Alzheimer's Disease Ontology
preferred prefix: ADO
activity status: active
depends on: Basic Formal Ontology
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.
license: CC BY 4.0
theme: health
bug-database: https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO/issues
access URL: http://purl.obolibrary.org/obo/ado.owl
contact point: Alpha Tom Kodamullil
distribution: ado.owl

Basic Formal Ontology
preferred prefix: BFO
activity status: active
description: The upper level ontology upon which OBO Foundry ontologies are built.
license: CC BY 4.0
theme: upper
bug-database: https://github.com/BFO-ontology/BFO/issues
mailing-list: https://groups.google.com/forum/#!forum/bfo-discuss
access URL: http://purl.obolibrary.org/obo/bfo.owl
contact point: Barry Smith
distribution: bfo.owl
distribution: bfo.obo

African Population Ontology
preferred prefix: AfPO
activity status: active
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.
license: CC BY 4.0
theme: organisms
bug-database: https://github.com/h3abionet/afpo/issues
access URL: AfPO (OWL edition)
contact point: Melek Chaouch
distribution: AfPO (OWL edition)
distribution: AfPO (OBO edition)
distribution: AfPO (obographs JSON edition)

AfPO (OWL edition)
description: The main ontology in OWL. Contains all MP terms and links to other OBO ontologies

AfPO (OBO edition)
description: A direct translation of the AfPO (OWL edition) into OBO format

AfPO (obographs JSON edition)
description: A direct translation of the AfPO (OWL edition) into OBOGraph JSON format

Agronomy Ontology
preferred prefix: AGRO
activity status: active
depends on: Basic Formal Ontology
depends on: Environment Ontology
depends on: Food Ontology
depends on: Gene Ontology
depends on: Information Artifact Ontology
depends on: NCBI organismal classification
depends on: Ontology for Biomedical Investigations
depends on: Phenotype And Trait Ontology
depends on: Plant Experimental Conditions Ontology
depends on: Plant Ontology
depends on: Relation Ontology
depends on: Plant Trait Ontology
depends on: Units of measurement ontology
depends on: Experimental condition ontology
description: Ontology of agronomic practices, agronomic techniques, and agronomic variables used in agronomic experiments
license: CC BY 4.0
publication: Data-driven Agricultural Research for Development: A Need for Data Harmonization Via Semantics.
theme: agriculture
bug-database: https://github.com/AgriculturalSemantics/agro/issues/
access URL: AgrO
contact point: Marie-Angélique Laporte
distribution: AgrO

Environment Ontology
preferred prefix: ENVO
activity status: active
depends on: Chemical Entities of Biological Interest
depends on: Food Ontology
depends on: Gene Ontology
depends on: NCBI organismal classification
depends on: Population and Community Ontology
depends on: Plant Ontology
depends on: Relation Ontology
depends on: Uberon multi-species anatomy ontology
description: An ontology of environmental systems, components, and processes.
license: CC0 1.0
publication: The environment ontology: contextualising biological and biomedical entities
publication: The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation
theme: environment
bug-database: https://github.com/EnvironmentOntology/envo/issues/
access URL: main ENVO OWL release
contact point: Pier Luigi Buttigieg
distribution: main ENVO OWL release
distribution: ENVO in obographs JSON format
distribution: ENVO in OBO Format. May be lossy
distribution: OBO-Basic edition of ENVO
distribution: Earth Microbiome Project subset
distribution: GSC Lite subset of ENVO

Food Ontology
preferred prefix: FOODON
activity status: active
depends on: Basic Formal Ontology
depends on: Chemical Entities of Biological Interest
depends on: Environment Ontology
depends on: Plant Environment Ontology
depends on: NCBI organismal classification
depends on: Ontology for Biomedical Investigations
depends on: Relation Ontology
depends on: Uberon multi-species anatomy ontology
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
license: CC BY 4.0
publication: FoodOn: a harmonized food ontology to increase global food traceability, quality control and data integration
theme: diet, metabolomics, and nutrition
bug-database: https://github.com/FoodOntology/foodon/issues/
access URL: FoodOn ontology with import file references and over 9,000 food products
contact point: Damion Dooley
distribution: FoodOn ontology with import file references and over 9,000 food products
distribution: FoodOn core ontology (currently the same as foodon.owl)

Gene Ontology
preferred prefix: GO
activity status: active
continuous integration server: http://build.berkeleybop.org/view/GO
depends on: Cell Ontology
depends on: GO bridge to NIFSTD
depends on: NCBI organismal classification
depends on: Relation Ontology
depends on: Uberon multi-species anatomy ontology
IAO_0000136: All life
description: An ontology for describing the function of genes and gene products
license: CC BY 4.0
publication: Gene ontology: tool for the unification of biology. The Gene Ontology Consortium
publication: The Gene Ontology resource: enriching a GOld mine
theme: biological systems
bug-database: https://github.com/geneontology/go-ontology/issues/
label: GO
access URL: GO (OWL edition)
contact point: Suzi Aleksander
distribution: GO (OWL edition)
distribution: GO (OBO Format edition)
distribution: GO (JSON edition)
distribution: GO-Plus
distribution: GO Base Module
distribution: GO-Basic, Filtered, for use with legacy tools
distribution: GO-Basic, Filtered, for use with legacy tools (JSON)
distribution: GO Taxon Groupings
distribution: GO (OWL edition), daily snapshot release
distribution: GO (OBO Format edition), daily snapshot release
account: news4go

Information Artifact Ontology
preferred prefix: IAO
activity status: active
has build information:
  method: owl2obo
  source url: http://purl.obolibrary.org/obo/iao.owl
description: An ontology of information entities.
license: CC BY 4.0
theme: information
bug-database: https://github.com/information-artifact-ontology/IAO/issues
access URL: http://purl.obolibrary.org/obo/iao.owl
contact point: Jie Zheng
distribution: iao.owl
distribution: IAO ontology metadata
distribution: IAO dev
distribution: ontology of document acts

NCBI organismal classification
preferred prefix: NCBITaxon
activity status: active
description: An ontology representation of the NCBI organismal taxonomy
license: CC0 1.0
theme: organisms
was derived from: ftp://ftp.ebi.ac.uk/pub/databases/taxonomy/taxonomy.dat
bug-database: https://github.com/obophenotype/ncbitaxon/issues
access URL: Main release
contact point: Frederic Bastian
distribution: Main release
distribution: OBO Format version of Main release
distribution: OBOGraphs JSON version of Main release
distribution: taxslim
distribution: taxslim disjointness axioms

Ontology for Biomedical Investigations
preferred prefix: OBI
activity status: active
continuous integration server: http://build.berkeleybop.org/job/build-obi/
has build information:
  source url: http://purl.obofoundry.org/obo/obi/repository/trunk/src/ontology/branches/
description: An integrated ontology for the description of life-science and clinical investigations
license: CC BY 4.0
publication: The Ontology for Biomedical Investigations
theme: investigations
bug-database: http://purl.obolibrary.org/obo/obi/tracker
mailing-list: http://groups.google.com/group/obi-users
access URL: OBI
contact point: Bjoern Peters
distribution: OBI
distribution: OBI in OBO
distribution: OBI Core
distribution: OBI Base module

Phenotype And Trait Ontology
preferred prefix: PATO
activity status: active
description: An ontology of phenotypic qualities (properties, attributes or characteristics)
license: CC BY 3.0
publication: The anatomy of phenotype ontologies: principles, properties and applications
publication: Using ontologies to describe mouse phenotypes
theme: phenotype
bug-database: https://github.com/pato-ontology/pato/issues
access URL: http://purl.obolibrary.org/obo/pato.owl
contact point: George Gkoutos
distribution: pato.owl
distribution: pato.obo
distribution: pato.json
distribution: pato-base.owl

Plant Experimental Conditions Ontology
preferred prefix: PECO
activity status: active
description: A structured, controlled vocabulary which describes the treatments, growing conditions, and/or study types used in plant biology experiments.
license: CC BY 4.0
publication: The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics.
theme: investigations
bug-database: https://github.com/Planteome/plant-experimental-conditions-ontology/issues
access URL: http://purl.obolibrary.org/obo/peco.owl
contact point: Pankaj Jaiswal
distribution: peco.owl
distribution: peco.obo

Plant Ontology
preferred prefix: PO
activity status: active
IAO_0000136: Viridiplantae
description: The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data.
license: CC BY 4.0
publication: The plant ontology as a tool for comparative plant anatomy and genomic analyses.
publication: The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics.
theme: anatomy and development
bug-database: https://github.com/Planteome/plant-ontology/issues
access URL: http://purl.obolibrary.org/obo/po.owl
contact point: Pankaj Jaiswal
distribution: po.owl
distribution: po.obo
account: planteome

Relation Ontology
preferred prefix: RO
activity status: active
description: Relationship types shared across multiple ontologies
license: CC0 1.0
theme: upper
bug-database: https://github.com/oborel/obo-relations/issues
mailing-list: https://groups.google.com/forum/#!forum/obo-relations
access URL: Relation Ontology
contact point: Chris Mungall
distribution: Relation Ontology
distribution: Relation Ontology in obo format
distribution: Relation Ontology in obojson format
distribution: RO Core relations
distribution: RO base ontology
distribution: Interaction relations
distribution: Ecology subset
distribution: Neuroscience subset

Plant Trait Ontology
preferred prefix: TO
activity status: active
IAO_0000136: Viridiplantae
description: A controlled vocabulary to describe phenotypic traits in plants.
license: CC BY 4.0
publication: The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics.
theme: phenotype
bug-database: https://github.com/Planteome/plant-trait-ontology/issues
access URL: http://purl.obolibrary.org/obo/to.owl
contact point: Pankaj Jaiswal
distribution: to.owl
distribution: to.obo

Units of measurement ontology
preferred prefix: UO
activity status: active
has build information:
  method: obo2owl
  source url: https://raw.githubusercontent.com/bio-ontology-research-group/unit-ontology/master/unit.obo
description: Metrical units for use in conjunction with PATO
license: CC BY 3.0
publication: The Units Ontology: a tool for integrating units of measurement in science
theme: phenotype
bug-database: https://github.com/bio-ontology-research-group/unit-ontology/issues
access URL: http://purl.obolibrary.org/obo/uo.owl
contact point: George Gkoutos
distribution: uo.owl
distribution: uo.obo
distribution: uo.json

Experimental condition ontology
preferred prefix: XCO
activity status: active
has build information:
  method: obo2owl
  source url: https://download.rgd.mcw.edu/ontology/experimental_condition/experimental_condition.obo
description: Conditions under which physiological and morphological measurements are made both in the clinic and in studies involving humans or model organisms.
license: CC0 1.0
publication: Three ontologies to define phenotype measurement data.
publication: The clinical measurement, measurement method and experimental condition ontologies: expansion, improvements and new applications.
theme: health
bug-database: https://github.com/rat-genome-database/XCO-experimental-condition-ontology/issues
access URL: http://purl.obolibrary.org/obo/xco.owl
contact point: Jennifer Smith
distribution: xco.owl
distribution: xco.obo

AgrO
description: Contains all AgrO terms and links to other relevant ontologies.

Ontology for the Anatomy of the Insect SkeletoMuscular system (AISM)
preferred prefix: AISM
activity status: active
depends on: Basic Formal Ontology
depends on: Biological Spatial Ontology
depends on: Common Anatomy Reference Ontology
depends on: Phenotype And Trait Ontology
depends on: Relation Ontology
depends on: Uberon multi-species anatomy ontology
has build information:
  checkout: git clone https://github.com/insect-morphology/aism
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.
license: CC BY 4.0
theme: anatomy and development
bug-database: https://github.com/insect-morphology/aism/issues
access URL: http://purl.obolibrary.org/obo/aism.owl
contact point: Jennifer C. Girón
distribution: aism.owl
distribution: aism.obo
distribution: aism.json

Biological Spatial Ontology
preferred prefix: BSPO
activity status: active
has build information:
  checkout: git clone https://github.com/obophenotype/biological-spatial-ontology.git
  method: vcs
description: An ontology for representing spatial concepts, anatomical axes, gradients, regions, planes, sides, and surfaces
license: CC BY 3.0
publication: Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology.
theme: anatomy and development
bug-database: https://github.com/obophenotype/biological-spatial-ontology/issues
access URL: http://purl.obolibrary.org/obo/bspo.owl
contact point: Chris Mungall
distribution: bspo.owl
distribution: bspo.obo

Common Anatomy Reference Ontology
preferred prefix: CARO
activity status: inactive
has build information:
  method: obo2owl
  source url: http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/caro/caro.obo
description: An upper level ontology to facilitate interoperability between existing anatomy ontologies for different species
license: CC BY 4.0
theme: anatomy and development
bug-database: https://github.com/obophenotype/caro/issues
contact point: Melissa Haendel
distribution: caro.owl

Uberon multi-species anatomy ontology
preferred prefix: UBERON
activity status: active
depends on: Basic Formal Ontology
depends on: Biological Spatial Ontology
depends on: Chemical Entities of Biological Interest
depends on: Cell Ontology
depends on: Environment Ontology
depends on: Gene Ontology
depends on: Neuro Behavior Ontology
depends on: NCBI organismal classification
depends on: OBO Metadata Ontology
depends on: Phenotype And Trait Ontology
depends on: PRotein Ontology (PRO)
depends on: Relation Ontology
has build information:
  checkout: git clone https://github.com/obophenotype/uberon.git
IAO_0000136: Metazoa
description: An integrated cross-species anatomy ontology covering animals and bridging multiple species-specific ontologies
license: CC BY 3.0
publication: Uberon, an integrative multi-species anatomy ontology
publication: Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon
theme: anatomy and development
funded by: NIH R24-OD011883
funded by: NIH R01-HG004838
funded by: NIH P41-HG002273
funded by: NSF DEB-0956049
bug-database: https://github.com/obophenotype/uberon/issues
mailing-list: https://lists.sourceforge.net/lists/listinfo/obo-anatomy
label: Uberon
access URL: Uberon
contact point: Chris Mungall
distribution: Uberon
distribution: Uberon base ontology
distribution: Uberon basic
distribution: Uberon collected metazoan ontology
distribution: Uberon composite metazoan ontology
distribution: Uberon composite vertebrate ontology
account: uberanat

The Amphioxus Development and Anatomy Ontology
preferred prefix: AMPHX
activity status: active
depends on: Uberon multi-species anatomy ontology
has build information:
  checkout: git clone https://github.com/EBISPOT/amphx_ontology.git
description: An ontology for the development and anatomy of Amphioxus (Branchiostoma lanceolatum).
license: CC BY 3.0
theme: anatomy and development
bug-database: https://github.com/EBISPOT/amphx_ontology/issues
access URL: http://purl.obolibrary.org/obo/amphx.owl
contact point: Hector Escriva
distribution: amphx.owl
distribution: amphx.obo

Ascomycete phenotype ontology
preferred prefix: APO
activity status: active
has build information:
  method: obo2owl
  source url: https://raw.githubusercontent.com/obophenotype/ascomycete-phenotype-ontology/master/apo.obo
IAO_0000136: Ascomycota
description: A structured controlled vocabulary for the phenotypes of Ascomycete fungi
license: CC BY 4.0
publication: New mutant phenotype data curation system in the Saccharomyces Genome Database
theme: phenotype
bug-database: https://github.com/obophenotype/ascomycete-phenotype-ontology/issues
access URL: http://purl.obolibrary.org/obo/apo.owl
contact point: Stacia R Engel
distribution: apo.owl
distribution: apo.obo

Apollo Structured Vocabulary
preferred prefix: APOLLO_SV
activity status: active
description: An OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation.
license: CC BY 4.0
publication: The Apollo Structured Vocabulary: an OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation
theme: health
bug-database: https://github.com/ApolloDev/apollo-sv/issues
access URL: http://purl.obolibrary.org/obo/apollo_sv.owl
contact point: William Hogan
distribution: apollo sv.owl

Antibiotic Resistance Ontology
preferred prefix: ARO
activity status: active
description: Antibiotic resistance genes and mutations
license: CC BY 4.0
publication: CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database.
theme: microbiology
bug-database: https://github.com/arpcard/aro/issues
mailing-list: https://mailman.mcmaster.ca/mailman/listinfo/card-l
access URL: http://purl.obolibrary.org/obo/aro.owl
contact point: Andrew G. McArthur
distribution: aro.owl

Biological Collections Ontology
preferred prefix: BCO
activity status: active
description: An ontology to support the interoperability of biodiversity data, including data on museum collections, environmental/metagenomic samples, and ecological surveys.
license: CC0 1.0
publication: Semantics in Support of Biodiversity Knowledge Discovery: An Introduction to the Biological Collections Ontology and Related Ontologies
theme: organisms
bug-database: https://github.com/BiodiversityOntologies/bco/issues
access URL: http://purl.obolibrary.org/obo/bco.owl
contact point: Ramona Walls
distribution: bco.owl

BioPortal Browser
label: BioPortal

Biomarker Ontology
preferred prefix: BMONT
activity status: active
description: An application ontology that represents comprehensive knowledge involving a variety of fields of medical and biological aspects.
license: CC BY 4.0
theme: health
bug-database: https://github.com/SCAI-BIO/BiomarkerOntology/issues
access URL: http://purl.obolibrary.org/obo/bmont.owl
contact point: Alpha Tom Kodamullil
distribution: BMONT.owl

BioPortal Ontology Browser
label: BioPortal

BMONT.owl
description: Includes axioms linking to other ontologies, but no imports of those ontologies

BRENDA tissue / enzyme source
preferred prefix: BTO
activity status: active
has build information:
  checkout: git clone https://github.com/BRENDA-Enzymes/BTO.git
description: A structured controlled vocabulary for the source of an enzyme comprising tissues, cell lines, cell types and cell cultures.
license: CC BY 4.0
publication: The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources
theme: anatomy and development
bug-database: https://github.com/BRENDA-Enzymes/BTO/issues
access URL: http://purl.obolibrary.org/obo/bto.owl
contact point: Christian-Alexander Dudek
distribution: bto.owl
distribution: bto.obo
distribution: bto.json

