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

Last updated Thu Jul 2 00:00:26 2015