https://github.com/vaccineontology/VO
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
  examples:
    description: A specific vaccine ‘Allogeneic Tumor Cell Vaccine’ curated in VO for VIOLIN vaccine record
    url: https://violinet.org/vaxquery/query_detail.php#vaccine_5878
  user: https://violinet.org
usages:
  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
  user: https://www.niaid.nih.gov/research/vaccine-adjuvant-compendium-vac
usages:
  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/
usages:
  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/

Vertebrate trait ontology
activity status: active
contact:
  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
  url: https://creativecommons.org/licenses/by/4.0/
ontology purl: http://purl.obolibrary.org/obo/vt.owl
preferred prefix: VT
products:
  id: vt.owl
  ontology purl: http://purl.obolibrary.org/obo/vt.owl
repository: https://github.com/AnimalGenome/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
  user: https://www.animalgenome.org/cgi-bin/QTLdb/index
usages:
  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
  user: https://rgd.mcw.edu/rgdweb/ontology/view.html
usages:
  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

Vertebrate Taxonomy Ontology
activity status: active
contact:
  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
  url: http://creativecommons.org/publicdomain/zero/1.0/
ontology purl: http://purl.obolibrary.org/obo/vto.owl
preferred prefix: VTO
products:
  id: vto.owl
  ontology purl: http://purl.obolibrary.org/obo/vto.owl
products:
  id: vto.obo
  ontology purl: http://purl.obolibrary.org/obo/vto.obo
publications: The vertebrate taxonomy ontology: a framework for reasoning across model organism and species phenotypes
  id: https://doi.org/10.1186/2041-1480-4-34
repository: https://github.com/phenoscape/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

C. elegans Gross Anatomy Ontology
activity status: active
contact:
  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
  url: https://creativecommons.org/licenses/by/4.0/
ontology purl: http://purl.obolibrary.org/obo/wbbt.owl
preferred prefix: WBbt
products:
  id: wbbt.owl
  ontology purl: http://purl.obolibrary.org/obo/wbbt.owl
products:
  id: wbbt.obo
  ontology purl: http://purl.obolibrary.org/obo/wbbt.obo
publications: Building a cell and anatomy ontology of Caenorhabditis elegans
  id: https://www.ncbi.nlm.nih.gov/pubmed/18629098
repository: https://github.com/obophenotype/c-elegans-gross-anatomy-ontology
taxon:
  id: NCBITaxon:6237
  label: Caenorhabditis
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
  publications: WormBase: a modern Model Organism Information Resource
    id: https://www.ncbi.nlm.nih.gov/pubmed/31642470
  type: annotation
  user: https://www.wormbase.org/

C. elegans development ontology
activity status: active
contact:
  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
  url: https://creativecommons.org/licenses/by/4.0/
ontology purl: http://purl.obolibrary.org/obo/wbls.owl
preferred prefix: WBls
products:
  id: wbls.owl
  ontology purl: http://purl.obolibrary.org/obo/wbls.owl
products:
  id: wbls.obo
  ontology purl: http://purl.obolibrary.org/obo/wbls.obo
publications: WormBase: a modern Model Organism Information Resource
  id: https://www.ncbi.nlm.nih.gov/pubmed/31642470
repository: https://github.com/obophenotype/c-elegans-development-ontology
tags: developemental life stage
taxon:
  id: NCBITaxon:6237
  label: Caenorhabditis
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
  publications: WormBase: a modern Model Organism Information Resource
    id: https://www.ncbi.nlm.nih.gov/pubmed/31642470
  type: annotation
  user: https://www.wormbase.org/

C. elegans phenotype
activity status: active
contact:
  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
  url: http://creativecommons.org/licenses/by/4.0/
ontology purl: http://purl.obolibrary.org/obo/wbphenotype.owl
preferred prefix: WBPhenotype
products:
  id: wbphenotype.owl
  ontology purl: http://purl.obolibrary.org/obo/wbphenotype.owl
products:
  id: wbphenotype.obo
  ontology purl: http://purl.obolibrary.org/obo/wbphenotype.obo
products:
  id: wbphenotype/wbphenotype-base.owl
  ontology purl: http://purl.obolibrary.org/obo/wbphenotype/wbphenotype-base.owl
publications: Worm Phenotype Ontology: integrating phenotype data within and beyond the C. elegans community.
  id: https://www.ncbi.nlm.nih.gov/pubmed/21261995
repository: https://github.com/obophenotype/c-elegans-phenotype-ontology
taxon:
  id: NCBITaxon:6237
  label: Caenorhabditis
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
  publications: WormBase: a modern Model Organism Information Resource
    id: https://www.ncbi.nlm.nih.gov/pubmed/31642470
  type: annotation
  user: https://www.wormbase.org/
usages:
  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: The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species
    id: https://www.ncbi.nlm.nih.gov/pubmed/27899636
  type: annotation
  user: https://monarchinitiative.org/

