The OBO Foundry is a collaborative experiment involving developers of science-based ontologies who are establishing a set of principles for ontology development with the goal of creating a suite of orthogonal interoperable reference ontologies in the biomedical domain. The groups developing ontologies who have expressed an interest in this goal are listed below, followed by other relevant efforts in this domain.

In addition to a listing of OBO ontologies, this site also provides a statement of the OBO Foundry principles, discussion fora, technical infrastructure, and other services to facilitate ontology development. We welcome feedback and encourage participation.

Click any column header to sort the table by that column. The paw prints link to the term request trackers for the listed ontologies.

OBO Foundry ontologies
Title Domain Prefix File Last changed
Molecular function biological function GO go.obo   [Tracker]
Biological process biological process GO go.obo   [Tracker]
Cellular component anatomy GO go.obo   [Tracker]
Ontology for biomedical investigations experiments OBI obi.owl   [Tracker]
Phenotypic quality phenotype PATO quality.obo   [Tracker]
Chemical entities of biological interest biochemistry CHEBI chebi.obo   [Tracker]
PRotein Ontology (PRO) proteins PR pro.obo   [Tracker]
Zebrafish anatomy and development anatomy ZFA zfa.obo   [Tracker]
Xenopus anatomy and development anatomy XAO xenopus_anatomy.obo   [Tracker]
Plant Ontology anatomy and development PO plant_ontology.obo?view=co   [Tracker]
OBO Foundry candidate ontologies and other ontologies of interest
Title Domain Prefix File Last changed
NCBI organismal classification taxonomy NCBITaxon taxonomy.dat
Vertebrate Taxonomy Ontology VTO vto.owl   [Tracker]
RNA ontology molecular structure RNAO rnao.obo
Cell Line Ontology CLO clo.owl
Cardiovascular Disease Ontology health CVDO cvdo.owl   [Tracker]
Exposure ontology health ExO CTD_exposure_ontology.obo
Beta Cell Genomics Ontology experiments BCGO bcgo.owl   [Tracker]
Ontology of Biological and Clinical Statistics statistics OBCS obcs.owl   [Tracker]
Drosophila Phenotype Ontology FBcv dpo.owl
Informed Consent Ontology health ICO ico.owl   [Tracker]
NIF Cell neuroscience NIF_Cell NIF-Cell.owl
Chemical Methods Ontology health CHMO chmo.owl   [Tracker]
Sample processing and separation techniques provenance SEP sep.obo
Physico-chemical methods and properties FIX fix.obo
Basic Formal Ontology upper BFO 1.1
The Drug Ontology health DRON dron.owl   [Tracker]
Emotion Ontology health MFOEM mfoem.owl   [Tracker]
microRNA Ontology miRNAO mirnao.owl
Molecular Process Ontology MOP mop.obo   [Tracker]
Epidemiology Ontology EPO epo.owl
Mathematical modeling ontology MAMO mamo-xml.owl   [Tracker]
Mental Functioning Ontology MF mf.owl   [Tracker]
Ontology of Biological Attributes phenotype OBA oba.owl
Ontology of Vaccine Adverse Events OVAE ovae.owl   [Tracker]
Mouse adult gross anatomy anatomy MA ma.obo   [Tracker]
Comparative Data Analysis Ontology CDAO cdao.owl
Mouse gross anatomy and development, timed anatomy EMAP EMAP_combined.obo
Infectious disease health IDO ido.owl   [Tracker]
Population and Community Ontology PCO pco.owl   [Tracker]
Ontology of Adverse Events adverse events, health OAE oae.owl
NIF Dysfunction neuroscience NIF_Dysfunction NIF-Dysfunction.owl
Plant Trait Ontology phenotype TO trait.obo?view=co   [Tracker]
Mouse gross anatomy and development, abstract anatomy EMAPA EMAPA.obo
Mammalian phenotype phenotype MP MPheno_OBO.ontology   [Tracker]
NCI Thesaurus health ncithesaurus EVS/
Symptom Ontology health SYMP gemina_symptom.obo
Foundational Model of Anatomy (subset) anatomy FMA fma.obo   [Tracker]
Adverse Event Reporting Ontology health AERO aero.owl
Geographical Entity Ontology GEO geo.owl   [Tracker]
Mosquito gross anatomy anatomy TGMA tgma.obo
Uber anatomy ontology, basic version anatomy uberon-basic basic.obo
Ontology for General Medical Science medicine OGMS ogms.owl   [Tracker]
Ontology for Biobanking health OBIB obib.owl   [Tracker]
Sequence types and features biological sequence SO so-xp.obo?format=raw   [Tracker]
eagle-i resource ontology resources ERO ero.owl   [Tracker]
Kinetic Simulation Algorithm Ontology algorithms KISAO KISAO   [Tracker]
Plant Environmental Conditions environment EO environment_ontology.obo
Systems Biology biochemistry SBO SBO_OBO.obo   [Tracker]