Comparative Data Analysis Ontology
preferred prefix: CDAO
activity status: active
has build information:
  method: owl2obo
  source url: http://purl.obolibrary.org/obo/cdao.owl
description: a formalization of concepts and relations relevant to evolutionary comparative analysis
license: CC0 1.0
publication: Initial Implementation of a Comparative Data Analysis Ontology
theme: organisms
bug-database: https://github.com/evoinfo/cdao/issues
access URL: http://purl.obolibrary.org/obo/cdao.owl
contact point: Jim Balhoff
distribution: cdao.owl

Compositional Dietary Nutrition Ontology
preferred prefix: CDNO
activity status: active
depends on: Basic Formal Ontology
depends on: Chemical Entities of Biological Interest
depends on: Environment Ontology
depends on: Phenotype And Trait Ontology
depends on: Relation Ontology
has build information:
  checkout: git clone https://github.com/CompositionalDietaryNutritionOntology/cdno.git
description: CDNO provides structured terminologies to describe nutritional attributes of material entities that contribute to human diet.
license: CC BY 3.0
publication: Establishing a Common Nutritional Vocabulary - From Food Production to Diet
theme: diet, metabolomics, and nutrition
bug-database: https://github.com/CompositionalDietaryNutritionOntology/cdno/issues
access URL: http://purl.obolibrary.org/obo/cdno.owl
contact point: Liliana Andres Hernandez
distribution: cdno.owl
distribution: cdno.obo

Chemical Entities of Biological Interest
preferred prefix: CHEBI
activity status: active
has build information:
  method: obo2owl
  source url: ftp://ftp.ebi.ac.uk/pub/databases/chebi/ontology/chebi.obo
description: A structured classification of molecular entities of biological interest focusing on 'small' chemical compounds.
license: CC BY 4.0
publication: ChEBI: re-engineered for a sustainable future
publication: ChEBI in 2016: Improved services and an expanding collection of metabolites.
theme: chemistry and biochemistry
bug-database: https://github.com/ebi-chebi/ChEBI/issues
access URL: http://purl.obolibrary.org/obo/chebi.owl
contact point: Adnan Malik
distribution: chebi.owl
distribution: chebi.obo
distribution: chebi.json
distribution: chebi, compressed owl
distribution: chebi_lite, no syns or xrefs
distribution: chebi_core, no xrefs
account: chebit

EBI CHEBI Browser
label: CHEBI

Chemical Information Ontology
preferred prefix: CHEMINF
activity status: active
has build information:
  method: owl2obo
  source url: https://raw.githubusercontent.com/semanticchemistry/semanticchemistry/master/ontology/cheminf.owl
description: Includes terms for the descriptors commonly used in cheminformatics software applications and the algorithms which generate them.
license: CC0 1.0
publication: The chemical information ontology: provenance and disambiguation for chemical data on the biological semantic web
theme: chemistry and biochemistry
bug-database: https://github.com/semanticchemistry/semanticchemistry/issues
mailing-list: https://groups.google.com/forum/#!forum/cheminf-ontology
access URL: http://purl.obolibrary.org/obo/cheminf.owl
contact point: Egon Willighagen
distribution: cheminf.owl

CHEBI Integrated Role Ontology
preferred prefix: CHIRO
activity status: active
depends on: Chemical Entities of Biological Interest
depends on: Gene Ontology
depends on: Human Phenotype Ontology (HPO)
depends on: Mammalian Phenotype Ontology
depends on: NCBI organismal classification
depends on: PRotein Ontology (PRO)
depends on: Uberon multi-species anatomy ontology
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.
license: CC0 1.0
publication: Extension of Roles in the ChEBI Ontology
theme: chemistry and biochemistry
bug-database: https://github.com/obophenotype/chiro/issues
access URL: http://purl.obolibrary.org/obo/chiro.owl
contact point: Nicole Vasilevsky
distribution: chiro.owl
distribution: chiro.obo

Human Phenotype Ontology (HPO)
preferred prefix: HP
activity status: active
IAO_0000136: Homo sapiens
description: The Human Phenotype Ontology (HPO) is a structured and controlled vocabulary for the phenotypic features encountered in human hereditary and other disease.
license: hpo
publication: The Human Phenotype Ontology: a tool for annotating and analyzing human hereditary disease.
publication: The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease.
publication: The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data.
publication: Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources.
theme: phenotype
bug-database: https://github.com/obophenotype/human-phenotype-ontology/issues/
mailing-list: https://groups.io/g/human-phenotype-ontology
access URL: Official HPO release in OWL
contact point: Sebastian Koehler
distribution: Official HPO release in obographs JSON format
distribution: Official HPO release in OBO format
distribution: Official HPO release in OWL
distribution: HPO base release in obographs JSON format
distribution: HPO base release in OBO format
distribution: HPO base release in OWL format
distribution: HPO full release in obographs JSON format
distribution: HPO full release in OBO format
distribution: HPO full release in OWL format
distribution: HPO International Edition in obographs JSON format
distribution: HPO International Edition in OBO format
distribution: HPO International Edition in OWL format
distribution: HPO simple, manually classified, without imports in obographs JSON format
distribution: HPO simple, manually classified, without imports in OBO format
distribution: HPO simple, manually classified, without imports in OWL format
distribution: HPO Annotations (Phenotype to Disease)
distribution: HPO phenotype to gene annotations
distribution: HPO gene to phenotype annotations
account: hp ontology

Mammalian Phenotype Ontology
preferred prefix: MP
activity status: active
IAO_0000136: Mammalia
description: Standard terms for annotating mammalian phenotypic data.
license: CC BY 4.0
publication: Expanding and refining the Mammalian Phenotype Ontology to enhance disease model discovery
publication: The Mammalian Phenotype Ontology as a unifying standard for experimental and high-throughput phenotyping data
publication: Expanding the mammalian phenotype ontology to support automated exchange of high throughput mouse phenotyping data generated by large-scale mouse knockout screens
theme: phenotype
bug-database: https://github.com/mgijax/mammalian-phenotype-ontology/issues
mailing-list: https://groups.google.com/forum/#!forum/phenotype-ontologies-editors
access URL: MP (OWL edition)
contact point: Sue Bello
distribution: MP (OWL edition)
distribution: MP (OBO edition)
distribution: MP (obographs JSON edition)
distribution: MP Base Module

PRotein Ontology (PRO)
preferred prefix: PR
activity status: active
has build information:
  method: obo2owl
  source url: https://proconsortium.org/download/current/pro_nonreasoned.obo
description: An ontological representation of protein-related entities
license: CC BY 4.0
publication: Protein Ontology (PRO): enhancing and scaling up the representation of protein entities
theme: chemistry and biochemistry
bug-database: https://github.com/PROconsortium/PRoteinOntology/issues
access URL: pro_reasoned.owl
contact point: Darren Natale
distribution: pro_reasoned.owl
distribution: pro_reasoned.obo
distribution: pro_nonreasoned.owl
distribution: pro_nonreasoned.obo

Chemical Methods Ontology
preferred prefix: CHMO
activity status: active
description: CHMO, the chemical methods ontology, describes methods used to
license: CC BY 4.0
theme: health
bug-database: https://github.com/rsc-ontologies/rsc-cmo/issues
access URL: http://purl.obolibrary.org/obo/chmo.owl
contact point: Colin Batchelor
distribution: chmo.owl

Coronavirus Infectious Disease Ontology
preferred prefix: CIDO
activity status: active
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.
license: CC BY 4.0
publication: A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology
theme: health
bug-database: https://github.com/cido-ontology/cido/issues
access URL: http://purl.obolibrary.org/obo/cido.owl
contact point: Yongqun Oliver He
distribution: cido.owl

Confidence Information Ontology
preferred prefix: CIO
activity status: active
description: An ontology to capture confidence information about annotations.
license: CC0 1.0
publication: The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations
theme: information
bug-database: https://github.com/BgeeDB/confidence-information-ontology
access URL: http://purl.obolibrary.org/obo/cio.owl
contact point: Frédéric Bastian
distribution: cio.owl
distribution: cio.obo

Cell Ontology
preferred prefix: CL
activity status: active
depends on: Gene Ontology
depends on: NCBI organismal classification
depends on: OBO Metadata Ontology
depends on: Phenotype And Trait Ontology
depends on: PRotein Ontology (PRO)
depends on: Relation Ontology
depends on: Uberon multi-species anatomy ontology
IAO_0000136: Metazoa
description: The Cell Ontology is a structured controlled vocabulary for cell types in animals.
license: CC BY 4.0
publication: The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability.
theme: anatomy and development
bug-database: https://github.com/obophenotype/cell-ontology/issues
mailing-list: https://groups.google.com/g/cl_edit
access URL: Main CL OWL edition
contact point: David Osumi-Sutherland
distribution: Main CL OWL edition
distribution: CL obo format edition
distribution: CL OBOGraph-JSON format edition
distribution: Basic CL
distribution: Basic CL (OBO version)
distribution: Basic CL (OBOGraph-JSON version)
distribution: CL base module
distribution: CL base module (OBO version)
distribution: CL base module (OBOGraph-JSON version)
account: CellOntology

OBO Metadata Ontology
preferred prefix: OMO
activity status: active
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).
license: CC0 1.0
theme: information
bug-database: https://github.com/information-artifact-ontology/ontology-metadata/issues
access URL: http://purl.obolibrary.org/obo/omo.owl
contact point: Chris Mungall
distribution: omo.owl

Main CL OWL edition
description: Complete ontology, plus inter-ontology axioms, and imports modules
format: owl-rdf/xml

CL obo format edition
description: Complete ontology, plus inter-ontology axioms, and imports modules merged in
format: obo

CL OBOGraph-JSON format edition
description: Complete ontology, plus inter-ontology axioms, and imports modules merged in
format: json

Basic CL
description: Basic version, no inter-ontology axioms
format: owl-rdf/xml

Basic CL (OBO version)
description: Basic version, no inter-ontology axioms
format: obo

Basic CL (OBOGraph-JSON version)
description: Basic version, no inter-ontology axioms
format: json

CL base module
description: complete CL but with no imports or external axioms
format: owl-rdf/xml

CL base module (OBO version)
description: complete CL but with no imports or external axioms
format: obo

CL base module (OBOGraph-JSON version)
description: complete CL but with no imports or external axioms
format: json

Collembola Anatomy Ontology
preferred prefix: CLAO
activity status: active
depends on: Relation Ontology
has build information:
  checkout: git clone https://github.com/luis-gonzalez-m/Collembola.git
description: CLAO is an ontology of anatomical terms employed in morphological descriptions for the Class Collembola (Arthropoda: Hexapoda).
license: CC0 1.0
theme: anatomy and development
bug-database: https://github.com/luis-gonzalez-m/Collembola/issues
access URL: http://purl.obolibrary.org/obo/clao.owl
contact point: Luis González-Montaña
distribution: clao.owl
distribution: clao.obo

Cell Line Ontology
preferred prefix: CLO
activity status: active
depends on: Cell Ontology
depends on: Human Disease Ontology
depends on: NCBI organismal classification
depends on: Uberon multi-species anatomy ontology
description: An ontology to standardize and integrate cell line information and to support computer-assisted reasoning.
license: CC BY 3.0
publication: CLO: The Cell Line Ontology
theme: anatomy and development
bug-database: https://github.com/CLO-Ontology/CLO/issues
access URL: http://purl.obolibrary.org/obo/clo.owl
contact point: Jie Zheng
distribution: clo.owl

Human Disease Ontology
preferred prefix: DOID
activity status: active
has build information:
  method: obo2owl
  source url: https://raw.githubusercontent.com/DiseaseOntology/HumanDiseaseOntology/master/src/ontology/doid.obo
IAO_0000136: Homo sapiens
description: An ontology for describing the classification of human diseases organized by etiology.
license: CC0 1.0
publication: Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data
publication: The Human Disease Ontology 2022 update
theme: health
bug-database: https://github.com/DiseaseOntology/HumanDiseaseOntology/issues
access URL: Disease Ontology, OWL format. This file contains DO's is_a asserted hierarchy plus equivalent axioms to other OBO Foundry ontologies.
contact point: Lynn Schriml
distribution: Disease Ontology, OWL format. This file contains DO's is_a asserted hierarchy plus equivalent axioms to other OBO Foundry ontologies.
distribution: Disease Ontology, OBO format. This file omits the equivalent axioms.
account: diseaseontology

Clytia hemisphaerica Development and Anatomy Ontology
preferred prefix: CLYH
activity status: active
depends on: Information Artifact Ontology
depends on: Relation Ontology
depends on: Uberon multi-species anatomy ontology
has build information:
  checkout: git clone https://github.com/EBISPOT/clyh_ontology.git
description: The Clytia hemisphaerica Development and Anatomy Ontology (CLYH) describes the anatomical and developmental features of the Clytia hemisphaerica life cycle.
license: CC BY 3.0
theme: anatomy and development
bug-database: https://github.com/EBISPOT/clyh_ontology/issues
access URL: http://purl.obolibrary.org/obo/clyh.owl
contact point: Lucas Leclere
distribution: clyh.owl
distribution: clyh.obo

Clinical measurement ontology
preferred prefix: CMO
activity status: active
has build information:
  method: obo2owl
  source url: https://download.rgd.mcw.edu/ontology/clinical_measurement/clinical_measurement.obo
description: Morphological and physiological measurement records generated from clinical and model organism research and health programs.
license: CC0 1.0
publication: Three ontologies to define phenotype measurement data.
publication: The clinical measurement, measurement method and experimental condition ontologies: expansion, improvements and new applications.
theme: health
bug-database: https://github.com/rat-genome-database/CMO-Clinical-Measurement-Ontology/issues
access URL: http://purl.obolibrary.org/obo/cmo.owl
contact point: Jennifer Smith
distribution: cmo.owl
distribution: cmo.obo

RGD Ontology Browser
label: RGD

Core Ontology for Biology and Biomedicine
preferred prefix: COB
activity status: active
description: COB brings together key terms from a wide range of OBO projects to improve interoperability.
license: CC0 1.0
theme: upper
bug-database: https://github.com/OBOFoundry/COB/issues
access URL: COB
contact point: Bjoern Peters
distribution: COB
distribution: COB base module
distribution: COB native module
distribution: COB to external
distribution: COB demo ontology (experimental)

COB
description: Core Ontology for Biology and Biomedicine, main ontology

COB base module
description: base module for COB

COB native module
description: COB with native IDs preserved rather than rewired to OBO IDs

COB to external
type: BridgeOntology

COB demo ontology (experimental)
description: demo of COB including subsets of other ontologies (Experimental, for demo purposes only)

Coleoptera Anatomy Ontology (COLAO)
preferred prefix: COLAO
activity status: active
depends on: Ontology for the Anatomy of the Insect SkeletoMuscular system (AISM)
depends on: Basic Formal Ontology
depends on: Biological Spatial Ontology
depends on: Common Anatomy Reference Ontology
depends on: Phenotype And Trait Ontology
depends on: Relation Ontology
depends on: Uberon multi-species anatomy ontology
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.
license: CC BY 4.0
theme: anatomy and development
bug-database: https://github.com/insect-morphology/colao/issues
access URL: http://purl.obolibrary.org/obo/colao.owl
contact point: Jennifer C. Giron
distribution: colao.owl
distribution: colao.obo

Contributor Role Ontology
preferred prefix: CRO
activity status: active
has build information:
  checkout: git clone https://github.com/data2health/contributor-role-ontology.git
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.
license: CC BY 2.0
theme: information
bug-database: https://github.com/data2health/contributor-role-ontology/issues
access URL: CRO
contact point: Marijane White
distribution: CRO

Ctenophore Ontology
preferred prefix: CTENO
activity status: active
depends on: Relation Ontology
depends on: Uberon multi-species anatomy ontology
IAO_0000136: Ctenophore
description: An anatomical and developmental ontology for ctenophores (Comb Jellies)
license: CC BY 3.0
theme: anatomy and development
bug-database: https://github.com/obophenotype/ctenophore-ontology/issues
access URL: http://purl.obolibrary.org/obo/cteno.owl
contact point: Chris Mungall
distribution: cteno.owl

CTO: Core Ontology of Clinical Trials
preferred prefix: CTO
activity status: active
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.
license: CC BY 4.0
theme: health
bug-database: https://github.com/ClinicalTrialOntology/CTO/issues
access URL: http://purl.obolibrary.org/obo/cto.owl
contact point: Dr. Alpha Tom Kodamullil
distribution: cto.owl

Cardiovascular Disease Ontology
preferred prefix: CVDO
activity status: active
has build information:
  method: owl2obo
  source url: http://purl.obolibrary.org/obo/cvdo.owl
  publication: The Cardiovascular Disease Ontology
description: An ontology to describe entities related to cardiovascular diseases
license: CC BY 4.0
theme: health
bug-database: https://github.com/OpenLHS/CVDO/issues
access URL: http://purl.obolibrary.org/obo/cvdo.owl
contact point: Paul Fabry
distribution: cvdo.owl

Dictyostelium discoideum anatomy
preferred prefix: DDANAT
activity status: active
has build information:
  method: obo2owl
  source url: https://raw.githubusercontent.com/dictyBase/migration-data/master/ontologies/dicty_anatomy.obo
IAO_0000136: Dictyostelium discoideum
description: A structured controlled vocabulary of the anatomy of the slime-mold Dictyostelium discoideum
license: CC0 1.0
publication: An anatomy ontology to represent biological knowledge in Dictyostelium discoideum
theme: anatomy and development
bug-database: https://github.com/dictyBase/migration-data/issues
access URL: http://purl.obolibrary.org/obo/ddanat.owl
contact point: Petra Fey
distribution: ddanat.owl
distribution: ddanat.obo
account: dictybase

Dictyostelium discoideum phenotype ontology
preferred prefix: DDPHENO
activity status: active
has build information:
  checkout: git clone https://github.com/obophenotype/dicty-phenotype-ontology.git
IAO_0000136: Dictyostelium discoideum
description: A structured controlled vocabulary of phenotypes of the slime-mould Dictyostelium discoideum.
license: CC0 1.0
publication: dictyBase and the Dicty Stock Center (version 2.0) - a progress report
theme: anatomy and development
bug-database: https://github.com/obophenotype/dicty-phenotype-ontology/issues
access URL: http://purl.obolibrary.org/obo/ddpheno.owl
contact point: Petra Fey
distribution: ddpheno.owl
distribution: ddpheno.obo
account: dictybase