Xenopus Anatomy Ontology
activity status: active
contact:
  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
id: xao
in foundry order: 1
layout: ontology_detail
license:
  label: CC BY 3.0
  url: http://creativecommons.org/licenses/by/3.0/
ontology purl: http://purl.obolibrary.org/obo/xao.owl
preferred prefix: XAO
products:
  id: xao.owl
  ontology purl: http://purl.obolibrary.org/obo/xao.owl
products:
  id: xao.obo
  ontology purl: http://purl.obolibrary.org/obo/xao.obo
publications: An ontology for Xenopus anatomy and development.
  id: https://www.ncbi.nlm.nih.gov/pubmed/18817563
publications: Enhanced XAO: the ontology of Xenopus anatomy and development underpins more accurate annotation of gene expression and queries on Xenbase.
  id: https://www.ncbi.nlm.nih.gov/pubmed/24139024
repository: https://github.com/xenopus-anatomy/xao
taxon:
  id: NCBITaxon:8353
  label: Xenopus
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
  user: http://www.xenbase.org

Experimental condition ontology
activity status: active
browsers: RGD Ontology Browser
  label: RGD
  url: http://rgd.mcw.edu/rgdweb/ontology/view.html
contact:
  github: jrsjrs
  label: Jennifer Smith
  orcid: 0000-0002-6443-9376
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
id: xco
layout: ontology_detail
license:
  label: CC0 1.0
  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/
preferred prefix: XCO
products:
  id: xco.owl
  ontology purl: http://purl.obolibrary.org/obo/xco.owl
products:
  id: xco.obo
  ontology purl: http://purl.obolibrary.org/obo/xco.obo
publications: Three ontologies to define phenotype measurement data.
  id: https://www.ncbi.nlm.nih.gov/pubmed/22654893
publications: The clinical measurement, measurement method and experimental condition ontologies: expansion, improvements and new applications.
  id: https://www.ncbi.nlm.nih.gov/pubmed/24103152
repository: https://github.com/rat-genome-database/XCO-experimental-condition-ontology
tags: clinical
tracker: https://github.com/rat-genome-database/XCO-experimental-condition-ontology/issues

HUPO-PSI cross-linking and derivatization reagents controlled vocabulary
activity status: active
contact:
  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
  url: https://creativecommons.org/licenses/by/3.0/
ontology purl: http://purl.obolibrary.org/obo/xlmod.owl
page: http://www.psidev.info/groups/controlled-vocabularies
preferred prefix: XLMOD
products:
  id: xlmod.obo
  ontology purl: http://purl.obolibrary.org/obo/xlmod.obo
products:
  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
tracker: https://github.com/HUPO-PSI/xlmod-CV/issues

Xenopus Phenotype Ontology
activity status: active
contact:
  github: seger
  label: Erik Segerdell
  orcid: 0000-0002-9611-1279
dependencies:
  id: bfo
dependencies:
  id: chebi
dependencies:
  id: cl
dependencies:
  id: go
dependencies:
  id: iao
dependencies:
  id: pato
dependencies:
  id: ro
dependencies:
  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
  url: http://creativecommons.org/licenses/by/3.0/
ontology purl: http://purl.obolibrary.org/obo/xpo.owl
preferred prefix: XPO
products:
  id: xpo.owl
  ontology purl: http://purl.obolibrary.org/obo/xpo.owl
products:
  id: xpo.obo
  ontology purl: http://purl.obolibrary.org/obo/xpo.obo
publications: The Xenopus phenotype ontology: bridging model organism phenotype data to human health and development.
  id: https://www.ncbi.nlm.nih.gov/pubmed/35317743
repository: https://github.com/obophenotype/xenopus-phenotype-ontology
taxon:
  id: NCBITaxon:8353
  label: Xenopus
tracker: https://github.com/obophenotype/xenopus-phenotype-ontology/issues