STATistics Ontology statistics STATO stato.owl   [Tracker]
Mental Disease Ontology health MFOMD mfomd.owl   [Tracker]
Zebrafish developmental stages anatomy ZFS zfs.obo
Ontology for MIRNA Target Prediction OMIT OMIT.owl
Information Artifact Ontology information IAO iao.owl   [Tracker]
Human disease ontology health DOID doid.obo   [Tracker]
The Ontology of Genes and Genomes OGG ogg.owl   [Tracker]
Environment Ontology environment ENVO envo-basic.obo   [Tracker]
Lipid Ontology lipids LiPrO LipidOntology
NMR-instrument specific component of metabolomics investigations experiments NMR NMR.owl
Mosquito insecticide resistance environment MIRO miro.obo
MIAPA Ontology MIAPA miapa.owl   [Tracker]
Protein modification proteins MOD PSI-MOD.obo
Platynereis stage ontology anatomy PD_ST Pdu_Stages.obo
Protein covalent bond proteins RESID RESIDUES.XML
Pathogen transmission health TRANS transmission_process.obo   [Tracker]
Ontology for genetic interval OGI ogi.owl   [Tracker]
Protein-protein interaction experiments MI psi-mi25.obo
Ontology of Medically Related Social Entities medicine OMRSE omrse.owl
Tick gross anatomy anatomy TADS tads.obo
C. elegans gross anatomy anatomy WBbt wbbt.obo   [Tracker]
Influenza Ontology health FLU flu.owl   [Tracker]
human phenotype ontology phenotype HP human-phenotype-ontology.obo   [Tracker]
CranioMaxilloFacial ontology health CMF cmf.owl   [Tracker]
Vertebrate Skeletal Anatomy Ontology anatomy VSAO vsao.obo   [Tracker]
Chemical Information Ontology biochemistry CHEMINF cheminf.owl
Mass spectrometry experiments MS psi-ms.obo
Neuro Behavior Ontology behavior NBO behavior.owl   [Tracker]
Evidence codes experiments ECO eco.obo
Pathway ontology biological process PW pathway.obo
Cell type anatomy CL cl.owl   [Tracker]
verteberate Homologous Organ Groups anatomy vHOG vHOG.obo
Variation Ontology VariO vario.obo
Biological Spatial Ontology anatomy BSPO bspo.obo   [Tracker]
C. elegans development anatomy WBls worm_development.obo
Biological Collections Ontology BCO bco.owl   [Tracker]
Porifera Ontology anatomy PORO poro.owl   [Tracker]
Physico-chemical process REX rex.obo
BRENDA tissue / enzyme source anatomy BTO BrendaTissueOBO
Fission Yeast Phenotype Ontology phenotype FYPO fypo.obo?format=raw   [Tracker]
Teleost Anatomy Ontology anatomy TAO tao.obo   [Tracker]
Dictyostelium discoideum phenotype anatomy DDPHENO dicty_phenotypes.obo
Relation ontology all RO ro.owl
Name Reaction Ontology RXNO rxno.obo   [Tracker]
Units of measurement phenotype UO unit.obo
Taxonomic rank vocabulary taxonomy TAXRANK taxrank.obo
Drosophila gross anatomy anatomy FBbt fbbt.obo   [Tracker]
Vaccine ontology health VO vo   [Tracker]
Ontology for Parasite LifeCycle OPL opl.owl   [Tracker]
C. elegans phenotype phenotype WBPhenotype wbphenotype.obo
Ontology of Genetic Susceptibility Factor OGSF ogsf.owl   [Tracker]
homology_ontology HOM hom.obo
Mouse pathology health MPATH mpath.obo
Human developmental anatomy, abstract version, v2 anatomy EHDAA2 ehdaa2.obo
Malaria Ontology health IDOMAL idomal.obo
Software ontology SWO swo_merged.owl
The Drug-drug Interaction Ontology DINTO dinto.owl   [Tracker]
Uber anatomy ontology anatomy UBERON ext.owl   [Tracker]
Microarray experimental conditions experiments MO MGEDOntology.owl
Hymenoptera Anatomy Ontology anatomy HAO hao.owl
Medaka fish anatomy and development anatomy MFO medaka_ontology.obo 2005/11/08
Fly taxonomy taxonomy FBsp fly_taxonomy.obo   [Tracker] 2007/04/10
OBO relationship types (legacy) all OBO_REL ro.obo   [Tracker] 2010/06/07
Drosophila development anatomy FBdv fly_development.obo   [Tracker] 2010/07/01
Common Anatomy Reference Ontology anatomy CARO caro.obo   [Tracker] 2011/12/14
Anatomical Entity Ontology anatomy AEO aeo.obo 2012/06/01
Teleost taxonomy taxonomy TTO teleost_taxonomy.obo   [Tracker] 2012/07/19
Dictyostelium discoideum anatomy anatomy DDANAT dicty_anatomy.obo   [Tracker] 2013/01/19
Biological imaging methods experiments FBbi image.obo 2013/11/05
Spider Ontology anatomy SPD spider_comparative_biology.obo   [Tracker] 2014/01/09
Fungal gross anatomy anatomy FAO fungal_anatomy.obo 2014/02/07
Ascomycete phenotype ontology phenotype APO ascomycete_phenotype.obo 2014/06/30
Mappings between, logical definitions for, bridging, and relations for combining, ontologies
Title Domain Prefix File Last changed
Gazetteer GAZ gaz.owl   [Tracker]

Last updated Fri Feb 20 00:00:33 2015