Drug-drug Interaction and Drug-drug Interaction Evidence Ontology
preferred prefix: DIDEO
activity status: active
description: The Potential Drug-drug Interaction and Potential Drug-drug Interaction Evidence Ontology
license: CC BY 4.0
theme: chemistry and biochemistry
bug-database: https://github.com/DIDEO/DIDEO/issues
access URL: http://purl.obolibrary.org/obo/dideo.owl
contact point: Mathias Brochhausen
distribution: dideo.owl

Disease Drivers Ontology
preferred prefix: DISDRIV
activity status: active
has build information:
  source url: https://raw.githubusercontent.com/DiseaseOntology/DiseaseDriversOntology/refs/heads/main/src/ontology/disdriv.owl
IAO_0000136: Homo sapiens
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.
license: CC0 1.0
theme: health
bug-database: https://github.com/DiseaseOntology/DiseaseDriversOntology/issues
access URL: http://purl.obolibrary.org/obo/disdriv.owl
contact point: Lynn Schriml
distribution: disdriv.owl
account: diseaseontology

DO Browser
label: DO

DO Browser
label: DO

Drosophila Phenotype Ontology
preferred prefix: FBcv
activity status: active
has build information:
  checkout: git clone https://github.com/FlyBase/drosophila-phenotype-ontolog.git
IAO_0000136: Drosophila
description: An ontology of commonly encountered and/or high level Drosophila phenotypes.
license: CC BY 4.0
publication: The Drosophila phenotype ontology.
theme: phenotype
bug-database: https://github.com/FlyBase/drosophila-phenotype-ontology/issues
access URL: http://purl.obolibrary.org/obo/dpo.owl
contact point: Clare Pilgrim
distribution: dpo.owl
distribution: dpo.obo
distribution: dpo.json

FlyBase Browser
label: FB

FlyBase Controlled Vocabulary
preferred prefix: FBcv
activity status: active
has build information:
  checkout: git clone https://github.com/FlyBase/flybase-controlled-vocabulary.git
description: A structured controlled vocabulary used for various aspects of annotation by FlyBase.
license: CC BY 4.0
theme: organisms
bug-database: https://github.com/FlyBase/flybase-controlled-vocabulary/issues
access URL: http://purl.obolibrary.org/obo/fbcv.owl
contact point: Clare Pilgrim
distribution: fbcv.owl
distribution: fbcv.obo
distribution: fbcv.json

The Drug Ontology
preferred prefix: DRON
activity status: active
has build information:
  method: owl2obo
  source url: http://purl.obolibrary.org/obo/dron.owl
description: An ontology to support comparative effectiveness researchers studying claims data.
license: CC BY 3.0
publication: Therapeutic indications and other use-case-driven updates in the drug ontology: anti-malarials, anti-hypertensives, opioid analgesics, and a large term request
theme: health
bug-database: https://github.com/ufbmi/dron/issues
access URL: http://purl.obolibrary.org/obo/dron.owl
contact point: William Hogan
distribution: dron.owl

Data Use Ontology
preferred prefix: DUO
activity status: active
depends on: Basic Formal Ontology
depends on: Information Artifact Ontology
description: DUO is an ontology which represent data use conditions.
license: CC BY 4.0
theme: information
bug-database: https://github.com/EBISPOT/DUO/issues
access URL: http://purl.obolibrary.org/obo/duo.owl
contact point: Melanie Courtot
distribution: duo.owl

The Echinoderm Anatomy and Development Ontology
preferred prefix: ECAO
activity status: active
depends on: Cell Ontology
depends on: Relation Ontology
depends on: Uberon multi-species anatomy ontology
has build information:
  checkout: git clone https://github.com/echinoderm-ontology/ecao_ontology.git
description: An ontology for the development and anatomy of the different species of the phylum Echinodermata (NCBITaxon:7586).
license: CC BY 3.0
theme: anatomy and development
bug-database: https://github.com/echinoderm-ontology/ecao_ontology/issues
access URL: http://purl.obolibrary.org/obo/ecao.owl
contact point: Charles Ettensohn
distribution: ecao.owl
distribution: ecao.obo

Evidence and Conclusion Ontology
preferred prefix: ECO
activity status: active
description: An ontology for experimental and other evidence statements.
license: CC0 1.0
publication: ECO: the Evidence and Conclusion Ontology, an update for 2022.
publication: ECO, the Evidence & Conclusion Ontology: community standard for evidence information.
publication: Standardized description of scientific evidence using the Evidence Ontology (ECO)
theme: investigations
funded by: NSF ABI-1458400
bug-database: https://github.com/evidenceontology/evidenceontology/issues
access URL: http://purl.obolibrary.org/obo/eco.owl
contact point: Michelle Giglio
distribution: eco.owl
distribution: eco.obo

ECO Browser
label: ECO

An ontology of core ecological entities
preferred prefix: ECOCORE
activity status: active
depends on: Basic Formal Ontology
depends on: Chemical Entities of Biological Interest
depends on: Environment Ontology
depends on: Gene Ontology
depends on: Information Artifact Ontology
depends on: Phenotype And Trait Ontology
depends on: Population and Community Ontology
depends on: Plant Ontology
depends on: Relation Ontology
depends on: Uberon multi-species anatomy ontology
description: Ecocore is a community ontology for the concise and controlled description of ecological traits of organisms.
license: CC BY 3.0
theme: environment
bug-database: https://github.com/EcologicalSemantics/ecocore/issues
access URL: http://purl.obolibrary.org/obo/ecocore.owl
contact point: Pier Luigi Buttigieg
distribution: ecocore.owl
distribution: ecocore.obo

Population and Community Ontology
preferred prefix: PCO
activity status: active
depends on: Basic Formal Ontology
depends on: Common Anatomy Reference Ontology
depends on: Environment Ontology
depends on: Gene Ontology
depends on: Information Artifact Ontology
depends on: NCBI organismal classification
depends on: Phenotype And Trait Ontology
depends on: Relation Ontology
description: An ontology about groups of interacting organisms such as populations and communities
license: CC0 1.0
theme: environment
bug-database: https://github.com/PopulationAndCommunityOntology/pco/issues
access URL: http://purl.obolibrary.org/obo/pco.owl
contact point: Ramona Walls
distribution: pco.owl

Environmental conditions, treatments and exposures ontology
preferred prefix: ECTO
activity status: active
depends on: Chemical Entities of Biological Interest
depends on: Environment Ontology
depends on: Exposure ontology
depends on: Gene Ontology
depends on: Information Artifact Ontology
depends on: Medical Action Ontology
depends on: Neuro Behavior Ontology
depends on: NCBI organismal classification
depends on: NCI Thesaurus OBO Edition
depends on: Phenotype And Trait Ontology
depends on: Relation Ontology
depends on: Uberon multi-species anatomy ontology
depends on: Experimental condition ontology
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).
license: CC0 1.0
theme: environment
bug-database: https://github.com/EnvironmentOntology/environmental-exposure-ontology/issues
access URL: http://purl.obolibrary.org/obo/ecto.owl
contact point: Anne Thessen
distribution: ecto.owl
distribution: ecto.obo
distribution: ecto.json
distribution: ecto-base.owl
distribution: ecto-base.obo
distribution: ecto-base.json

Exposure ontology
preferred prefix: ExO
activity status: active
description: Vocabularies for describing exposure data to inform understanding of environmental health.
license: CC BY 4.0
theme: health
bug-database: https://github.com/CTDbase/exposure-ontology/issues
access URL: http://purl.obolibrary.org/obo/exo.owl
contact point: Anne Thessen
distribution: exo.owl
distribution: exo.obo

Medical Action Ontology
preferred prefix: MAXO
activity status: active
depends on: Chemical Entities of Biological Interest
depends on: Food Ontology
depends on: Gene Ontology
depends on: Human Phenotype Ontology (HPO)
depends on: Information Artifact Ontology
depends on: Neuro Behavior Ontology
depends on: Ontology for Biomedical Investigations
depends on: Relation Ontology
depends on: Uberon multi-species anatomy ontology
has build information:
  checkout: git clone https://github.com/monarch-initiative/MAxO.git
description: The Medical Action Ontology (MAxO) provides a broad view of medical actions and includes terms for medical procedures, interventions, therapies, treatments, and recommendations.
license: CC BY 4.0
theme: health
bug-database: https://github.com/monarch-initiative/MAxO/issues
access URL: http://purl.obolibrary.org/obo/maxo.owl
contact point: Leigh Carmody
distribution: maxo.owl
distribution: maxo.obo
distribution: maxo.json
distribution: maxo-base.owl
distribution: maxo-base.obo
distribution: maxo-base.json

Neuro Behavior Ontology
preferred prefix: NBO
activity status: active
has build information:
  method: owl2obo
  source url: https://raw.githubusercontent.com/obo-behavior/behavior-ontology/master/nbo.owl
description: An ontology of human and animal behaviours and behavioural phenotypes
license: CC BY 3.0
publication: Analyzing gene expression data in mice with the Neuro Behavior Ontology
theme: biological systems
bug-database: https://github.com/obo-behavior/behavior-ontology/issues
access URL: http://purl.obolibrary.org/obo/nbo.owl
contact point: George Gkoutos
distribution: nbo.owl

NCI Thesaurus OBO Edition
preferred prefix: NCIT
activity status: active
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.
license: CC BY 4.0
theme: health
bug-database: https://github.com/ncit-obo-org/ncit-obo-edition/issues
access URL: NCIt OBO Edition OWL format
contact point: None
distribution: NCIt OBO Edition OWL format
distribution: NCIt OBO Edition OBO format

Mouse Developmental Anatomy Ontology
preferred prefix: EMAPA
activity status: active
has build information:
  method: obo2owl
  source url: ftp://ftp.hgu.mrc.ac.uk/pub/MouseAtlas/Anatomy/EMAPA.obo
IAO_0000136: Mus
description: An ontology for mouse anatomy covering embryonic development and postnatal stages.
license: CC BY 4.0
publication: An internet-accessible database of mouse developmental anatomy based on a systematic nomenclature
publication: EMAP/EMAPA ontology of mouse developmental anatomy: 2013 update
publication: Mouse Anatomy Ontologies: Enhancements and Tools for Exploring and Integrating Biomedical Data
publication: Textual Anatomics: the Mouse Developmental Anatomy Ontology and the Gene Expression Database for Mouse Development (GXD)
theme: anatomy and development
bug-database: https://github.com/obophenotype/developmental-mouse-anatomy-ontology/issues
access URL: http://purl.obolibrary.org/obo/emapa.owl
contact point: Terry Hayamizu
distribution: emapa.owl
distribution: emapa.obo

Epilepsy Ontology
preferred prefix: EPIO
activity status: active
depends on: Basic Formal Ontology
description: A application driven Epilepsy Ontology with official terms from the ILAE.
license: CC BY 4.0
theme: health
bug-database: https://github.com/SCAI-BIO/EpilepsyOntology/issues
access URL: http://purl.obolibrary.org/obo/epio.owl
contact point: Alpha Tom Kodamullil
distribution: epio.owl
distribution: EPIO merged.owl

Exercise Medicine Ontology
preferred prefix: EXMO
activity status: active
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.
license: CC BY 4.0
publication: Core reference ontology for individualized exercise prescription
theme: health
bug-database: https://github.com/Exercise-Medicine-Ontology/EXMO/issues
access URL: http://purl.obolibrary.org/obo/exmo.owl
contact point: Xingyun Liu
distribution: exmo.owl

Fungal gross anatomy
preferred prefix: FAO
activity status: active
has build information:
  checkout: git clone https://github.com/obophenotype/fungal-anatomy-ontology.git
  method: vcs
IAO_0000136: Fungal
description: A structured controlled vocabulary for the anatomy of fungi.
license: CC0 1.0
theme: anatomy and development
bug-database: https://github.com/obophenotype/fungal-anatomy-ontology/issues
access URL: http://purl.obolibrary.org/obo/fao.owl
contact point: Val Wood
distribution: fao.owl
distribution: fao.obo

Drosophila gross anatomy
preferred prefix: FBbt
activity status: active
has build information:
  checkout: git clone https://github.com/FlyBase/drosophila-anatomy-developmental-ontology.git
IAO_0000136: Drosophila
description: An ontology representing the gross anatomy of Drosophila melanogaster.
license: CC BY 4.0
publication: The Drosophila anatomy ontology
publication: A strategy for building neuroanatomy ontologies
publication: The Virtual Fly Brain Browser and Query Interface
publication: FlyBase: anatomical data, images and queries
theme: anatomy and development
bug-database: http://purl.obolibrary.org/obo/fbbt/tracker
access URL: http://purl.obolibrary.org/obo/fbbt.owl
contact point: Clare Pilgrim
distribution: fbbt.owl
distribution: fbbt.obo
distribution: fbbt.json
distribution: fbbt-simple.owl
distribution: fbbt-simple.obo

FlyBase Browser
label: FB

Virtual Fly Brain
label: VFB

BioPortal Browser
label: BioPortal

FlyBase Browser
label: FB

Drosophila development
preferred prefix: FBdv
activity status: active
has build information:
  checkout: git clone https://github.com/FlyBase/drosophila-developmental-ontology.git
IAO_0000136: Drosophila
description: A structured controlled vocabulary of the development of Drosophila melanogaster.
license: CC BY 4.0
theme: anatomy and development
bug-database: http://purl.obolibrary.org/obo/fbdv/tracker
access URL: http://purl.obolibrary.org/obo/fbdv.owl
contact point: Clare Pilgrim
distribution: fbdv.owl
distribution: fbdv.obo
distribution: fbdv.json
distribution: fbdv-simple.owl
distribution: fbdv-simple.obo

FlyBase Browser
label: FB

Food Interactions with Drugs Evidence Ontology
preferred prefix: FIDEO
activity status: active
description: Food-Drug interactions automatically extracted from scientific literature
license: CC0 1.0
theme: diet, metabolomics, and nutrition
bug-database: https://gitub.u-bordeaux.fr/erias/fideo/issues
access URL: http://purl.obolibrary.org/obo/fideo.owl
contact point: Georgeta Bordea
distribution: fideo.owl

Flora Phenotype Ontology
preferred prefix: FLOPO
activity status: active
has build information:
  method: owl2obo
  source url: https://github.com/flora-phenotype-ontology/flopoontology/raw/master/ontology/flopo.owl
IAO_0000136: Viridiplantae
description: Traits and phenotypes of flowering plants occurring in digitized Floras
license: CC0 1.0
publication: The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants
theme: phenotype
bug-database: https://github.com/flora-phenotype-ontology/flopoontology/issues
access URL: http://purl.obolibrary.org/obo/flopo.owl
contact point: Robert Hoehndorf
distribution: flopo.owl

Food-Biomarker Ontology
preferred prefix: FOBI
activity status: active
depends on: Chemical Entities of Biological Interest
depends on: Food Ontology
description: FOBI (Food-Biomarker Ontology) is an ontology to represent food intake data and associate it with metabolomic data
license: CC BY 3.0
publication: FOBI: an ontology to represent food intake data and associate it with metabolomic data
publication: The fobitools framework: the first steps towards food enrichment analysis
theme: diet, metabolomics, and nutrition
bug-database: https://github.com/pcastellanoescuder/FoodBiomarkerOntology/issues
access URL: FOBI is an ontology to represent food intake data and associate it with metabolomic data
contact point: Pol Castellano Escuder
distribution: FOBI is an ontology to represent food intake data and associate it with metabolomic data

FOBI is an ontology to represent food intake data and associate it with metabolomic data
format: owl-rdf/xml

Plant Environment Ontology
activity status: inactive
has build information:
  method: obo2owl
  source url: https://github.com/Planteome/plant-environment-ontology/blob/master/plant-environment-ontology.obo.owl
description: A structured, controlled vocabulary which describes the treatments, growing conditions, and/or study types used in plant biology experiments.
license: CC BY 4.0
publication: Ontologies as integrative tools for plant science.
theme: environment
bug-database: https://github.com/Planteome/plant-environment-ontology/issues
contact point: Pankaj Jaiswal
distribution: eo.owl
distribution: eo.obo

FoodOn ontology with import file references and over 9,000 food products
format: owl-rdf/xml

FoodOn core ontology (currently the same as foodon.owl)
format: owl-rdf/xml

FuTRES Ontology of Vertebrate Traits
preferred prefix: FOVT
activity status: active
depends on: Biological Collections Ontology
depends on: Basic Formal Ontology
depends on: Biological Spatial Ontology
depends on: Information Artifact Ontology
depends on: Ontology of Biological Attributes
depends on: Phenotype And Trait Ontology
depends on: Relation Ontology
depends on: Uberon multi-species anatomy ontology
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).
license: CC0 1.0
theme: phenotype
bug-database: https://github.com/futres/fovt/issues
access URL: http://purl.obolibrary.org/obo/fovt.owl
contact point: Meghan Balk
distribution: fovt.owl
distribution: fovt.obo
distribution: fovt-base.owl
distribution: fovt-base.obo

Ontology of Biological Attributes
preferred prefix: OBA
activity status: active
description: A collection of biological attributes (traits) covering all kingdoms of life.
license: CC0 1.0
publication: The Ontology of Biological Attributes (OBA) - computational traits for the life sciences
theme: phenotype
bug-database: https://github.com/obophenotype/bio-attribute-ontology/issues
access URL: http://purl.obolibrary.org/obo/oba.owl
contact point: Chris Mungall
distribution: oba.owl
distribution: oba.obo
distribution: oba-basic.obo

Fission Yeast Phenotype Ontology
preferred prefix: FYPO
activity status: active
has build information:
  method: obo2owl
  source url: https://raw.githubusercontent.com/pombase/fypo/master/release/fypo.owl
IAO_0000136: S. pombe
description: FYPO is a formal ontology of phenotypes observed in fission yeast.
license: CC BY 4.0
publication: FYPO: The Fission Yeast Phenotype Ontology.
theme: phenotype
bug-database: https://github.com/pombase/fypo/issues
access URL: http://purl.obolibrary.org/obo/fypo.owl
contact point: Val Wood
distribution: fypo.owl
distribution: fypo.obo

Plant Gall Ontology
preferred prefix: GALLONT
activity status: active
depends on: Common Anatomy Reference Ontology
depends on: Flora Phenotype Ontology
depends on: NCBI organismal classification
depends on: Ontology for Biomedical Investigations
depends on: Phenotype And Trait Ontology
depends on: Plant Ontology
depends on: Porifera Ontology
depends on: Relation Ontology
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.
license: CC0 1.0
theme: phenotype
bug-database: https://github.com/adeans/gallont/issues
access URL: http://purl.obolibrary.org/obo/gallont.owl
contact point: Andy Deans
distribution: gallont.owl
distribution: gallont.json
distribution: gallont.obo

Porifera Ontology
preferred prefix: PORO
activity status: active
depends on: Relation Ontology
depends on: Uberon multi-species anatomy ontology
IAO_0000136: Porifera
description: An ontology covering the anatomy of the taxon Porifera (sponges)
license: CC BY 3.0
publication: The Porifera Ontology (PORO): enhancing sponge systematics with an anatomy ontology
theme: anatomy and development
bug-database: https://github.com/obophenotype/porifera-ontology/issues
access URL: http://purl.obolibrary.org/obo/poro.owl
contact point: Bob Thacker
distribution: poro.owl
distribution: poro.obo

Gazetteer
preferred prefix: GAZ
activity status: active
description: A gazetteer constructed on ontological principles. The countries are actively maintained.
license: CC0 1.0
theme: environment
bug-database: https://github.com/EnvironmentOntology/gaz/issues
mailing-list: https://groups.google.com/forum/#!forum/obo-gazetteer
access URL: http://purl.obolibrary.org/obo/gaz.owl
contact point: Lynn Schriml
distribution: gaz.owl
distribution: gaz.obo
distribution: GAZ countries

GAZ countries
description: A country specific subset of the GAZ.