Zebrafish Experimental Conditions Ontology
activity status: active
contact:
  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
  url: http://creativecommons.org/licenses/by/3.0/
ontology purl: http://purl.obolibrary.org/obo/zeco.owl
preferred prefix: ZECO
products:
  id: zeco.obo
  ontology purl: http://purl.obolibrary.org/obo/zeco.obo
products:
  id: zeco.owl
  ontology purl: http://purl.obolibrary.org/obo/zeco.owl
products:
  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
tracker: https://github.com/ybradford/zebrafish-experimental-conditions-ontology/issues

Zebrafish anatomy and development ontology
activity status: active
contact:
  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
  url: http://creativecommons.org/licenses/by/3.0/
ontology purl: http://purl.obolibrary.org/obo/zfa.owl
preferred prefix: ZFA
products:
  id: zfa.owl
  ontology purl: http://purl.obolibrary.org/obo/zfa.owl
products:
  id: zfa.obo
  ontology purl: http://purl.obolibrary.org/obo/zfa.obo
publications: The zebrafish anatomy and stage ontologies: representing the anatomy and development of Danio rerio.
  id: https://www.ncbi.nlm.nih.gov/pubmed/24568621
repository: https://github.com/cerivs/zebrafish-anatomical-ontology
taxon:
  id: NCBITaxon:7954
  label: Danio
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

Zebrafish developmental stages ontology
activity status: active
contact:
  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
  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
preferred prefix: ZFS
products:
  id: zfs.owl
  ontology purl: http://purl.obolibrary.org/obo/zfs.owl
products:
  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
tracker: https://github.com/cerivs/zebrafish-anatomical-ontology/issues

Zebrafish Phenotype Ontology
activity status: active
contact:
  github: ybradford
  label: Yvonne Bradford
  orcid: 0000-0002-9900-7880
dependencies:
  id: bfo
dependencies:
  id: bspo
dependencies:
  id: go
dependencies:
  id: pato
dependencies:
  id: ro
dependencies:
  id: uberon
dependencies:
  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
  url: http://creativecommons.org/licenses/by/3.0/
ontology purl: http://purl.obolibrary.org/obo/zp.owl
preferred prefix: ZP
products:
  id: zp.owl
  ontology purl: http://purl.obolibrary.org/obo/zp.owl
products:
  id: zp.obo
  ontology purl: http://purl.obolibrary.org/obo/zp.obo
repository: https://github.com/obophenotype/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: The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species
    id: https://www.ncbi.nlm.nih.gov/pubmed/27899636
  type: annotation
  user: https://monarchinitiative.org/

Gender, Sex, and Sexual Orientation (GSSO) ontology
activity status: active
contact:
  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
preferred prefix: GSSO
products:
  id: gsso.owl
  ontology purl: http://purl.obolibrary.org/obo/gsso.owl
products:
  id: gsso.obo
  ontology purl: http://purl.obolibrary.org/obo/gsso.obo
products:
  id: gsso.json
  ontology purl: http://purl.obolibrary.org/obo/gsso.json
repository: https://github.com/Superraptor/GSSO
tracker: https://github.com/Superraptor/GSSO/issues

Human Phenotype Ontology (HPO)
activity status: active
browsers: JAX HPO Browser
  label: HPO
  url: https://hpo.jax.org/app/
browsers: Monarch Phenotype Page
  label: Monarch
  url: http://monarchinitiative.org/phenotype/HP:0000118
contact:
  github: drseb
  label: Sebastian Koehler
  orcid: 0000-0002-5316-1399
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
preferred prefix: HP
products: 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 obographs JSON format.
  format: json
  id: hp.json
  ontology purl: http://purl.obolibrary.org/obo/hp.json
products: Official HPO release in OBO 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
products: Official HPO release in OWL
  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
products: 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 obographs JSON file format.
  format: obo
  id: hp/hp-base.json
  ontology purl: http://purl.obolibrary.org/obo/hp/hp-base.json
products: HPO base release in OBO 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
products: HPO base release in OWL 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
products: 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 obographs JSON file format.
  format: json
  id: hp/hp-full.json
  ontology purl: http://purl.obolibrary.org/obo/hp/hp-full.json
products: HPO full release in OBO 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
products: HPO full release in OWL 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
products: 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 obographs JSON file format.
  format: json
  id: hp/hp-international.json
  ontology purl: http://purl.obolibrary.org/obo/hp/hp-international.json
products: HPO International Edition in OBO 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
products: HPO International Edition in OWL 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
products: 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 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
products: HPO simple, manually classified, without imports in OBO 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
products: HPO simple, manually classified, without imports in OWL 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
products: HPO Annotations (Phenotype to Disease)
  description: https://hpo.jax.org/app/data/annotations
  format: tsv
  id: hp/phenotype.hpoa
  ontology purl: http://purl.obolibrary.org/obo/hp/phenotype.hpoa
products: HPO phenotype to gene annotations
  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
products: HPO gene to phenotype 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
publications: The Human Phenotype Ontology: a tool for annotating and analyzing human hereditary disease.
  id: https://www.ncbi.nlm.nih.gov/pubmed/18950739
publications: The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease.
  id: https://www.ncbi.nlm.nih.gov/pubmed/26119816
publications: The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data.
  id: https://www.ncbi.nlm.nih.gov/pubmed/24217912
publications: Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources.
  id: https://www.ncbi.nlm.nih.gov/pubmed/30476213
repository: https://github.com/obophenotype/human-phenotype-ontology
taxon:
  id: NCBITaxon:9606
  label: Homo sapiens
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/

