ontologies.yml

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