Genomics Cohorts Knowledge Ontology
preferred prefix: GECKO
activity status: active
description: An ontology to represent genomics cohort attributes
license: CC BY 4.0
theme: organisms
bug-database: https://github.com/IHCC-cohorts/GECKO/issues
access URL: http://purl.obolibrary.org/obo/gecko.owl
contact point: Rebecca Jackson
distribution: gecko.owl

Genomic Epidemiology Ontology
preferred prefix: GENEPIO
activity status: active
depends on: Chemical Entities of Biological Interest
depends on: NCBI organismal classification
depends on: Plant Ontology
depends on: Relation Ontology
depends on: Uberon multi-species anatomy ontology
description: The Genomic Epidemiology Ontology (GenEpiO) covers vocabulary necessary to identify, document and research foodborne pathogens and associated outbreaks.
license: CC BY 3.0
theme: health
bug-database: https://github.com/GenEpiO/genepio/issues/
access URL: http://purl.obolibrary.org/obo/genepio.owl
contact point: Damion Dooley
distribution: genepio.owl

Genotype Ontology
preferred prefix: GENO
activity status: active
has build information:
  checkout: git clone https://github.com/monarch-initiative/GENO-ontology.git
description: An integrated ontology for representing the genetic variations described in genotypes, and their causal relationships to phenotype and diseases.
license: CC BY 4.0
theme: biological systems
bug-database: https://github.com/monarch-initiative/GENO-ontology/issues
access URL: GENO
contact point: Matthew Brush
distribution: GENO

Geographical Entity Ontology
preferred prefix: GEO
activity status: active
description: An ontology of geographical entities
license: CC BY 4.0
theme: environment
bug-database: https://github.com/ufbmi/geographical-entity-ontology/issues
access URL: http://purl.obolibrary.org/obo/geo.owl
contact point: Bill Hogan
distribution: geo.owl

Glycan Naming and Subsumption Ontology (GNOme)
preferred prefix: GNO
activity status: active
has build information:
  checkout: git clone https://github.com/glygen-glycan-data/GNOme.git
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.
license: CC BY 4.0
publication: GNOme - Glycan Naming and Subsumption Ontology
theme: chemistry and biochemistry
bug-database: https://github.com/glygen-glycan-data/GNOme/issues
access URL: http://purl.obolibrary.org/obo/gno.owl
contact point: Nathan Edwards
distribution: gno.owl
distribution: gno.obo
distribution: gno.json

GNOme Glycan Structure Browser
label: Structure Browser

GNOme Glycan Composition Browser
label: Composition Browser

gno.owl
description: Glycan Naming and Subsumption Ontology, OWL format (primary)

gno.obo
description: Glycan Naming and Subsumption Ontology, OBO format (automated conversion from OWL)

gno.json
description: Glycan Naming and Subsumption Ontology, JSON format (automated conversion from OWL)

GO bridge to NIFSTD
description: Bridging axioms between nifstd and go
publication: The Gene Ontology (GO) Cellular Component Ontology: integration with SAO (Subcellular Anatomy Ontology) and other recent developments.
type: BridgeOntology

Gene Ontology AmiGO 2 Browser
label: AmiGO

GO (OWL edition)
description: The main ontology in OWL. This is self contained and does not have connections to other OBO ontologies

GO (OBO Format edition)
description: Equivalent to go.owl, in obo format

GO (JSON edition)
description: Equivalent to go.owl, in obograph json format

GO-Plus
description: The main ontology plus axioms connecting to select external ontologies, with subsets of those ontologies

GO Base Module
description: The main ontology plus axioms connecting to select external ontologies, excluding the external ontologies themselves

GO-Plus
description: As go-plus.owl, in obographs json format

GO-Basic, Filtered, for use with legacy tools
description: Basic version of the GO, filtered such that the graph is guaranteed to be acyclic and annotations can be propagated up the graph. The relations included are is a, part of, regulates, negatively regulates and positively regulates. This version excludes relationships that cross the 3 GO hierarchies.

GO-Basic, Filtered, for use with legacy tools (JSON)
description: As go-basic.obo, in json format

GO Taxon Groupings
description: Classes added to ncbitaxon for groupings such as prokaryotes

GO (OWL edition), daily snapshot release
description: Equivalent to go.owl, but released daily. Note the snapshot release is not archived.

GO (OBO Format edition), daily snapshot release
description: Equivalent to go.owl, but released daily. Note the snapshot release is not archived.

Human Ancestry Ontology
preferred prefix: HANCESTRO
activity status: active
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.
license: CC BY 4.0
publication: A standardized framework for representation of ancestry data in genomics studies, with application to the NHGRI-EBI GWAS Catalog
theme: organisms
bug-database: https://github.com/EBISPOT/hancestro/issues
access URL: HANCESTRO
contact point: Danielle Welter
distribution: HANCESTRO
distribution: HANCESTRO Base

HANCESTRO
description: The full version of HANCESTRO in OWL format, with BFO upper hierarchy for easier integration with other ontologies

HANCESTRO Base
description: Base version of HANCESTRO

Hymenoptera Anatomy Ontology
preferred prefix: HAO
activity status: active
has build information:
  checkout: git clone https://github.com/hymao/hao.git
IAO_0000136: Hymenoptera
description: A structured controlled vocabulary of the anatomy of the Hymenoptera (bees, wasps, and ants)
license: CC0 1.0
publication: A gross anatomy ontology for hymenoptera
theme: anatomy and development
bug-database: https://github.com/hymao/hao/issues
access URL: http://purl.obolibrary.org/obo/hao.owl
contact point: Matt Yoder
distribution: hao.owl
distribution: hao.obo
distribution: depictions.owl

Homology Ontology
preferred prefix: HOM
activity status: active
has build information:
  checkout: git clone https://github.com/BgeeDB/homology-ontology.git
  method: vcs
description: This ontology represents concepts related to homology, as well as other concepts used to describe similarity and non-homology.
license: CC0 1.0
publication: An ontology to clarify homology-related concepts
theme: anatomy and development
bug-database: https://github.com/BgeeDB/homology-ontology/issues
access URL: http://purl.obolibrary.org/obo/hom.owl
contact point: Frederic Bastian
distribution: hom.owl

Human Developmental Stages
preferred prefix: HsapDv
activity status: active
description: Life cycle stages for Human
license: CC BY 3.0
theme: anatomy and development
bug-database: https://github.com/obophenotype/developmental-stage-ontologies/issues
access URL: http://purl.obolibrary.org/obo/hsapdv.owl
contact point: Frédéric Bastian
distribution: hsapdv.owl
distribution: hsapdv.obo

Health Surveillance Ontology
preferred prefix: HSO
activity status: active
depends on: Basic Formal Ontology
depends on: NCBI organismal classification
depends on: Ontology for Biomedical Investigations
depends on: Relation Ontology
depends on: Uberon multi-species anatomy ontology
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.
license: CC BY 3.0
theme: health
bug-database: https://github.com/SVA-SE/HSO/issues/
access URL: http://purl.obolibrary.org/obo/hso.owl
contact point: Fernanda Dorea
distribution: hso.owl

Hypertension Ontology
preferred prefix: HTN
activity status: active
description: An ontology for representing clinical data about hypertension, intended to support classification of patients according to various diagnostic guidelines
license: CC BY 4.0
theme: health
bug-database: https://github.com/aellenhicks/htn_owl/issues
access URL: HTN
contact point: Amanda Hicks
distribution: HTN

ontology of document acts
description: An ontology based on a theory of document acts describing what people can do with documents
contact point: Mathias Brochhausen

Integrative and Conjugative Element Ontology
preferred prefix: ICEO
activity status: active
description: ICEO is an integrated biological ontology for the description of bacterial integrative and conjugative elements (ICEs).
license: CC BY 4.0
publication: ICEO, a biological ontology for representing and analyzing bacterial integrative and conjugative elements
theme: microbiology
bug-database: https://github.com/ontoice/ICEO/issues
access URL: http://purl.obolibrary.org/obo/iceo.owl
contact point: Meng LIU
distribution: iceo.owl

Informed Consent Ontology
preferred prefix: ICO
activity status: active
description: An ontology of clinical informed consents
license: CC BY 4.0
theme: investigations
bug-database: https://github.com/ICO-ontology/ICO/issues
access URL: http://purl.obolibrary.org/obo/ico.owl
contact point: Yongqun Oliver He
distribution: ico.owl

Infectious Disease Ontology
preferred prefix: IDO
activity status: active
has build information:
  method: owl2obo
  source url: http://purl.obolibrary.org/obo/ido.owl
IAO_0000136: Homo sapiens
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.
license: CC BY 3.0
publication: The Infectious Disease Ontology in the age of COVID-19
theme: health
bug-database: https://github.com/infectious-disease-ontology/infectious-disease-ontology/issues
access URL: http://purl.obolibrary.org/obo/ido.owl
contact point: Lindsay Cowell
distribution: ido.owl

Interaction Network Ontology
preferred prefix: INO
activity status: active
description: An ontology of interactions and interaction networks
license: CC BY 3.0
publication: Development and application of an Interaction Network Ontology for literature mining of vaccine-associated gene-gene interactions
theme: biological systems
bug-database: https://github.com/INO-ontology/ino/issues
access URL: http://purl.obolibrary.org/obo/ino.owl
contact point: Yongqun Oliver He
distribution: ino.owl

clinical LABoratory Ontology
preferred prefix: LABO
activity status: active
depends on: Information Artifact Ontology
depends on: Ontology for Biomedical Investigations
depends on: Ontology for General Medical Science
depends on: Ontologized MIABIS
depends on: Ontology for Modeling and Representation of Social Entities
depends on: Ontology of Precision Medicine and Investigation
IAO_0000136: Homo sapiens
description: LABO is an ontology of informational entities formalizing clinical laboratory tests prescriptions and reporting documents.
license: CC BY 4.0
publication: LABO: An Ontology for Laboratory Test Prescription and Reporting
theme: information
bug-database: https://github.com/OpenLHS/LABO/issues
access URL: http://purl.obolibrary.org/obo/labo.owl
contact point: Paul Fabry
distribution: labo.owl

Ontology for General Medical Science
preferred prefix: OGMS
activity status: active
IAO_0000136: Homo sapiens
description: An ontology for representing treatment of disease and diagnosis and on carcinomas and other pathological entities
license: CC BY 4.0
publication: Toward an ontological treatment of disease and diagnosis
publication: Biomarkers in the Ontology for General Medical Science
theme: health
bug-database: https://github.com/OGMS/ogms/issues
access URL: http://purl.obolibrary.org/obo/ogms.owl
contact point: Brian Aevermann
distribution: ogms.owl

Ontologized MIABIS
activity status: inactive
description: An ontological version of MIABIS (Minimum Information About BIobank data Sharing)
license: CC BY 3.0
theme: health
bug-database: https://github.com/OMIABIS/omiabis-dev/issues
contact point: Mathias Brochhausen
distribution: omiabis.owl

Ontology for Modeling and Representation of Social Entities
preferred prefix: OMRSE
activity status: active
has build information:
  method: owl2obo
  source url: https://github.com/mcwdsi/OMRSE
IAO_0000136: Homo sapiens
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.
license: CC BY 4.0
publication: The ontology of medically related social entities: recent developments
theme: health
bug-database: https://github.com/mcwdsi/OMRSE/issues
access URL: http://purl.obolibrary.org/obo/omrse.owl
contact point: Bill Hogan
distribution: omrse.owl

Ontology of Precision Medicine and Investigation
preferred prefix: OPMI
activity status: active
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.
license: CC BY 4.0
theme: investigations
bug-database: https://github.com/OPMI/opmi/issues
mailing-list: http://groups.google.com/group/opmi-discuss
access URL: http://purl.obolibrary.org/obo/opmi.owl
contact point: Yongqun Oliver He
distribution: opmi.owl

Lepidoptera Anatomy Ontology
preferred prefix: LEPAO
activity status: active
depends on: Ontology for the Anatomy of the Insect SkeletoMuscular system (AISM)
depends on: Basic Formal Ontology
depends on: Biological Spatial Ontology
depends on: Common Anatomy Reference Ontology
depends on: Phenotype And Trait Ontology
depends on: Relation Ontology
depends on: Uberon multi-species anatomy ontology
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).
license: CC BY 4.0
theme: anatomy and development
bug-database: https://github.com/insect-morphology/lepao/issues
access URL: http://purl.obolibrary.org/obo/lepao.owl
contact point: Luis A. Gonzalez-Montana
distribution: lepao.owl
distribution: lepao.obo

Mouse adult gross anatomy
preferred prefix: MA
activity status: active
IAO_0000136: Mus
description: A structured controlled vocabulary of the adult anatomy of the mouse (Mus).
license: CC BY 4.0
theme: anatomy and development
bug-database: https://github.com/obophenotype/adult-mouse-anatomy-ontology/issues
access URL: http://purl.obolibrary.org/obo/ma.owl
contact point: Terry Hayamizu
distribution: ma.owl
distribution: ma.obo

Microbial Conditions Ontology
preferred prefix: MCO
activity status: active
depends on: Basic Formal Ontology
depends on: Chemical Entities of Biological Interest
depends on: Cell Ontology
depends on: Cell Line Ontology
depends on: Ontology of Prokaryotic Phenotypic and Metabolic Characters
depends on: NCBI organismal classification
depends on: NCI Thesaurus OBO Edition
depends on: Ontology for Biomedical Investigations
depends on: Ontology for MIRNA Target
depends on: Ontology of Microbial Phenotypes
depends on: Phenotype And Trait Ontology
depends on: Plant Experimental Conditions Ontology
depends on: Uberon multi-species anatomy ontology
depends on: Zebrafish Experimental Conditions Ontology
description: Microbial Conditions Ontology is an ontology...
license: CC BY 3.0
theme: investigations
bug-database: https://github.com/microbial-conditions-ontology/microbial-conditions-ontology/issues
access URL: http://purl.obolibrary.org/obo/mco.owl
contact point: Citlalli Mejía-Almonte
distribution: mco.owl
distribution: mco.obo

Ontology of Prokaryotic Phenotypic and Metabolic Characters
preferred prefix: MICRO
activity status: inactive
description: An ontology of prokaryotic phenotypic and metabolic characters
license: CC BY 2.0
theme: phenotype
bug-database: https://github.com/carrineblank/MicrO/issues
access URL: http://purl.obolibrary.org/obo/micro.owl
contact point: Carrine Blank
distribution: micro.owl

Ontology for MIRNA Target
preferred prefix: OMIT
activity status: active
description: Ontology to establish data exchange standards and common data elements in the microRNA (miR) domain
license: CC BY 3.0
theme: chemistry and biochemistry
bug-database: https://github.com/OmniSearch/omit/issues
access URL: http://purl.obolibrary.org/obo/omit.owl
contact point: Jingshan Huang
distribution: omit.owl

Ontology of Microbial Phenotypes
preferred prefix: OMP
activity status: active
has build information:
  method: obo2owl
  source url: https://raw.githubusercontent.com/microbialphenotypes/OMP-ontology-files/master/omp.obo
description: An ontology of phenotypes covering microbes
license: CC BY 3.0
publication: An ontology for microbial phenotypes
theme: phenotype
bug-database: https://github.com/microbialphenotypes/OMP-ontology/issues
access URL: http://purl.obolibrary.org/obo/omp.owl
contact point: James C. Hu
distribution: omp.owl
distribution: omp.obo

Zebrafish Experimental Conditions Ontology
preferred prefix: ZECO
activity status: active
has build information:
  method: obo2owl
  source url: https://raw.githubusercontent.com/ybradford/zebrafish-experimental-conditions-ontology/master/zeco.obo
IAO_0000136: Danio
description: Experimental conditions applied to zebrafish, developed to facilitate experiment condition annotation at ZFIN
license: CC BY 3.0
theme: environment
bug-database: https://github.com/ybradford/zebrafish-experimental-conditions-ontology/issues
access URL: http://purl.obolibrary.org/obo/zeco.owl
contact point: Yvonne Bradford
distribution: zeco.obo
distribution: zeco.owl
distribution: zeco.json

Model Card Report Ontology
preferred prefix: MCRO
activity status: active
depends on: Information Artifact Ontology
depends on: Software ontology
description: An ontology representing the structure of model card reports - reports that describe basic characteristics of machine learning models for the public and consumers.
license: CC BY 4.0
publication: Toward a standard formal semantic representation of the model card report
theme: information technology
bug-database: https://github.com/UTHealth-Ontology/MCRO/issues
access URL: http://purl.obolibrary.org/obo/mcro.owl
contact point: Tuan Amith
distribution: mcro.owl