Kinetic Simulation Algorithm Ontology
activity status: active
browsers: Ontology Lookup Service
  label: OLS
  url: https://www.ebi.ac.uk/ols/ontologies/kisao
browsers: BioPortal
  label: BioPortal
  url: https://bioportal.bioontology.org/ontologies/KISAO
browsers: OntoBee
  label: OntoBee
  url: https://www.ontobee.org/ontology/KISAO
contact:
  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: NIH P41EB023912
  id: https://grantome.com/search
funded by: NIH R35GM119771
  id: https://grantome.com/search
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
preferred prefix: KISAO
products:
  id: kisao.owl
  ontology purl: http://purl.obolibrary.org/obo/kisao.owl
publications: Controlled vocabularies and semantics in systems biology
  id: https://www.ncbi.nlm.nih.gov/pubmed/22027554
repository: https://github.com/SED-ML/KiSAO
tags: systems biology
tags: computational biology
tags: mathematical modeling
tags: numerical simulation
tags: simulation algorithms
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/
usages:
  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/
usages:
  description: runBioSimulations is a web application for execution biological simulations.
  examples:
    description: Example simulation runs
    url: https://run.biosimulations.org/runs
  type: annotation
  user: https://run.biosimulations.org/
usages:
  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
  see also: https://arxiv.org/abs/2203.06732
  type: annotation
  user: https://biosimulators.org/

Systems Biology Ontology
activity status: active
contact:
  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
preferred prefix: SBO
products:
  id: sbo.owl
  ontology purl: http://purl.obolibrary.org/obo/sbo.owl
repository: https://github.com/EBI-BioModels/SBO
tracker: https://github.com/EBI-BioModels/SBO/issues

Sickle Cell Disease Ontology
activity status: active
contact:
  github: JadeHotchkiss
  label: Jade Hotchkiss
  orcid: 0000-0002-2193-0704
dependencies:
  id: apollo_sv
dependencies:
  id: aro
dependencies:
  id: chebi
dependencies:
  id: chmo
dependencies:
  id: cmo
dependencies:
  id: doid
dependencies:
  id: dron
dependencies:
  id: duo
dependencies:
  id: envo
dependencies:
  id: eupath
dependencies:
  id: exo
dependencies:
  id: gaz
dependencies:
  id: gsso
dependencies:
  id: hp
dependencies:
  id: hsapdv
dependencies:
  id: ico
dependencies:
  id: ido
dependencies:
  id: idomal
dependencies:
  id: mp
dependencies:
  id: nbo
dependencies:
  id: ncit
dependencies:
  id: obi
dependencies:
  id: ogms
dependencies:
  id: opmi
dependencies:
  id: pr
dependencies:
  id: sbo
dependencies:
  id: stato
dependencies:
  id: symp
dependencies:
  id: uo
dependencies:
  id: vo
dependencies:
  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
preferred prefix: SCDO
products:
  id: scdo.owl
  ontology purl: http://purl.obolibrary.org/obo/scdo.owl
products:
  id: scdo.obo
  ontology purl: http://purl.obolibrary.org/obo/scdo.obo
publications: The Sickle Cell Disease Ontology: recent development and expansion of the universal sickle cell knowledge representation.
  id: https://www.ncbi.nlm.nih.gov/pubmed/35363306
publications: The Sickle Cell Disease Ontology: Enabling Collaborative Research and Co-Designing of New Planetary Health Applications.
  id: https://www.ncbi.nlm.nih.gov/pubmed/33021900
publications: The Sickle Cell Disease Ontology: enabling universal sickle cell-based knowledge representation.
  id: https://www.ncbi.nlm.nih.gov/pubmed/31769834
repository: https://github.com/scdodev/scdo-ontology
tags: disease
tracker: https://github.com/scdodev/scdo-ontology/issues

Physico-chemical methods and properties
activity status: orphaned
contact:
  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
products:
  id: fix.obo
  ontology purl: http://purl.obolibrary.org/obo/fix.obo

Mathematical modeling ontology
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
preferred prefix: MAMO
products:
  id: mamo.owl
  ontology purl: http://purl.obolibrary.org/obo/mamo.owl
repository: http://sourceforge.net/p/mamo-ontology
tracker: http://sourceforge.net/p/mamo-ontology/tickets/

Physico-chemical process
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

Social Insect Behavior Ontology
activity status: orphaned
contact:
  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
  url: http://creativecommons.org/licenses/by/3.0/
ontology purl: http://purl.obolibrary.org/obo/sibo.owl
preferred prefix: SIBO
products:
  id: sibo.owl
  ontology purl: http://purl.obolibrary.org/obo/sibo.owl
products:
  id: sibo.obo
  ontology purl: http://purl.obolibrary.org/obo/sibo.obo
repository: https://github.com/obophenotype/sibo
tags: behavior
tracker: https://github.com/obophenotype/sibo/issues

Variation Ontology
activity status: orphaned
contact:
  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
  url: https://creativecommons.org/licenses/by/4.0/
ontology purl: http://purl.obolibrary.org/obo/vario.owl
preferred prefix: VariO
products: VariO main release in OWL
  id: vario.owl
  ontology purl: http://purl.obolibrary.org/obo/vario.owl
products: VariO in OBO format
  id: vario.obo
  ontology purl: http://purl.obolibrary.org/obo/vario.obo
publications: Variation Ontology for annotation of variation effects and mechanisms
  id: https://www.ncbi.nlm.nih.gov/pubmed/24162187
publications: Variation ontology: annotator guide
  id: https://www.ncbi.nlm.nih.gov/pubmed/24533660
publications: Types and effects of protein variations
  id: https://www.ncbi.nlm.nih.gov/pubmed/25616435
tracker: http://variationontology.org/instructions.shtml

VEuPathDB ontology
activity status: inactive
contact:
  github: zhengj2007
  label: Jie Zheng
  orcid: 0000-0002-2999-0103
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
  url: http://creativecommons.org/licenses/by/4.0/
ontology purl: http://purl.obolibrary.org/obo/eupath.owl
preferred prefix: EUPATH
products:
  id: eupath.owl
  ontology purl: http://purl.obolibrary.org/obo/eupath.owl
publications: Malaria study data integration and information retrieval based on OBO Foundry ontologies.
  id: https://doi.org/10.5281/zenodo.6685957
repository: https://github.com/VEuPathDB-ontology/VEuPathDB-ontology
tags: functional genomics
tags: population biology
tags: clinical epidemiology
tags: microbiomes
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
usages:
  description: The VEuPathDB ontology is used in the clinical epidemiology resources.
  type: annotation and query
  user: https://clinepidb.org
usages:
  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

Mammalian Feeding Muscle Ontology
activity status: inactive
contact:
  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
  url: http://creativecommons.org/licenses/by/3.0/
ontology purl: http://purl.obolibrary.org/obo/mfmo.owl
preferred prefix: 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
tracker: https://github.com/RDruzinsky/feedontology/issues

Ontology of Prokaryotic Phenotypic and Metabolic Characters
activity status: inactive
contact:
  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
  url: https://creativecommons.org/licenses/by/2.0/
ontology purl: http://purl.obolibrary.org/obo/micro.owl
preferred prefix: MICRO
products:
  id: micro.owl
  ontology purl: http://purl.obolibrary.org/obo/micro.owl
repository: https://github.com/carrineblank/MicrO
tracker: https://github.com/carrineblank/MicrO/issues

Ontology of Genetic Susceptibility Factor
activity status: inactive
contact:
  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
  url: https://creativecommons.org/licenses/by/3.0/
ontology purl: http://purl.obolibrary.org/obo/ogsf.owl
preferred prefix: OGSF
products:
  id: ogsf.owl
  ontology purl: http://purl.obolibrary.org/obo/ogsf.owl
repository: https://github.com/linikujp/OGSF
tracker: https://github.com/linikujp/OGSF/issues