Software ontology
preferred prefix: SWO
activity status: active
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.
license: CC BY 4.0
publication: The Software Ontology (SWO): a resource for reproducibility in biomedical data analysis, curation and digital preservation
theme: information technology
bug-database: https://github.com/allysonlister/swo/issues
access URL: http://purl.obolibrary.org/obo/swo.owl
contact point: Allyson Lister
distribution: swo.owl
distribution: swo.json

Mental Functioning Ontology
preferred prefix: MF
activity status: active
has build information:
  method: owl2obo
  source url: http://purl.obolibrary.org/obo/mf.owl
description: The Mental Functioning Ontology is an overarching ontology for all aspects of mental functioning.
license: CC BY 3.0
theme: health
bug-database: https://github.com/jannahastings/mental-functioning-ontology/issues
access URL: http://purl.obolibrary.org/obo/mf.owl
contact point: Janna Hastings
distribution: mf.owl

Emotion Ontology
preferred prefix: MFOEM
activity status: active
has build information:
  method: owl2obo
  source url: http://purl.obolibrary.org/obo/mfoem.owl
description: An ontology of affective phenomena such as emotions, moods, appraisals and subjective feelings.
license: CC BY 3.0
theme: health
bug-database: https://github.com/jannahastings/emotion-ontology/issues
access URL: http://purl.obolibrary.org/obo/mfoem.owl
contact point: Janna Hastings
distribution: mfoem.owl

Mental Disease Ontology
preferred prefix: MFOMD
activity status: active
description: An ontology to describe and classify mental diseases such as schizophrenia, annotated with DSM-IV and ICD codes where applicable
license: CC BY 3.0
theme: health
bug-database: https://github.com/jannahastings/mental-functioning-ontology/issues
access URL: http://purl.obolibrary.org/obo/mfomd.owl
contact point: Janna Hastings
distribution: mfomd.owl

Molecular Interactions Controlled Vocabulary
preferred prefix: MI
activity status: active
has build information:
  method: obo2owl
  source url: https://raw.githubusercontent.com/HUPO-PSI/psi-mi-CV/master/psi-mi.obo
description: A structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions.
license: CC BY 4.0
theme: investigations
bug-database: https://github.com/HUPO-PSI/psi-mi-CV/issues
access URL: http://purl.obolibrary.org/obo/mi.owl
contact point: Luana Licata
distribution: mi.owl
distribution: mi.obo

MIAPA Ontology
preferred prefix: MIAPA
activity status: active
description: An application ontology to formalize annotation of phylogenetic data.
license: CC0 1.0
publication: Taking the First Steps towards a Standard for Reporting on Phylogenies: Minimum Information about a Phylogenetic Analysis (MIAPA)
theme: information
bug-database: https://github.com/evoinfo/miapa/issues
mailing-list: http://groups.google.com/group/miapa-discuss
access URL: http://purl.obolibrary.org/obo/miapa.owl
contact point: Hilmar Lapp
distribution: miapa.owl

Measurement method ontology
preferred prefix: MMO
activity status: active
has build information:
  method: obo2owl
  source url: https://download.rgd.mcw.edu/ontology/measurement_method/measurement_method.obo
description: A representation of the variety of methods used to make clinical and phenotype measurements.
license: CC0 1.0
publication: Three ontologies to define phenotype measurement data.
publication: The clinical measurement, measurement method and experimental condition ontologies: expansion, improvements and new applications.
theme: health
bug-database: https://github.com/rat-genome-database/MMO-Measurement-Method-Ontology/issues
access URL: http://purl.obolibrary.org/obo/mmo.owl
contact point: Jennifer Smith
distribution: mmo.owl
distribution: mmo.obo

RGD Ontology Browser
label: RGD

Mouse Developmental Stages
preferred prefix: MmusDv
activity status: active
has build information:
  method: obo2owl
  source url: https://raw.githubusercontent.com/obophenotype/developmental-stage-ontologies/master/src/mmusdv/mmusdv.obo
description: Life cycle stages for Mus Musculus
license: CC BY 3.0
theme: anatomy and development
bug-database: https://github.com/obophenotype/developmental-stage-ontologies/issues
access URL: http://purl.obolibrary.org/obo/mmusdv.owl
contact point: Frédéric Bastian
distribution: mmusdv.owl
distribution: mmusdv.obo

Protein modification
preferred prefix: MOD
activity status: active
has build information:
  method: obo2owl
  source url: https://raw.githubusercontent.com/HUPO-PSI/psi-mod-CV/master/PSI-MOD.obo
description: PSI-MOD is an ontology consisting of terms that describe protein chemical modifications
license: CC BY 4.0
publication: The PSI-MOD community standard for representation of protein modification data
theme: chemistry and biochemistry
bug-database: https://github.com/HUPO-PSI/psi-mod-CV/issues
access URL: PSI-MOD.owl
contact point: Pierre-Alain Binz
distribution: PSI-MOD.owl
distribution: PSI-MOD.obo

PSI-MOD.owl
description: PSI-MOD Ontology, OWL format

PSI-MOD.obo
description: PSI-MOD Ontology, OBO format

Mondo Disease Ontology
preferred prefix: MONDO
activity status: active
IAO_0000136: Metazoa
description: A global community effort to harmonize multiple disease resources to yield a coherent merged ontology.
license: CC BY 4.0
publication: Mondo: Integrating Disease Terminology Across Communities
publication: Mondo: Unifying diseases for the world, by the world
theme: health
bug-database: https://github.com/monarch-initiative/mondo/issues
mailing-list: https://groups.google.com/group/mondo-users
label: Mondo
access URL: Mondo OWL edition
contact point: Sabrina Toro
distribution: Mondo OWL edition
distribution: Mondo OBO Format edition
distribution: Mondo JSON edition
distribution: Mondo Base Release
distribution: Mondo Simple Release

Monarch Initiative Disease Browser
label: Monarch

Mondo OWL edition
description: Complete ontology with merged imports.
format: owl-rdf/xml

Mondo OBO Format edition
description: OBO serialization of mondo.owl.
format: obo

Mondo JSON edition
description: Obographs serialization of mondo.owl.
format: obo

Mondo Base Release
description: The main ontology plus axioms connecting to select external ontologies, excluding the external ontologies themselves
format: owl

Mondo Simple Release
description: The main ontology classes and their hierarchies, without references to external terms.
format: owl

Molecular Process Ontology
preferred prefix: MOP
activity status: active
has build information:
  method: owl2obo
  source url: https://raw.githubusercontent.com/rsc-ontologies/rxno/master/mop.owl
description: Processes at the molecular level
license: CC BY 4.0
theme: chemistry and biochemistry
bug-database: https://github.com/rsc-ontologies/rxno/issues
access URL: Molecular Process Ontology
contact point: Colin Batchelor
distribution: Molecular Process Ontology

Mammalia
label: Mammalian

MGI MP Browser
label: MGI

RGD MP Browser
label: RGD

Monarch Phenotype Page
label: Monarch

MP (OWL edition)
description: The main ontology in OWL. Contains all MP terms and links to other OBO ontologies.

MP (OBO edition)
description: A direct translation of the MP (OWL edition) into OBO format.

MP (obographs JSON edition)
description: For a description of the format see https://github.com/geneontology/obographs.

MP Base Module
description: The main ontology plus axioms connecting to select external ontologies, excluding axioms from the the external ontologies themselves.

Mouse pathology ontology
preferred prefix: MPATH
activity status: active
has build information:
  method: obo2owl
  source url: https://raw.githubusercontent.com/PaulNSchofield/mpath/master/mpath.obo
IAO_0000136: Mus
description: A structured controlled vocabulary of mutant and transgenic mouse pathology phenotypes
license: CC BY 3.0
theme: health
bug-database: https://github.com/PaulNSchofield/mpath/issues
access URL: http://purl.obolibrary.org/obo/mpath.owl
contact point: Paul Schofield
distribution: mpath.owl

Minimum PDDI Information Ontology
preferred prefix: MPIO
activity status: active
description: An ontology of minimum information regarding potential drug-drug interaction information.
license: CC BY 4.0
theme: health
bug-database: https://github.com/MPIO-Developers/MPIO/issues
access URL: http://purl.obolibrary.org/obo/mpio.owl
contact point: Mathias Brochhausen
distribution: mpio.owl

MHC Restriction Ontology
preferred prefix: MRO
activity status: active
description: An ontology for Major Histocompatibility Complex (MHC) restriction in experiments
license: CC BY 3.0
theme: chemistry and biochemistry
bug-database: https://github.com/IEDB/MRO/issues
access URL: http://purl.obolibrary.org/obo/mro.owl
contact point: Bjoern Peters
distribution: mro.owl

Mass spectrometry ontology
preferred prefix: MS
activity status: active
continuous integration server: https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master
depends on: Phenotype And Trait Ontology
depends on: Units of measurement ontology
has build information:
  method: obo2owl
  source url: https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo
description: A structured controlled vocabulary for the annotation of experiments concerned with proteomics mass spectrometry.
license: CC BY 3.0
publication: The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary.
theme: investigations
bug-database: https://github.com/HUPO-PSI/psi-ms-CV/issues
label: MS
access URL: http://purl.obolibrary.org/obo/ms.owl
contact point: Joshua Klein
distribution: ms.obo
distribution: ms.owl

BioPortal Ontology Browser
label: BioPortal

NCBI Taxonomy Browser
label: NCBI

NCIt OBO Edition OWL format
description: A direct transformation of the standard NCIt content using OBO-style term and ontology IRIs and annotation properties.

Non-Coding RNA Ontology
preferred prefix: NCRO
activity status: active
has build information:
  method: owl2obo
  source url: http://purl.obolibrary.org/obo/ncro/prebuild/ncro.owl
description: An ontology for non-coding RNA, both of biological origin, and engineered.
license: CC BY 4.0
theme: investigations
bug-database: https://github.com/OmniSearch/ncro/issues
mailing-list: ncro-devel@googlegroups.com, ncro-discuss@googlegroups.com
access URL: http://purl.obolibrary.org/obo/ncro.owl
contact point: Jingshan Huang
distribution: NCRO development version

Next Generation Biobanking Ontology
preferred prefix: NGBO
activity status: active
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.
license: CC BY 4.0
theme: investigations
bug-database: https://github.com/Dalalghamdi/NGBO/issues
access URL: http://purl.obolibrary.org/obo/ngbo.owl
contact point: Dalia Alghamdi
distribution: ngbo.owl

NOMEN - A nomenclatural ontology for biological names
preferred prefix: NOMEN
activity status: active
has build information:
  checkout: git clone https://github.com/SpeciesFileGroup/nomen.git
description: NOMEN is a nomenclatural ontology for biological names (not concepts). It encodes the goverened rules of nomenclature.
license: CC0 1.0
theme: information
funded by: NSF ABI-1356381
bug-database: https://github.com/SpeciesFileGroup/nomen/issues
mailing-list: https://groups.google.com/forum/#!forum/nomen-discuss
label: NOMEN
access URL: NOMEN
contact point: Matt Yoder
distribution: NOMEN

NOMEN
description: core ontology
type: Ontology

Ontology of Adverse Events
preferred prefix: OAE
activity status: active
has build information:
  method: owl2obo
  source url: https://raw.githubusercontent.com/OAE-ontology/OAE/master/src/oae_merged.owl
description: A biomedical ontology in the domain of adverse events
license: CC BY 3.0
theme: health
bug-database: https://github.com/OAE-ontology/OAE/issues
access URL: http://purl.obolibrary.org/obo/oae.owl
contact point: Yongqunh He
distribution: oae.owl

Ontology of Arthropod Circulatory Systems
preferred prefix: OARCS
activity status: active
description: OArCS is an ontology describing the Arthropod ciruclatory system.
license: CC BY 3.0
theme: anatomy and development
bug-database: https://github.com/aszool/oarcs/issues
access URL: http://purl.obolibrary.org/obo/oarcs.owl
contact point: Matt Yoder
distribution: oarcs.owl

Ontology of Biological and Clinical Statistics
preferred prefix: OBCS
activity status: active
description: A biomedical ontology in the domain of biological and clinical statistics.
license: CC BY 4.0
theme: information technology
bug-database: https://github.com/obcs/obcs/issues
access URL: http://purl.obolibrary.org/obo/obcs.owl
contact point: Jie Zheng
distribution: obcs.owl

BioPortal Browser
label: BioPortal

OBI
description: The full version of OBI in OWL format

OBI in OBO
description: The OBO-format version of OBI

OBI Core
description: A collection of important high-level terms and their relations from OBI and other ontologies

OBI Base module
description: Base module for OBI

Ontology for Biobanking
preferred prefix: OBIB
activity status: active
description: An ontology built for annotation and modeling of biobank repository and biobanking administration
license: CC BY 4.0
theme: investigations
bug-database: https://github.com/biobanking/biobanking/issues
access URL: http://purl.obolibrary.org/obo/obib.owl
contact point: Justin Whorton
distribution: obib.owl

Occupation Ontology
preferred prefix: OCCO
activity status: active
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.
license: CC BY 4.0
theme: information
bug-database: https://github.com/Occupation-Ontology/OccO/issues
access URL: http://purl.obolibrary.org/obo/occo.owl
contact point: Jie Zheng
distribution: occo.owl

BioPortal Ontology Browser
label: BioPortal

The Ontology of Genes and Genomes
preferred prefix: OGG
activity status: active
description: A formal ontology of genes and genomes of biological organisms.
license: CC BY 3.0
theme: biological systems
bug-database: https://bitbucket.org/hegroup/ogg/issues/
access URL: http://purl.obolibrary.org/obo/ogg.owl
contact point: Yongqun Oliver He
distribution: ogg.owl

Oral Health and Disease Ontology
preferred prefix: OHD
activity status: active
has build information:
  method: owl2obo
  source url: http://purl.obolibrary.org/obo/ohd.owl
description: The Oral Health and Disease Ontology is used for representing the diagnosis and treatment of dental maladies.
license: CC BY 4.0
publication: Structuring, reuse and analysis of electronic dental data using the Oral Health and Disease Ontology
theme: health
bug-database: https://github.com/oral-health-and-disease-ontologies/ohd-ontology/issues
access URL: http://purl.obolibrary.org/obo/ohd.owl
contact point: Bill Duncan
distribution: ohd.owl
distribution: OHD dev

Ontology of Host-Microbiome Interactions
preferred prefix: OHMI
activity status: active
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.
license: CC BY 4.0
theme: organisms
bug-database: https://github.com/ohmi-ontology/ohmi/issues
mailing-list: http://groups.google.com/group/ohmi-discuss
access URL: http://purl.obolibrary.org/obo/ohmi.owl
contact point: Yongqun Oliver He
distribution: ohmi.owl

Ontology of Host Pathogen Interactions
preferred prefix: OHPI
activity status: active
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.
license: CC BY 4.0
publication: Victors: a web-based knowledge base of virulence factors in human and animal pathogens
theme: biological systems
bug-database: https://github.com/OHPI/ohpi/issues
mailing-list: http://groups.google.com/group/ohpi-discuss
access URL: http://purl.obolibrary.org/obo/ohpi.owl
contact point: Edison Ong
distribution: ohpi.owl

Ontology for Nutritional Epidemiology
preferred prefix: ONE
activity status: active
depends on: Food Ontology
depends on: Ontology for Biomedical Investigations
depends on: Ontology for Nutritional Studies
description: An ontology to standardize research output of nutritional epidemiologic studies.
license: CC BY 4.0
theme: diet, metabolomics, and nutrition
bug-database: https://github.com/cyang0128/Nutritional-epidemiologic-ontologies/issues
access URL: http://purl.obolibrary.org/obo/one.owl
contact point: Chen Yang
distribution: one.owl

Ontology for Nutritional Studies
preferred prefix: ONS
activity status: active
depends on: Basic Formal Ontology
depends on: Chemical Entities of Biological Interest
depends on: Environment Ontology
depends on: Food Ontology
depends on: NCBI organismal classification
depends on: Ontology for Biomedical Investigations
depends on: Relation Ontology
depends on: Uberon multi-species anatomy ontology
description: An ontology for description of concepts in the nutritional studies domain.
license: CC BY 4.0
publication: ONS: an ontology for a standardized description of interventions and observational studies in nutrition
theme: diet, metabolomics, and nutrition
bug-database: https://github.com/enpadasi/Ontology-for-Nutritional-Studies/issues
access URL: ONS latest release
contact point: Francesco Vitali
distribution: ONS latest release

OntoAvida: ontology for Avida digital evolution platform
preferred prefix: ONTOAVIDA
activity status: active
depends on: FlyBase Controlled Vocabulary
depends on: Gender, Sex, and Sexual Orientation (GSSO) ontology
depends on: NCI Thesaurus OBO Edition
depends on: Relation Ontology
depends on: The Statistical Methods Ontology
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).
license: CC BY 4.0
publication: Ontology for the Avida digital evolution platform
theme: simulation
bug-database: https://gitlab.com/fortunalab/ontoavida/-/issues
access URL: OWL
contact point: Miguel A. Fortuna
distribution: OWL
distribution: OBO

Gender, Sex, and Sexual Orientation (GSSO) ontology
preferred prefix: GSSO
activity status: active
has build information:
  checkout: git clone https://github.com/Superraptor/GSSO.git
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.
license: Apache 2.0 License
theme: organisms
bug-database: https://github.com/Superraptor/GSSO/issues
access URL: http://purl.obolibrary.org/obo/gsso.owl
contact point: Clair Kronk
distribution: gsso.owl
distribution: gsso.obo
distribution: gsso.json

The Statistical Methods Ontology
preferred prefix: STATO
activity status: active
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.
license: CC BY 3.0
publication: Experiment design driven FAIRification of omics data matrices, an exemplar
publication: Semantic concept schema of the linear mixed model of experimental observations
theme: information technology
bug-database: https://github.com/ISA-tools/stato/issues
access URL: http://purl.obolibrary.org/obo/stato.owl
contact point: Philippe Rocca-Serra
distribution: stato.owl

Ontoavida HTML Browser
label: Human-readable (HTML)