Medaka Developmental Stages
activity status: inactive
contact:
  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
  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
preferred prefix: OlatDv
products:
  id: olatdv.obo
  ontology purl: http://purl.obolibrary.org/obo/olatdv.obo
products:
  id: olatdv.owl
  ontology purl: http://purl.obolibrary.org/obo/olatdv.owl
repository: https://github.com/obophenotype/developmental-stage-ontologies
tracker: https://github.com/obophenotype/developmental-stage-ontologies/issues

Platynereis Developmental Stages
activity status: inactive
contact:
  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
  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
preferred prefix: PdumDv
products:
  id: pdumdv.owl
  ontology purl: http://purl.obolibrary.org/obo/pdumdv.owl
products:
  id: pdumdv.obo
  ontology purl: http://purl.obolibrary.org/obo/pdumdv.obo
repository: https://github.com/obophenotype/developmental-stage-ontologies
tracker: https://github.com/obophenotype/developmental-stage-ontologies/issues

Anatomical Entity Ontology
activity status: inactive
contact:
  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
  url: https://creativecommons.org/licenses/by/4.0/
ontology purl: http://purl.obolibrary.org/obo/aeo.owl
preferred prefix: AEO
products:
  id: aeo.owl
  ontology purl: http://purl.obolibrary.org/obo/aeo.owl
repository: https://github.com/obophenotype/human-developmental-anatomy-ontology
tracker: https://github.com/obophenotype/human-developmental-anatomy-ontology/issues

Cephalopod Ontology
activity status: inactive
contact:
  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
  url: http://creativecommons.org/licenses/by/3.0/
ontology purl: http://purl.obolibrary.org/obo/ceph.owl
products: main version
  id: ceph.owl
  ontology purl: http://purl.obolibrary.org/obo/ceph.owl
products: oboformat edition
  id: ceph.obo
  ontology purl: http://purl.obolibrary.org/obo/ceph.obo
repository: https://github.com/obophenotype/cephalopod-ontology
taxon:
  id: NCBITaxon:6605
  label: Cephalopod
tracker: https://github.com/obophenotype/cephalopod-ontology/issues

Human developmental anatomy, abstract
activity status: inactive
contact:
  label: Jonathan Bard
dependencies:
  id: aeo
dependencies:
  id: caro
dependencies:
  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
  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
products:
  id: ehdaa2.obo
  ontology purl: http://purl.obolibrary.org/obo/ehdaa2.obo
publications: A new ontology (structured hierarchy) of human developmental anatomy for the first 7 weeks (Carnegie stages 1-20).
  id: https://www.ncbi.nlm.nih.gov/pubmed/22973865
repository: https://github.com/obophenotype/human-developmental-anatomy-ontology
taxon:
  id: NCBITaxon:9606
  label: Homo sapiens
tracker: https://github.com/obophenotype/human-developmental-anatomy-ontology/issues

Foundational Model of Anatomy Ontology (subset)
activity status: inactive
contact:
  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
  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
preferred prefix: FMA
products:
  id: fma.owl
  ontology purl: http://purl.obolibrary.org/obo/fma.owl
publications: Translating the Foundational Model of Anatomy into OWL
  id: https://www.ncbi.nlm.nih.gov/pubmed/18688289
publications: The foundational model of anatomy in OWL: Experience and perspectives
  id: https://www.ncbi.nlm.nih.gov/pubmed/18360535
publications: Challenges in converting frame-based ontology into OWL: the Foundational Model of Anatomy case-study
  id: https://www.ncbi.nlm.nih.gov/pubmed/16779026
repository: https://bitbucket.org/uwsig/fma
taxon:
  id: NCBITaxon:9606
  label: Homo sapiens
tracker: https://bitbucket.org/uwsig/fma/issues

Malaria Ontology
activity status: inactive
contact:
  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
  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
products:
  id: idomal.obo
  ontology purl: http://purl.obolibrary.org/obo/idomal.obo
repository: https://github.com/VEuPathDB-ontology/IDOMAL

Mosquito insecticide resistance
activity status: inactive
contact:
  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
products:
  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

RNA ontology
activity status: inactive
browsers: RNA Ontology jOWL Browser
  label: RNAO
  url: http://bgsu-rna.github.io/rnao/
contact:
  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
  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
products:
  id: rnao.obo
  ontology purl: http://purl.obolibrary.org/obo/rnao.obo
repository: https://github.com/BGSU-RNA/rnao
tags: molecular structure
tracker: https://github.com/BGSU-RNA/rnao/issues

Tick Anatomy Ontology
activity status: inactive
contact:
  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
  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
products:
  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

Mosquito gross anatomy ontology
activity status: inactive
contact:
  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
  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
products:
  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

Unipathway
activity status: inactive
contact:
  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
  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
products:
  id: upa.obo
  ontology purl: http://purl.obolibrary.org/obo/upa.obo
publications: UniPathway: a resource for the exploration and annotation of metabolic pathways
  id: https://www.ncbi.nlm.nih.gov/pubmed/22102589
repository: https://github.com/geneontology/unipathway
tags: pathways
tracker: https://github.com/geneontology/unipathway/issues

Amphibian gross anatomy
activity status: inactive
contact:
  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

Animal natural history and life history
activity status: inactive
contact:
  label: Animal Diversity Web technical staff
domain: organisms
homepage: http://www.animaldiversity.org
id: adw
is obsolete: true
layout: ontology_detail

Adverse Event Reporting Ontology
activity status: inactive
contact:
  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
  url: http://creativecommons.org/licenses/by/3.0/
products:
  id: aero.owl
  ontology purl: http://purl.obolibrary.org/obo/aero.owl

Amphibian taxonomy
activity status: inactive
contact:
  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

Beta Cell Genomics Ontology
activity status: inactive
contact:
  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
  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
tracker: https://github.com/obi-bcgo/bcgo/issues

Bilateria anatomy
activity status: inactive
contact:
  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

Gene Regulation Ontology
activity status: inactive
contact:
  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

Common Anatomy Reference Ontology
activity status: inactive
contact:
  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
  url: https://creativecommons.org/licenses/by/4.0/
preferred prefix: CARO
products:
  id: caro.owl
  ontology purl: http://purl.obolibrary.org/obo/caro.owl
repository: https://github.com/obophenotype/caro
tracker: https://github.com/obophenotype/caro/issues

CranioMaxilloFacial ontology
activity status: inactive
contact:
  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

Dendritic cell
activity status: inactive
contact:
  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

The Drug-Drug Interactions Ontology
activity status: inactive
contact:
  label: Maria Herrero
description: A formal represention for drug-drug interactions knowledge.
domain: health
homepage: http://labda.inf.uc3m.es/doku.php
id: dinto
is obsolete: true
layout: ontology_detail
license:
  label: CC BY 3.0
  url: https://creativecommons.org/licenses/by/3.0/
products:
  id: dinto.owl
  ontology purl: http://purl.obolibrary.org/obo/dinto.owl
publications: DINTO: Using OWL Ontologies and SWRL Rules to Infer Drug–Drug Interactions and Their Mechanisms.
  id: https://www.ncbi.nlm.nih.gov/pubmed/26147071
repository: https://github.com/labda/DINTO
tracker: https://github.com/labda/DINTO/issues

Human developmental anatomy, timed version
activity status: inactive
contact:
  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

Human developmental anatomy, abstract version
activity status: inactive
contact:
  label: Jonathan Bard
domain: anatomy and development
id: ehdaa
is obsolete: true
layout: ontology_detail
replaced by: ehdaa2
taxon:
  id: NCBITaxon:9606
  label: Homo sapiens

Mouse gross anatomy and development, timed
activity status: inactive
contact:
  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

Plant Environment Ontology
activity status: inactive
contact:
  github: jaiswalp
  label: Pankaj Jaiswal
  orcid: 0000-0002-1005-8383
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
  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
products:
  id: eo.obo
  ontology purl: http://purl.obolibrary.org/obo/eo.obo
publications: Ontologies as integrative tools for plant science.
  id: https://www.ncbi.nlm.nih.gov/pubmed/22847540
replaced by: peco
repository: https://github.com/Planteome/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/
usages:
  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
  user: http://gramene.org/

Epidemiology Ontology
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

eagle-i resource ontology
activity status: inactive
contact:
  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
  url: https://creativecommons.org/licenses/by/2.0/
products:
  id: ero.owl
  ontology purl: http://purl.obolibrary.org/obo/ero.owl
tags: resources

eVOC (Expressed Sequence Annotation for Humans)
activity status: inactive
contact:
  label: eVOC mailing list
domain: anatomy and development
id: ev
is obsolete: true
layout: ontology_detail

Fly taxonomy
activity status: inactive
contact:
  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

Influenza Ontology
activity status: inactive
contact:
  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
tracker: http://purl.obolibrary.org/obo/flu/tracker

Cereal Plant Gross Anatomy
activity status: inactive
contact:
  label: Plant Ontology Administrators
domain: anatomy and development
homepage: http://www.gramene.org/plant_ontology/
id: gro
is obsolete: true
layout: ontology_detail