OWL
description: The main ontology in OWL

OBO
description: Equivalent to ontoavida.owl, in obo format

Obstetric and Neonatal Ontology
preferred prefix: ONTONEO
activity status: active
has build information:
  source url: https://raw.githubusercontent.com/ontoneo-project/Ontoneo/master/ontoneo.owl
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.
license: CC BY 4.0
publication: OntONeo: The Obstetric and Neonatal Ontology
publication: Formal Ontologies in Knowledge Organization within the Obstetric and Neonatal Domain
theme: health
bug-database: https://github.com/ontoneo-project/Ontoneo/issues
mailing-list: http://groups.google.com/group/ontoneo-discuss
access URL: ONTONEO
contact point: Fernanda Farinelli
distribution: ONTONEO

BioPortal Browser
label: BioPortal

OntoBee Browser
label: OntoBee

ONTONEO
description: The full version of ONTONEO in OWL format

Ontology of Organizational Structures of Trauma centers and Trauma systems
preferred prefix: OOSTT
activity status: active
description: An ontology built for representating the organizational components of trauma centers and trauma systems.
license: CC BY 4.0
theme: health
bug-database: https://github.com/OOSTT/OOSTT/issues
access URL: http://purl.obolibrary.org/obo/oostt.owl
contact point: Mathias Brochhausen
distribution: oostt.owl

Ontology for Parasite LifeCycle
preferred prefix: OPL
activity status: active
description: A reference ontology for parasite life cycle stages.
license: CC BY 4.0
theme: organisms
bug-database: https://github.com/OPL-ontology/OPL/issues
access URL: http://purl.obolibrary.org/obo/opl.owl
contact point: Jie Zheng
distribution: opl.owl

Ontology of RNA Sequencing
preferred prefix: ORNASEQ
activity status: active
description: An application ontology designed to annotate next-generation sequencing experiments performed on RNA.
license: CC BY 4.0
theme: investigations
bug-database: https://github.com/safisher/ornaseq/issues
access URL: http://purl.obolibrary.org/obo/ornaseq.owl
contact point: Stephen Fisher
distribution: ornaseq.owl

Ontology of Vaccine Adverse Events
preferred prefix: OVAE
activity status: active
description: A biomedical ontology in the domain of vaccine adverse events.
license: CC BY 3.0
theme: health
bug-database: https://github.com/OVAE-Ontology/ovae/issues
access URL: http://purl.obolibrary.org/obo/ovae.owl
contact point: Yongqunh He
distribution: ovae.owl

BioPortal Ontology Browser
label: BioPortal

pato-base.owl
description: Includes axioms linking to other ontologies, but no imports of those ontologies

Provisional Cell Ontology
preferred prefix: PCL
activity status: active
depends on: Basic Formal Ontology
depends on: Chemical Entities of Biological Interest
depends on: Cell Ontology
depends on: Gene Ontology
depends on: Neuro Behavior Ontology
depends on: NCBI organismal classification
depends on: OBO Metadata Ontology
depends on: Phenotype And Trait Ontology
depends on: PRotein Ontology (PRO)
depends on: Relation Ontology
depends on: Sequence types and features ontology
depends on: Uberon multi-species anatomy ontology
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.
license: CC BY 4.0
theme: phenotype
bug-database: https://github.com/obophenotype/provisional_cell_ontology/issues
access URL: http://purl.obolibrary.org/obo/pcl.owl
contact point: David Osumi-Sutherland
distribution: pcl.owl
distribution: pcl.obo
distribution: pcl.json
distribution: pcl-base.owl
distribution: pcl-base.obo
distribution: pcl-base.json
distribution: pcl-full.owl
distribution: pcl-full.obo
distribution: pcl-full.json
distribution: pcl-simple.owl
distribution: pcl-simple.obo
distribution: pcl-simple.json

Sequence types and features ontology
preferred prefix: SO
activity status: active
has build information:
  method: obo2owl
  source url: https://raw.githubusercontent.com/The-Sequence-Ontology/SO-Ontologies/master/so.obo
description: A structured controlled vocabulary for sequence annotation, for the exchange of annotation data and for the description of sequence objects in databases.
license: CC BY 4.0
publication: The Sequence Ontology: a tool for the unification of genome annotations.
publication: Evolution of the Sequence Ontology terms and relationships.
theme: chemistry and biochemistry
bug-database: https://github.com/The-Sequence-Ontology/SO-Ontologies/issues
mailing-list: https://sourceforge.net/p/song/mailman/song-devel/
access URL: Main SO OWL release
contact point: Karen Eilbeck
distribution: Main SO OWL release
distribution: Main SO release in OBO Format
distribution: Sequence Ontology Feature Annotation (SOFA) subset (OWL)
distribution: Sequence Ontology Feature Annotation (SOFA) subset (OBO Format)

The Prescription of Drugs Ontology
preferred prefix: PDRO
activity status: active
has build information:
  method: owl2obo
  source url: http://purl.obolibrary.org/obo/pdro.owl
description: An ontology to describe entities related to prescription of drugs
license: CC BY 4.0
publication: The Prescription of Drug Ontology 2.0 (PDRO): More Than the Sum of Its Parts
theme: information
bug-database: https://github.com/OpenLHS/PDRO/issues
access URL: http://purl.obolibrary.org/obo/pdro.owl
contact point: Paul Fabry
distribution: pdro.owl

Pathogen Host Interaction Phenotype Ontology
preferred prefix: PHIPO
activity status: active
depends on: Phenotype And Trait Ontology
description: PHIPO is a formal ontology of species-neutral phenotypes observed in pathogen-host interactions.
license: CC BY 3.0
publication: PHI-base in 2022: a multi-species phenotype database for Pathogen-Host Interactions
theme: phenotype
bug-database: https://github.com/PHI-base/phipo/issues
access URL: http://purl.obolibrary.org/obo/phipo.owl
contact point: Alayne Cuzick
distribution: phipo.owl
distribution: phipo.obo

planaria-ontology
preferred prefix: PLANA
activity status: active
depends on: Relation Ontology
depends on: Uberon multi-species anatomy ontology
description: PLANA, the planarian anatomy ontology, encompasses the anatomy and life cycle stages for both __Schmidtea mediterranea__ biotypes.
license: CC BY 3.0
publication: Planarian Anatomy Ontology: a resource to connect data within and across experimental platforms
theme: anatomy and development
bug-database: https://github.com/obophenotype/planaria-ontology/issues
access URL: http://purl.obolibrary.org/obo/plana.owl
contact point: Sofia Robb
distribution: plana.owl
distribution: plana.obo

Planarian Phenotype Ontology
preferred prefix: PLANP
activity status: active
depends on: Gene Ontology
depends on: Phenotype And Trait Ontology
depends on: planaria-ontology
depends on: Relation Ontology
description: Planarian Phenotype Ontology is an ontology of phenotypes observed in the planarian Schmidtea mediterranea.
license: CC BY 3.0
theme: phenotype
bug-database: https://github.com/obophenotype/planarian-phenotype-ontology/issues
access URL: http://purl.obolibrary.org/obo/planp.owl
contact point: Sofia Robb
distribution: planp.owl
distribution: planp.obo

Planteome browser
label: Planteome

Plant Phenology Ontology
preferred prefix: PPO
activity status: active
IAO_0000136: Viridiplantae
description: An ontology for describing the phenology of individual plants and populations of plants, and for integrating plant phenological data across sources and scales.
license: CC BY 3.0
theme: phenotype
bug-database: https://github.com/PlantPhenoOntology/PPO/issues
access URL: http://purl.obolibrary.org/obo/ppo.owl
contact point: Ramona Walls
distribution: ppo.owl

BioPortal Browser
label: BioPortal

PRO Home
label: PRO

pro_reasoned.owl
description: PRO after reasoning has been applied, OWL format. Add '.gz' for compressed.

pro_reasoned.obo
description: PRO after reasoning has been applied, OBO format.

pro_nonreasoned.owl
description: PRO without reasoning applied, OWL format. Add '.gz' for compressed.

pro_nonreasoned.obo
description: PRO without reasoning applied, OBO format.

Process Chemistry Ontology
preferred prefix: PROCO
activity status: active
depends on: Chemical Entities of Biological Interest
depends on: Chemical Information Ontology
depends on: Ontology for Biomedical Investigations
depends on: Phenotype And Trait Ontology
depends on: Relation Ontology
depends on: Systems Biology Ontology
description: PROCO covers process chemistry, the chemical field concerned with scaling up laboratory syntheses to commercially viable processes.
license: CC BY 4.0
theme: chemistry and biochemistry
bug-database: https://github.com/proco-ontology/PROCO/issues
access URL: http://purl.obolibrary.org/obo/proco.owl
contact point: Wes Schafer
distribution: proco.owl

Systems Biology Ontology
preferred prefix: SBO
activity status: active
has build information:
  method: obo2owl
  source url: http://www.ebi.ac.uk/sbo/exports/Main/SBO_OBO.obo
description: Terms commonly used in Systems Biology, and in particular in computational modeling.
license: Artistic License 2.0
theme: chemistry and biochemistry
bug-database: https://github.com/EBI-BioModels/SBO/issues
access URL: http://purl.obolibrary.org/obo/sbo.owl
contact point: Rahuman Sheriff
distribution: sbo.owl

Performance Summary Display Ontology
preferred prefix: PSDO
activity status: active
depends on: Basic Formal Ontology
depends on: Information Artifact Ontology
depends on: Relation Ontology
depends on: The Statistical Methods Ontology
has build information:
  checkout: https://github.com/Display-Lab/psdo.git
description: Ontology to reproducibly study visualizations of clinical performance
license: CC BY 3.0
theme: information
bug-database: https://github.com/Display-Lab/psdo/issues
access URL: http://purl.obolibrary.org/obo/psdo.owl
contact point: Zach Landis-Lewis
distribution: psdo.owl

Plant Stress Ontology
preferred prefix: PSO
activity status: active
depends on: Relation Ontology
description: The Plant Stress Ontology describes biotic and abiotic stresses that a plant may encounter.
license: CC BY 3.0
publication: The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics.
theme: agriculture
bug-database: https://github.com/Planteome/plant-stress-ontology/issues
access URL: http://purl.obolibrary.org/obo/pso.owl
contact point: Laurel Cooper
distribution: pso.owl
distribution: pso.obo

Pathway ontology
preferred prefix: PW
activity status: active
has build information:
  method: obo2owl
  source url: https://download.rgd.mcw.edu/ontology/pathway/pathway.obo
description: A controlled vocabulary for annotating gene products to pathways.
license: CC BY 4.0
publication: The Rat Genome Database pathway portal.
publication: The pathway ontology - updates and applications.
theme: biological systems
bug-database: https://github.com/rat-genome-database/PW-Pathway-Ontology/issues
access URL: http://purl.obolibrary.org/obo/pw.owl
contact point: G. Thomas Hayman
distribution: pw.owl
distribution: pw.obo

RGD Ontology Browser
label: RGD

Radiation Biology Ontology
preferred prefix: RBO
activity status: active
depends on: Basic Formal Ontology
depends on: Chemical Methods Ontology
depends on: Environment Ontology
depends on: Ontology for Biomedical Investigations
depends on: Phenotype And Trait Ontology
depends on: Relation Ontology
depends on: Units of measurement ontology
description: RBO is an ontology for the effects of radiation on biota in terrestrial and space environments.
license: CC BY 3.0
theme: environment
bug-database: https://github.com/Radiobiology-Informatics-Consortium/RBO/issues
access URL: http://purl.obolibrary.org/obo/rbo.owl
contact point: Daniel C. Berrios
distribution: rbo.owl
distribution: rbo.obo
distribution: rbo.json
distribution: rbo-base.owl
distribution: rbo-base.obo
distribution: rbo-base.json

Relation Ontology
description: Canonical edition

Relation Ontology in obo format
description: The obo edition is less expressive than the OWL, and has imports merged in

RO Core relations
description: Minimal subset intended to work with BFO-classes

RO base ontology
description: Axioms defined within RO and to be used in imports for other ontologies

Interaction relations
description: For use in ecology and environmental science

Neuroscience subset
description: For use in neuroscience

Rat Strain Ontology
preferred prefix: RS
activity status: active
has build information:
  method: obo2owl
  source url: https://download.rgd.mcw.edu/ontology/rat_strain/rat_strain.obo
IAO_0000136: Rattus
description: Ontology of rat strains
license: CC BY 4.0
publication: Rat Strain Ontology: structured controlled vocabulary designed to facilitate access to strain data at RGD.
theme: organisms
bug-database: https://github.com/rat-genome-database/RS-Rat-Strain-Ontology/issues
access URL: http://purl.obolibrary.org/obo/rs.owl
contact point: Shur-Jen Wang
distribution: rs.owl
distribution: rs.obo

RGD Ontology Browser
label: RGD

Name Reaction Ontology
preferred prefix: RXNO
activity status: active
has build information:
  method: owl2obo
  source url: https://raw.githubusercontent.com/rsc-ontologies/rxno/master/rxno.owl
description: Connects organic name reactions to their roles in an organic synthesis and to processes in MOP
license: CC BY 4.0
theme: chemistry and biochemistry
bug-database: https://github.com/rsc-ontologies/rxno/issues
access URL: Name Reaction Ontology
contact point: Colin Batchelor
distribution: Name Reaction Ontology

Scientific Evidence and Provenance Information Ontology
preferred prefix: SEPIO
activity status: active
has build information:
  checkout: git clone https://github.com/monarch-initiative/SEPIO-ontology.git
description: An ontology for representing the provenance of scientific claims and the evidence that supports them.
license: CC BY 3.0
theme: investigations
bug-database: https://github.com/monarch-initiative/SEPIO-ontology/issues
access URL: SEPIO
contact point: Matthew Brush
distribution: SEPIO

Space Life Sciences Ontology
preferred prefix: SLSO
activity status: active
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.
license: CC BY 3.0
theme: investigations
bug-database: https://github.com/nasa/LSDAO/issues
access URL: http://purl.obolibrary.org/obo/slso.owl
contact point: Dan Berrios
distribution: slso.owl
distribution: slso.obo
distribution: slso.json
distribution: slso-base.owl

BioPortal Ontology Browser
label: BioPortal

slso-base.owl
description: Includes axioms linking to other ontologies, but no imports of those ontologies

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

Sequence Ontology Feature Annotation (SOFA) subset (OBO Format)
description: This subset includes only locatable sequence features and is designed for use in such outputs as GFF3

Spider Ontology
preferred prefix: SPD
activity status: active
has build information:
  method: obo2owl
  source url: https://raw.githubusercontent.com/obophenotype/spider-ontology/master/spider_comparative_biology.obo
IAO_0000136: spiders
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).
license: CC BY 3.0
publication: The Spider Anatomy Ontology (SPD)—A Versatile Tool to Link Anatomy with Cross-Disciplinary Data
theme: anatomy and development
bug-database: https://github.com/obophenotype/spider-ontology/issues
access URL: http://purl.obolibrary.org/obo/spd.owl
contact point: Martin Ramirez
distribution: spd.owl

Symptom Ontology
preferred prefix: SYMP
activity status: active
has build information:
  method: obo2owl
  source url: https://raw.githubusercontent.com/DiseaseOntology/SymptomOntology/master/src/ontology/symp.obo
IAO_0000136: Homo sapiens
description: An ontology of disease symptoms, with symptoms encompasing perceived changes in function, sensations or appearance reported by a patient indicative of a disease.
license: CC0 1.0
publication: GeMInA, Genomic Metadata for Infectious Agents, a geospatial surveillance pathogen database
publication: The Human Disease Ontology 2022 update
theme: health
bug-database: https://github.com/DiseaseOntology/SymptomOntology/issues
access URL: http://purl.obolibrary.org/obo/symp.owl
contact point: Lynn Schriml
distribution: symp.owl
distribution: symp.obo

terms4FAIRskills
preferred prefix: T4FS
activity status: active
description: A terminology for the skills necessary to make data FAIR and to keep it FAIR.
license: CC BY 4.0
publication: EOSC Co-creation funded project 074: Delivery of a proof of concept for terms4FAIRskills: Technical report
theme: information
bug-database: https://github.com/terms4fairskills/FAIRterminology/issues
access URL: http://purl.obolibrary.org/obo/t4fs.owl
contact point: Allyson Lister
distribution: t4fs.owl
distribution: t4fs.obo
distribution: t4fs.json
distribution: 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.
distribution: 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.
distribution: 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.