Habronattus courtship
activity status: inactive
contact:
  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

Event (INOH pathway ontology)
activity status: inactive
domain: chemistry and biochemistry
homepage: http://www.inoh.org
id: iev
is obsolete: true
layout: ontology_detail

Molecule role (INOH Protein name/family name ontology)
activity status: inactive
contact:
  label: INOH curators
domain: chemistry and biochemistry
homepage: http://www.inoh.org
id: imr
is obsolete: true
layout: ontology_detail

Protein Domains
activity status: inactive
contact:
  label: InterPro Help
domain: chemistry and biochemistry
homepage: http://www.ebi.ac.uk/interpro/index.html
id: ipr
is obsolete: true
layout: ontology_detail

Lipid Ontology
activity status: inactive
contact:
  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

Loggerhead nesting
activity status: inactive
contact:
  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

Multiple alignment
activity status: inactive
contact:
  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

Minimal anatomical terminology
activity status: inactive
contact:
  label: Jonathan Bard
domain: anatomy and development
id: mat
is obsolete: true
layout: ontology_detail

Medaka fish anatomy and development
activity status: inactive
contact:
  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

microRNA Ontology
activity status: inactive
contact:
  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
  url: https://creativecommons.org/publicdomain/zero/1.0/
products:
  id: mirnao.owl
  ontology purl: http://purl.obolibrary.org/obo/mirnao.owl

Microarray experimental conditions
activity status: inactive
contact:
  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

NIF Cell
activity status: inactive
contact:
  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

NIF Dysfunction
activity status: inactive
contact:
  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

NIF Gross Anatomy
activity status: inactive
contact:
  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

NMR-instrument specific component of metabolomics investigations
activity status: inactive
contact:
  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

OBO relationship types (legacy)
activity status: inactive
contact:
  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

Ontology for genetic interval
activity status: inactive
contact:
  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
tracker: https://code.google.com/p/ontology-for-genetic-interval/issues/list

Ontologized MIABIS
activity status: inactive
contact:
  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
  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
tracker: https://github.com/OMIABIS/omiabis-dev/issues

Plant Anatomy Ontology
activity status: inactive
contact:
  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

Platynereis stage ontology
activity status: inactive
contact:
  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

Plant Growth and Development Stage
activity status: inactive
contact:
  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

Plasmodium life cycle
activity status: inactive
contact:
  label: Matt Berriman
domain: anatomy and development
homepage: http://www.sanger.ac.uk/Users/mb4/PLO/
id: plo
is obsolete: true
layout: ontology_detail

Proteomics data and process provenance
activity status: inactive
contact:
  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

Protein covalent bond
activity status: inactive
contact:
  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

Subcellular anatomy ontology
activity status: inactive
contact:
  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

Sample processing and separation techniques
activity status: inactive
contact:
  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
id: sep
is obsolete: true
layout: ontology_detail
page: http://psidev.info/index.php
products:
  id: sep.owl
  ontology purl: http://purl.obolibrary.org/obo/sep.owl
tags: provenance

Suggested Ontology for Pharmacogenomics
activity status: inactive
contact:
  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

Terminology of Anatomy of Human Embryology
activity status: inactive
contact:
  label: Pierre Sprumont
domain: anatomy and development
id: tahe
is obsolete: true
layout: ontology_detail
taxon:
  id: NCBITaxon:9606
  label: Homo sapiens

Terminology of Anatomy of Human Histology
activity status: inactive
contact:
  label: Pierre Sprumont
domain: health
id: tahh
is obsolete: true
layout: ontology_detail
taxon:
  id: NCBITaxon:9606
  label: Homo sapiens

Teleost Anatomy Ontology
activity status: inactive
contact:
  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
  url: http://creativecommons.org/publicdomain/zero/1.0/
products:
  id: tao.owl
  ontology purl: http://purl.obolibrary.org/obo/tao.owl
publications: The teleost anatomy ontology: anatomical representation for the genomics age
  id: https://www.ncbi.nlm.nih.gov/pubmed/20547776
replaced by: uberon
taxon:
  id: NCBITaxon:32443
  label: Teleostei

Vertebrate Homologous Ontology Group Ontology
activity status: inactive
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

Vertebrate Skeletal Anatomy Ontology-
activity status: inactive
contact:
  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

Yeast phenotypes
activity status: inactive
contact:
  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

Maize gross anatomy
activity status: inactive
contact:
  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