Taxonomic rank vocabulary
preferred prefix: TAXRANK
activity status: active
description: A vocabulary of taxonomic ranks (species, family, phylum, etc)
license: CC0 1.0
publication: The vertebrate taxonomy ontology: a framework for reasoning across model organism and species phenotypes
theme: organisms
bug-database: https://github.com/phenoscape/taxrank/issues
access URL: http://purl.obolibrary.org/obo/taxrank.owl
contact point: Jim Balhoff
distribution: taxrank.owl
distribution: taxrank.obo

Planteome browser
label: Planteome

Pathogen Transmission Ontology
preferred prefix: TRANS
activity status: active
has build information:
  method: obo2owl
  source url: https://raw.githubusercontent.com/DiseaseOntology/PathogenTransmissionOntology/master/src/ontology/trans.obo
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.
license: CC0 1.0
publication: GeMInA, Genomic Metadata for Infectious Agents, a geospatial surveillance pathogen database
publication: The Human Disease Ontology 2022 update
theme: health
bug-database: https://github.com/DiseaseOntology/PathogenTransmissionOntology/issues
access URL: http://purl.obolibrary.org/obo/trans.owl
contact point: Lynn Schriml
distribution: trans.owl
distribution: trans.obo

Teleost taxonomy ontology
preferred prefix: TTO
activity status: active
IAO_0000136: Teleostei
description: An ontology covering the taxonomy of teleosts (bony fish)
license: CC0 1.0
publication: The Teleost Taxonomy Ontology
theme: organisms
bug-database: https://github.com/phenoscape/teleost-taxonomy-ontology/issues
access URL: http://purl.obolibrary.org/obo/tto.owl
contact point: Jim Balhoff
distribution: tto.obo
distribution: tto.owl

Toxic Process Ontology
preferred prefix: TXPO
activity status: active
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.
license: CC BY 3.0
publication: Ontological approach to the knowledge systematization of a toxic process and toxic course representation framework for early drug risk management
theme: chemistry and biochemistry
bug-database: https://github.com/txpo-ontology/TXPO/issues
access URL: http://purl.obolibrary.org/obo/txpo.owl
contact point: Yuki Yamagata
distribution: txpo.owl

BioPortal Browser
label: BioPortal

TOXPILOT

Gene Ontology AmiGO 2 Browser
label: RGD

Gene Ontology AmiGO 2 Browser
label: AmiGO (SUBSET)

Bgee gene expression queries
label: Bgee (gene expression)

FANTOM5 Data Portal
label: FANTOM5

INCF KnowledgeSpace Portal
label: KnowledgeSpace

Uberon
description: core ontology
type: Ontology

Uberon base ontology
description: Axioms defined within Uberon and to be used in imports for other ontologies

Uberon basic
description: Uberon edition that excludes external ontologies and most relations
format: obo
type: obo-basic-ontology

Uberon collected metazoan ontology
IAO_0000136: Metazoa
description: Uberon plus all metazoan ontologies
type: MergedOntology

Uberon composite metazoan ontology
IAO_0000136: Metazoa
description: Uberon and all metazoan ontologies with redundant species-specific terms removed
type: MergedOntology

Uberon composite vertebrate ontology
IAO_0000136: Vertebrata
type: MergedOntology

Unified Phenotype Ontology (uPheno)
preferred prefix: UPHENO
activity status: active
has build information:
  method: archive
  source url: http://build.berkeleybop.org/job/build-pheno-ontologies/lastSuccessfulBuild/artifact/*zip*/archive.zip
description: The uPheno ontology integrates multiple phenotype ontologies into a unified cross-species phenotype ontology.
license: CC0 1.0
publication: The Unified Phenotype Ontology (uPheno): A framework for cross-species integrative phenomics
publication: Phenotype Ontologies Traversing All The Organisms (POTATO) workshop aims to reconcile logical definitions across species
publication: Phenotype Ontologies Traversing All The Organisms (POTATO) workshop: 2nd edition
theme: phenotype
bug-database: https://github.com/obophenotype/upheno/issues
mailing-list: https://groups.google.com/forum/#!forum/phenotype-ontologies-editors
access URL: uPheno 1 (inactive)
contact point: James McLaughlin
distribution: uPheno 1 (inactive)
distribution: uPheno MP-HP equivalence axioms
distribution: uPheno 2

uPheno 1 (inactive)
description: uPheno 1 is no longer actively maintained, please start using uPheno 2 (see below).

uPheno MP-HP equivalence axioms
description: No longer actively maintained.

uPheno 2
description: The new version of uPheno, along with species independent phenotypes and additional phenotype relations. The ontology is still in Beta status, but we recommend users to migrate their infrastructures to uPheno 2 as uPheno 1 is no longer actively maintained.

Vertebrate Breed Ontology
preferred prefix: VBO
activity status: active
depends on: NCBI organismal classification
description: Vertebrate Breed Ontology is an ontology created to serve as a single computable resource for vertebrate breed names.
license: CC BY 4.0
publication: The Vertebrate Breed Ontology: Toward Effective Breed Data Standardization
theme: organisms
bug-database: https://github.com/monarch-initiative/vertebrate-breed-ontology/issues
mailing-list: https://groups.google.com/group/VBO-users
access URL: http://purl.obolibrary.org/obo/vbo.owl
contact point: Sabrina Toro
distribution: vbo.owl
distribution: vbo.obo
distribution: vbo.json
distribution: vbo-base.owl
distribution: vbo-base.obo
distribution: vbo-base.json

Vaccine Ontology
preferred prefix: VO
activity status: active
has build information:
  source url: https://raw.githubusercontent.com/vaccineontology/VO/master/src/VO_merged.owl
description: VO is a biomedical ontology in the domain of vaccine and vaccination.
license: CC BY 4.0
publication: Ontology representation and analysis of vaccine formulation and administration and their effects on vaccine immune responses
publication: Mining of vaccine-associated IFN-γ gene interaction networks using the Vaccine Ontology
theme: health
bug-database: https://github.com/vaccineontology/VO/issues
access URL: http://purl.obolibrary.org/obo/vo.owl
contact point: Yongqunh He
distribution: vo.owl

Vertebrate trait ontology
preferred prefix: VT
activity status: active
has build information:
  checkout: svn co http://phenotype-ontologies.googlecode.com/svn/trunk/src/ontology/vt
  method: vcs
description: An ontology of traits covering vertebrates
license: CC BY 4.0
theme: phenotype
bug-database: https://github.com/AnimalGenome/vertebrate-trait-ontology/issues
access URL: http://purl.obolibrary.org/obo/vt.owl
contact point: Carissa Park
distribution: vt.owl

Vertebrate Taxonomy Ontology
preferred prefix: VTO
activity status: active
description: Comprehensive hierarchy of extinct and extant vertebrate taxa.
license: CC0 1.0
publication: The vertebrate taxonomy ontology: a framework for reasoning across model organism and species phenotypes
theme: organisms
bug-database: https://github.com/phenoscape/vertebrate-taxonomy-ontology/issues
access URL: http://purl.obolibrary.org/obo/vto.owl
contact point: Jim Balhoff
distribution: vto.owl
distribution: vto.obo

C. elegans Gross Anatomy Ontology
preferred prefix: WBbt
activity status: active
has build information:
  checkout: git clone https://github.com/obophenotype/c-elegans-gross-anatomy-ontology.git
IAO_0000136: Caenorhabditis
description: A structured controlled vocabulary of the anatomy of Caenorhabditis elegans.
license: CC BY 4.0
publication: Building a cell and anatomy ontology of Caenorhabditis elegans
theme: anatomy and development
bug-database: https://github.com/obophenotype/c-elegans-gross-anatomy-ontology/issues
access URL: http://purl.obolibrary.org/obo/wbbt.owl
contact point: Raymond Lee
distribution: wbbt.owl
distribution: wbbt.obo

C. elegans development ontology
preferred prefix: WBls
activity status: active
has build information:
  checkout: git clone https://github.com/obophenotype/c-elegans-development-ontology.git
IAO_0000136: Caenorhabditis
description: A structured controlled vocabulary of the development of Caenorhabditis elegans.
license: CC BY 4.0
publication: WormBase: a modern Model Organism Information Resource
theme: anatomy and development
bug-database: https://github.com/obophenotype/c-elegans-development-ontology/issues
access URL: http://purl.obolibrary.org/obo/wbls.owl
contact point: Chris Grove
distribution: wbls.owl
distribution: wbls.obo

C. elegans phenotype
preferred prefix: WBPhenotype
activity status: active
has build information:
  checkout: git clone https://github.com/obophenotype/c-elegans-phenotype-ontology.git
IAO_0000136: Caenorhabditis
description: A structured controlled vocabulary of Caenorhabditis elegans phenotypes
license: CC BY 4.0
publication: Worm Phenotype Ontology: integrating phenotype data within and beyond the C. elegans community.
theme: phenotype
bug-database: https://github.com/obophenotype/c-elegans-phenotype-ontology/issues
access URL: http://purl.obolibrary.org/obo/wbphenotype.owl
contact point: Chris Grove
distribution: wbphenotype.owl
distribution: wbphenotype.obo
distribution: wbphenotype-base.owl

Xenopus Anatomy Ontology
preferred prefix: XAO
activity status: active
has build information:
  method: obo2owl
  source url: https://raw.githubusercontent.com/xenopus-anatomy/xao/master/xenopus_anatomy.obo
IAO_0000136: Xenopus
description: XAO represents the anatomy and development of the African frogs Xenopus laevis and tropicalis.
license: CC BY 3.0
publication: An ontology for Xenopus anatomy and development.
publication: Enhanced XAO: the ontology of Xenopus anatomy and development underpins more accurate annotation of gene expression and queries on Xenbase.
theme: anatomy and development
bug-database: https://github.com/xenopus-anatomy/xao/issues
access URL: http://purl.obolibrary.org/obo/xao.owl
contact point: Erik Segerdell
distribution: xao.owl
distribution: xao.obo

RGD Ontology Browser
label: RGD

HUPO-PSI cross-linking and derivatization reagents controlled vocabulary
preferred prefix: XLMOD
activity status: active
description: A structured controlled vocabulary for cross-linking reagents used with proteomics mass spectrometry.
license: CC BY 3.0
theme: chemistry and biochemistry
bug-database: https://github.com/HUPO-PSI/xlmod-CV/issues
label: xlmod
access URL: http://purl.obolibrary.org/obo/xlmod.owl
contact point: Lutz Fischer
distribution: xlmod.obo
distribution: xlmod.owl

Xenopus Phenotype Ontology
preferred prefix: XPO
activity status: active
depends on: Basic Formal Ontology
depends on: Chemical Entities of Biological Interest
depends on: Cell Ontology
depends on: Gene Ontology
depends on: Information Artifact Ontology
depends on: Phenotype And Trait Ontology
depends on: Relation Ontology
depends on: Xenopus Anatomy Ontology
IAO_0000136: Xenopus
description: XPO represents anatomical, cellular, and gene function phenotypes occurring throughout the development of the African frogs Xenopus laevis and tropicalis.
license: CC BY 3.0
publication: The Xenopus phenotype ontology: bridging model organism phenotype data to human health and development.
theme: phenotype
bug-database: https://github.com/obophenotype/xenopus-phenotype-ontology/issues
access URL: http://purl.obolibrary.org/obo/xpo.owl
contact point: Erik Segerdell
distribution: xpo.owl
distribution: xpo.obo

Zebrafish anatomy and development ontology
preferred prefix: ZFA
activity status: active
has build information:
  method: obo2owl
  source url: https://raw.githubusercontent.com/cerivs/zebrafish-anatomical-ontology/master/src/zebrafish_anatomy.obo
IAO_0000136: Danio
description: A structured controlled vocabulary of the anatomy and development of the Zebrafish
license: CC BY 3.0
publication: The zebrafish anatomy and stage ontologies: representing the anatomy and development of Danio rerio.
theme: anatomy and development
bug-database: https://github.com/cerivs/zebrafish-anatomical-ontology/issues
access URL: http://purl.obolibrary.org/obo/zfa.owl
contact point: Ceri Van Slyke
distribution: zfa.owl
distribution: zfa.obo

Zebrafish developmental stages ontology
preferred prefix: ZFS
activity status: active
has build information:
  method: obo2owl
  source url: https://raw.githubusercontent.com/obophenotype/developmental-stage-ontologies/master/src/zfs/zfs.obo
IAO_0000136: Danio
description: Developmental stages of the Zebrafish
license: CC BY 3.0
theme: anatomy and development
bug-database: https://github.com/cerivs/zebrafish-anatomical-ontology/issues
access URL: http://purl.obolibrary.org/obo/zfs.owl
contact point: Ceri Van Slyke
distribution: zfs.owl
distribution: zfs.obo

Zebrafish Phenotype Ontology
preferred prefix: ZP
activity status: active
depends on: Basic Formal Ontology
depends on: Biological Spatial Ontology
depends on: Gene Ontology
depends on: Phenotype And Trait Ontology
depends on: Relation Ontology
depends on: Uberon multi-species anatomy ontology
depends on: Zebrafish anatomy and development ontology
description: The Zebrafish Phenotype Ontology formally defines all phenotypes of the Zebrafish model organism.
license: CC BY 3.0
theme: phenotype
bug-database: https://github.com/obophenotype/zebrafish-phenotype-ontology/issues
access URL: http://purl.obolibrary.org/obo/zp.owl
contact point: Yvonne Bradford
distribution: zp.owl
distribution: zp.obo

JAX HPO Browser
label: HPO

Monarch Phenotype Page
label: Monarch

Official HPO release in obographs JSON format
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

Official HPO release in OBO format
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

Official HPO release in OWL
description: Manually classified version of the ontology without the use of a reasoner, with imported terms, in OWL format (RDF/XML).
format: owl

HPO base release in obographs JSON format
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

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 OBO file format.
format: obo

HPO base release in OWL format
description: Manually curated version of the ontology without the use of a reasoner, with references to imported terms, in OWL (RDF/XML) file format.
format: owl

HPO full release in obographs JSON format
description: Version of the ontology automatically classified with the use of a reasoner, including all imported terms, in obographs JSON file format.
format: json

HPO full release in OBO format
description: Version of the ontology automatically classified with the use of a reasoner, including all imported terms, in OBO file format.
format: obo

HPO full release in OWL format
description: Version of the ontology automatically classified with the use of a reasoner, including all imported terms, in OWL (RDF/XML) file format.
format: owl

HPO International Edition in obographs JSON format
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

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 OBO file format.
format: obo

HPO International Edition in OWL format
description: Version of the ontology corresponding to the primary release (hp.owl), with translated labels, synonyms, and definitions, in OWL (RDF/XML) file format.
format: owl

HPO simple, manually classified, without imports in obographs JSON format
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

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 OBO file format.
format: obo

HPO simple, manually classified, without imports in OWL format
description: Simple, manually curated version of the ontology without the use of a reasoner, and without any imported terms, in OWL (RDF/XML) file format.
format: owl

HPO Annotations (Phenotype to Disease)
description: https://hpo.jax.org/app/data/annotations
format: tsv

HPO phenotype to gene annotations
description: https://hpo.jax.org/app/data/annotations
format: tsv

HPO gene to phenotype annotations
description: https://hpo.jax.org/app/data/annotations
format: tsv

Kinetic Simulation Algorithm Ontology
preferred prefix: KISAO
activity status: active
has build information:
  method: owl2obo
  source url: https://raw.githubusercontent.com/SED-ML/KiSAO/deploy/kisao.owl
description: A classification of algorithms for simulating biology, their parameters, and their outputs
license: Artistic License 2.0
publication: Controlled vocabularies and semantics in systems biology
theme: simulation
funded by: NIH P41EB023912
funded by: NIH R35GM119771
bug-database: https://github.com/SED-ML/KiSAO/issues
access URL: http://purl.obolibrary.org/obo/kisao.owl
contact point: Jonathan Karr
distribution: kisao.owl

Ontology Lookup Service
label: OLS

BioPortal

OntoBee

Sickle Cell Disease Ontology
preferred prefix: SCDO
activity status: active
depends on: Apollo Structured Vocabulary
depends on: Antibiotic Resistance Ontology
depends on: Chemical Entities of Biological Interest
depends on: Chemical Methods Ontology
depends on: Clinical measurement ontology
depends on: Human Disease Ontology
depends on: The Drug Ontology
depends on: Data Use Ontology
depends on: Environment Ontology
depends on: VEuPathDB ontology
depends on: Exposure ontology
depends on: Gazetteer
depends on: Gender, Sex, and Sexual Orientation (GSSO) ontology
depends on: Human Phenotype Ontology (HPO)
depends on: Human Developmental Stages
depends on: Informed Consent Ontology
depends on: Infectious Disease Ontology
depends on: Malaria Ontology
depends on: Mammalian Phenotype Ontology
depends on: Neuro Behavior Ontology
depends on: NCI Thesaurus OBO Edition
depends on: Ontology for Biomedical Investigations
depends on: Ontology for General Medical Science
depends on: Ontology of Precision Medicine and Investigation
depends on: PRotein Ontology (PRO)
depends on: Systems Biology Ontology
depends on: The Statistical Methods Ontology
depends on: Symptom Ontology
depends on: Units of measurement ontology
depends on: Vaccine Ontology
depends on: Vertebrate trait ontology
has build information:
  checkout: git clone https://github.com/scdodev/scdo-ontology.git
description: An ontology for the standardization of terminology and integration of knowledge about Sickle Cell Disease.
license: GPL-3.0
publication: The Sickle Cell Disease Ontology: recent development and expansion of the universal sickle cell knowledge representation.
publication: The Sickle Cell Disease Ontology: Enabling Collaborative Research and Co-Designing of New Planetary Health Applications.
publication: The Sickle Cell Disease Ontology: enabling universal sickle cell-based knowledge representation.
theme: health
bug-database: https://github.com/scdodev/scdo-ontology/issues
access URL: http://purl.obolibrary.org/obo/scdo.owl
contact point: Jade Hotchkiss
distribution: scdo.owl
distribution: scdo.obo

VEuPathDB ontology
preferred prefix: EUPATH
activity status: inactive
description: An ontology is developed to support Eukaryotic Pathogen, Host & Vector Genomics Resource (VEuPathDB; https://veupathdb.org).
license: CC BY 4.0
publication: Malaria study data integration and information retrieval based on OBO Foundry ontologies.
theme: organisms
bug-database: https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues
access URL: http://purl.obolibrary.org/obo/eupath.owl
contact point: Jie Zheng
distribution: eupath.owl

Malaria Ontology
activity status: inactive
description: An application ontology to cover all aspects of malaria as well as the intervention attempts to control it.
license: CC0 1.0
theme: health
access URL: http://purl.obolibrary.org/obo/idomal.owl
contact point: Pantelis Topalis
distribution: idomal.owl
distribution: idomal.obo

Physico-chemical methods and properties
activity status: orphaned
has build information:
  method: obo2owl
  source url: ftp://ftp.ebi.ac.uk/pub/databases/chebi/ontology/fix.obo
description: An ontology of physico-chemical methods and properties.
theme: chemistry and biochemistry
access URL: http://purl.obolibrary.org/obo/fix.owl
contact point: chEBI
distribution: fix.owl
distribution: fix.obo

Mathematical modeling ontology
preferred prefix: MAMO
activity status: orphaned
has build information:
  method: owl2obo
  source url: https://svn.code.sf.net/p/mamo-ontology/code/tags/latest/mamo-xml.owl
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.
license: Artistic License 2.0
theme: simulation
bug-database: http://sourceforge.net/p/mamo-ontology/tickets/
access URL: http://purl.obolibrary.org/obo/mamo.owl
distribution: mamo.owl

Physico-chemical process
activity status: orphaned
has build information:
  method: obo2owl
  source url: http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/physicochemical/rex.obo
description: An ontology of physico-chemical processes, i.e. physico-chemical changes occurring in course of time.
theme: chemistry and biochemistry
access URL: http://purl.obolibrary.org/obo/rex.owl
distribution: rex.owl

Social Insect Behavior Ontology
preferred prefix: SIBO
activity status: orphaned
has build information:
  checkout: git clone https://github.com/obophenotype/sibo.git
  method: vcs
description: Social Behavior in insects
license: CC BY 3.0
theme: biological systems
bug-database: https://github.com/obophenotype/sibo/issues
access URL: http://purl.obolibrary.org/obo/sibo.owl
contact point: Chris Mungall
distribution: sibo.owl
distribution: sibo.obo

Variation Ontology
preferred prefix: VariO
activity status: orphaned
has build information:
  method: obo2owl
  source url: http://variationontology.org/vario_download/vario.obo
description: Variation Ontology, VariO, is an ontology for standardized, systematic description of effects, consequences and mechanisms of variations.
license: CC BY 4.0
publication: Variation Ontology for annotation of variation effects and mechanisms
publication: Variation ontology: annotator guide
publication: Types and effects of protein variations
theme: biological systems
bug-database: http://variationontology.org/instructions.shtml
access URL: VariO main release in OWL
contact point: Mauno Vihinen
distribution: VariO main release in OWL
distribution: VariO in OBO format

Biological Imaging Methods Ontology
preferred prefix: FBbi
activity status: inactive
has build information:
  method: obo2owl
  source url: https://raw.githubusercontent.com/dosumis/fbbi/master/src/ontology/fbbi.obo
description: A structured controlled vocabulary of sample preparation, visualization and imaging methods used in biomedical research.
license: CC BY 4.0
theme: investigations
bug-database: https://github.com/CRBS/Biological_Imaging_Methods_Ontology/issues
access URL: http://purl.obolibrary.org/obo/fbbi.owl
contact point: Willy Wong
distribution: fbbi.owl

Mammalian Feeding Muscle Ontology
preferred prefix: MFMO
activity status: inactive
depends on: Uberon multi-species anatomy ontology
IAO_0000136: Mammalia
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.
license: CC BY 3.0
theme: anatomy and development
bug-database: https://github.com/RDruzinsky/feedontology/issues
access URL: http://purl.obolibrary.org/obo/mfmo.owl
contact point: Robert Druzinsky
distribution: mfmo.owl

Ontology of Genetic Susceptibility Factor
preferred prefix: OGSF
activity status: inactive
description: An application ontology to represent genetic susceptibility to a specific disease, adverse event, or a pathological process.
license: CC BY 3.0
theme: investigations
bug-database: https://github.com/linikujp/OGSF/issues
access URL: http://purl.obolibrary.org/obo/ogsf.owl
contact point: Asiyah Yu Lin
distribution: ogsf.owl

Medaka Developmental Stages
preferred prefix: OlatDv
activity status: inactive
has build information:
  method: obo2owl
  source url: https://raw.githubusercontent.com/obophenotype/developmental-stage-ontologies/master/src/olatdv/olatdv.obo
description: Life cycle stages for Medaka
license: CC BY 3.0
theme: anatomy and development
bug-database: https://github.com/obophenotype/developmental-stage-ontologies/issues
access URL: http://purl.obolibrary.org/obo/olatdv.owl
contact point: Frédéric Bastian
distribution: olatdv.obo
distribution: olatdv.owl

Platynereis Developmental Stages
preferred prefix: PdumDv
activity status: inactive
has build information:
  method: obo2owl
  source url: https://raw.githubusercontent.com/obophenotype/developmental-stage-ontologies/master/src/pdumdv/pdumdv.obo
description: Life cycle stages for Platynereis dumerilii
license: CC BY 3.0
theme: anatomy and development
bug-database: https://github.com/obophenotype/developmental-stage-ontologies/issues
access URL: http://purl.obolibrary.org/obo/pdumdv.owl
contact point: Frédéric Bastian
distribution: pdumdv.owl
distribution: pdumdv.obo

Anatomical Entity Ontology
preferred prefix: AEO
activity status: inactive
has build information:
  checkout: git clone https://github.com/obophenotype/human-developmental-anatomy-ontology.git
  method: vcs
description: AEO is an ontology of anatomical structures that expands CARO, the Common Anatomy Reference Ontology
license: CC BY 4.0
theme: anatomy and development
bug-database: https://github.com/obophenotype/human-developmental-anatomy-ontology/issues
access URL: http://purl.obolibrary.org/obo/aeo.owl
contact point: Jonathan Bard
distribution: aeo.owl

Cephalopod Ontology
activity status: inactive
IAO_0000136: Cephalopod
description: An anatomical and developmental ontology for cephalopods
license: CC BY 3.0
theme: anatomy and development
bug-database: https://github.com/obophenotype/cephalopod-ontology/issues
access URL: main version
contact point: Chris Mungall
distribution: main version
distribution: oboformat edition

Human developmental anatomy, abstract
activity status: inactive
depends on: Anatomical Entity Ontology
depends on: Common Anatomy Reference Ontology
depends on: Cell Ontology
has build information:
  checkout: git clone https://github.com/obophenotype/human-developmental-anatomy-ontology.git
  method: vcs
IAO_0000136: Homo sapiens
description: A structured controlled vocabulary of stage-specific anatomical structures of the developing human.
license: CC BY 4.0
publication: A new ontology (structured hierarchy) of human developmental anatomy for the first 7 weeks (Carnegie stages 1-20).
theme: anatomy and development
bug-database: https://github.com/obophenotype/human-developmental-anatomy-ontology/issues
access URL: http://purl.obolibrary.org/obo/ehdaa2.owl
contact point: Jonathan Bard
distribution: ehdaa2.owl
distribution: ehdaa2.obo

Foundational Model of Anatomy Ontology (subset)
preferred prefix: FMA
activity status: inactive
has build information:
  method: obo2owl
  source url: http://svn.code.sf.net/p/obo/svn/fma-conversion/trunk/fma2_obo.obo
IAO_0000136: Homo sapiens
description: This is currently a slimmed down version of FMA
license: CC BY 3.0
publication: Translating the Foundational Model of Anatomy into OWL
publication: The foundational model of anatomy in OWL: Experience and perspectives
publication: Challenges in converting frame-based ontology into OWL: the Foundational Model of Anatomy case-study
theme: anatomy and development
bug-database: https://bitbucket.org/uwsig/fma/issues
access URL: http://purl.obolibrary.org/obo/fma.owl
contact point: Onard Mejino
distribution: fma.owl

Mosquito insecticide resistance
activity status: inactive
IAO_0000136: Anopheles
description: Application ontology for entities related to insecticide resistance in mosquitos
theme: environment
access URL: http://purl.obolibrary.org/obo/miro.owl
contact point: Christos (Kitsos) Louis
distribution: miro.owl
distribution: miro.obo

RNA ontology
activity status: inactive
has build information:
  checkout: git clone https://github.com/BGSU-RNA/rnao.git
  method: vcs
description: Controlled vocabulary pertaining to RNA function and based on RNA sequences, secondary and three-dimensional structures.
license: CC0 1.0
theme: chemistry and biochemistry
bug-database: https://github.com/BGSU-RNA/rnao/issues
access URL: http://purl.obolibrary.org/obo/rnao.owl
contact point: Colin Batchelor
distribution: rnao.owl
distribution: rnao.obo

RNA Ontology jOWL Browser
label: RNAO

Tick Anatomy Ontology
activity status: inactive
IAO_0000136: Ixodidae
description: The anatomy of the Tick, Families: Ixodidae, Argassidae
license: CC BY 4.0
theme: anatomy and development
access URL: http://purl.obolibrary.org/obo/tads.owl
contact point: Daniel Sonenshine
distribution: tads.owl
distribution: tads.obo

Mosquito gross anatomy ontology
activity status: inactive
IAO_0000136: Anopheles
description: A structured controlled vocabulary of the anatomy of mosquitoes.
license: CC0 1.0
theme: anatomy and development
access URL: http://purl.obolibrary.org/obo/tgma.owl
contact point: Pantelis Topalis
distribution: tgma.owl
distribution: tgma.obo

Unipathway
activity status: inactive
depends on: Relation Ontology
description: A manually curated resource for the representation and annotation of metabolic pathways
license: CC BY 3.0
publication: UniPathway: a resource for the exploration and annotation of metabolic pathways
theme: biological systems
bug-database: https://github.com/geneontology/unipathway/issues
access URL: http://purl.obolibrary.org/obo/upa.owl
contact point: Anne Morgat
distribution: upa.owl
distribution: upa.obo

Amphibian gross anatomy
activity status: inactive
IAO_0000136: Amphibia
theme: anatomy and development
contact point: David Blackburn

Animal natural history and life history
activity status: inactive
theme: organisms
contact point: Animal Diversity Web technical staff

Adverse Event Reporting Ontology
activity status: inactive
has build information:
  method: owl2obo
  source url: http://purl.obolibrary.org/obo/aero.owl
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
license: CC BY 3.0
theme: health
contact point: Melanie Courtot
distribution: aero.owl

Amphibian taxonomy
activity status: inactive
IAO_0000136: Amphibia
theme: organisms
contact point: David Blackburn

Beta Cell Genomics Ontology
activity status: inactive
description: An application ontology built for beta cell genomics studies.
license: CC BY 3.0
theme: anatomy and development
bug-database: https://github.com/obi-bcgo/bcgo/issues
contact point: Jie Zheng
distribution: bcgo.owl

Bilateria anatomy
activity status: inactive
has build information:
  method: obo2owl
  source url: http://4dx.embl.de/4DXpress_4d/edocs/bilateria_mrca.obo
IAO_0000136: Bilateria
theme: anatomy and development
contact point: Thorsten Henrich
distribution: bila.owl

Gene Regulation Ontology
activity status: inactive
theme: chemistry and biochemistry
contact point: Vivian Lee

CranioMaxilloFacial ontology
activity status: inactive
theme: health
contact point: Mark Engelstad

Dendritic cell
activity status: inactive
IAO_0000136: all
theme: anatomy and development
contact point: Lindsay Cowell

The Drug-Drug Interactions Ontology
activity status: inactive
description: A formal represention for drug-drug interactions knowledge.
license: CC BY 3.0
publication: DINTO: Using OWL Ontologies and SWRL Rules to Infer Drug–Drug Interactions and Their Mechanisms.
theme: health
bug-database: https://github.com/labda/DINTO/issues
contact point: Maria Herrero
distribution: dinto.owl

Human developmental anatomy, timed version
activity status: inactive
IAO_0000136: Homo sapiens
theme: anatomy and development
contact point: Jonathan Bard

Human developmental anatomy, abstract version
activity status: inactive
IAO_0000136: Homo sapiens
theme: anatomy and development
contact point: Jonathan Bard

Mouse gross anatomy and development, timed
activity status: inactive
has build information:
  method: obo2owl
  source url: ftp://ftp.hgu.mrc.ac.uk/pub/MouseAtlas/Anatomy/EMAP_combined.obo
IAO_0000136: Mus
description: A structured controlled vocabulary of stage-specific anatomical structures of the mouse (Mus).
theme: anatomy and development
contact point: Terry Hayamizu
distribution: emap.owl

Epidemiology Ontology
activity status: inactive
has build information:
  method: owl2obo
  source url: http://purl.obolibrary.org/obo/epo.owl
description: An ontology designed to support the semantic annotation of epidemiology resources
theme: health
distribution: epo.owl

eagle-i resource ontology
activity status: inactive
has build information:
  method: owl2obo
  source url: http://purl.obolibrary.org/obo/ero.owl
description: An ontology of research resources such as instruments. protocols, reagents, animal models and biospecimens.
license: CC BY 2.0
theme: information
contact point: Marc Ciriello
distribution: ero.owl

eVOC (Expressed Sequence Annotation for Humans)
activity status: inactive
theme: anatomy and development
contact point: eVOC mailing list

Fly taxonomy
activity status: inactive
has build information:
  method: obo2owl
  source url: http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/taxonomy/fly_taxonomy.obo
IAO_0000136: Drosophila
description: The taxonomy of the family Drosophilidae (largely after Baechli) and of other taxa referred to in FlyBase.
theme: organisms
contact point: Clare Pilgrim
distribution: fbsp.owl

Influenza Ontology
activity status: inactive
has build information:
  method: owl2obo
  source url: http://purl.obolibrary.org/obo/flu.owl
theme: health
bug-database: http://purl.obolibrary.org/obo/flu/tracker
contact point: Burke Squires
distribution: flu.owl

Cereal Plant Gross Anatomy
activity status: inactive
theme: anatomy and development
contact point: Plant Ontology Administrators

Habronattus courtship
activity status: inactive
theme: organisms
contact point: Peter Midford

Event (INOH pathway ontology)
activity status: inactive
has build information:
  method: obo2owl
  source url: http://download.baderlab.org/INOH/ontologies/EventOntology_172.obo
theme: chemistry and biochemistry

Molecule role (INOH Protein name/family name ontology)
activity status: inactive
has build information:
  method: obo2owl
  source url: https://web.archive.org/web/20131127090937/http://www.inoh.org/ontologies/MoleculeRoleOntology.obo
theme: chemistry and biochemistry
contact point: INOH curators

Protein Domains
activity status: inactive
theme: chemistry and biochemistry
contact point: InterPro Help

Lipid Ontology
activity status: inactive
has build information:
  method: owl2obo
  source url: http://www.lipidprofiles.com/LipidOntology
description: An ontology representation of the LIPIDMAPS nomenclature classification.
theme: chemistry and biochemistry
contact point: Christopher Baker

Loggerhead nesting
activity status: inactive
theme: organisms
contact point: Peter Midford

Multiple alignment
activity status: inactive
theme: chemistry and biochemistry
contact point: Julie Thompson

Minimal anatomical terminology
activity status: inactive
theme: anatomy and development
contact point: Jonathan Bard

Medaka fish anatomy and development
activity status: inactive
IAO_0000136: Oryzias
description: A structured controlled vocabulary of the anatomy and development of the Japanese medaka fish, Oryzias latipes.
theme: anatomy and development
contact point: Thorsten Henrich
distribution: mfo.owl

microRNA Ontology
activity status: inactive
description: An application ontology for use with miRNA databases.
license: CC0 1.0
theme: chemistry and biochemistry
contact point: Pantelis Topalis
distribution: mirnao.owl

Microarray experimental conditions
activity status: inactive
description: A standardized description of a microarray experiment in support of MAGE v.1.
theme: investigations
contact point: Chris Stoeckert
distribution: mo.owl

NIF Cell
activity status: inactive
description: Neuronal cell types
theme: anatomy and development
contact point: Fahim Imam

NIF Dysfunction
activity status: inactive
theme: health
contact point: Fahim Imam

NIF Gross Anatomy
activity status: inactive
theme: anatomy and development
contact point: Fahim Imam

NMR-instrument specific component of metabolomics investigations
activity status: inactive
has build information:
  method: owl2obo
  source url: https://msi-workgroups.svn.sourceforge.net/svnroot/msi-workgroups/ontology/NMR.owl
description: Descriptors relevant to the experimental conditions of the Nuclear Magnetic Resonance (NMR) component in a metabolomics investigation.
theme: investigations
contact point: Schober Daniel
distribution: nmr.owl

OBO relationship types (legacy)
activity status: inactive
theme: upper
contact point: Chris Mungall

Ontology for genetic interval
activity status: inactive
description: An ontology that formalizes the genomic element by defining an upper class genetic interval
theme: chemistry and biochemistry
bug-database: https://code.google.com/p/ontology-for-genetic-interval/issues/list
contact point: Asiyah Yu Lin
distribution: ogi.owl

Plant Anatomy Ontology
activity status: inactive
IAO_0000136: Viridiplantae
theme: anatomy and development
contact point: Pankaj Jaiswal

Platynereis stage ontology
activity status: inactive
IAO_0000136: Platynereis
theme: anatomy and development
contact point: Thorsten Henrich

Plant Growth and Development Stage
activity status: inactive
IAO_0000136: Viridiplantae
theme: anatomy and development
contact point: Plant Ontology Administrators

Plasmodium life cycle
activity status: inactive
theme: anatomy and development
contact point: Matt Berriman

Proteomics data and process provenance
activity status: inactive
theme: chemistry and biochemistry
contact point: Satya S. Sahoo

Protein covalent bond
activity status: inactive
description: For the description of covalent bonds in proteins.
theme: chemistry and biochemistry
contact point: John Garavelli

Subcellular anatomy ontology
activity status: inactive
IAO_0000136: Homo sapiens
theme: anatomy and development
contact point: Stephen Larson

Sample processing and separation techniques
activity status: inactive
has build information:
  method: obo2owl
  source url: https://raw.githubusercontent.com/HUPO-PSI/gelml/master/CV/sep.obo
description: A structured controlled vocabulary for the annotation of sample processing and separation techniques in scientific experiments.
theme: investigations
contact point: SEP developers via the PSI and MSI mailing lists
distribution: sep.owl

Suggested Ontology for Pharmacogenomics
activity status: inactive
IAO_0000136: Homo sapiens
theme: chemistry and biochemistry
contact point: Adrien Coulet

Terminology of Anatomy of Human Embryology
activity status: inactive
IAO_0000136: Homo sapiens
theme: anatomy and development
contact point: Pierre Sprumont

Terminology of Anatomy of Human Histology
activity status: inactive
IAO_0000136: Homo sapiens
theme: health
contact point: Pierre Sprumont

Teleost Anatomy Ontology
activity status: inactive
has build information:
  method: obo2owl
  source url: http://purl.obolibrary.org/obo/tao.obo
IAO_0000136: Teleostei
description: Multispecies fish anatomy ontology. Originally seeded from ZFA, but intended to cover terms relevant to other taxa
license: CC0 1.0
publication: The teleost anatomy ontology: anatomical representation for the genomics age
theme: anatomy and development
contact point: Wasila Dahdul
distribution: tao.owl

Vertebrate Homologous Ontology Group Ontology
activity status: inactive
theme: anatomy and development
distribution: vhog.owl

Vertebrate Skeletal Anatomy Ontology-
activity status: inactive
has build information:
  method: obo2owl
  source url: http://phenoscape.svn.sourceforge.net/svnroot/phenoscape/tags/vocab-releases/VSAO/vsao.obo
IAO_0000136: Vertebrata
description: Vertebrate skeletal anatomy ontology.
theme: anatomy and development
contact point: Wasila Dahdul
distribution: vsao.owl

Yeast phenotypes
activity status: inactive
IAO_0000136: Saccharomyces cerevisiae
theme: phenotype
contact point: Mike Cherry

Maize gross anatomy
activity status: inactive
IAO_0000136: Zea
theme: anatomy and development
contact point: Leszek Vincent