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
Xenopus anatomy and development anatomy XAO xenopus_anatomy.obo   [Tracker]
Cellular component anatomy GO go.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 quality.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
Cell Line Ontology CLO clo.owl
Population and Community Ontology PCO pco.owl   [Tracker]
Epidemiology Ontology EPO epo.owl
Ontology of Genetic Susceptibility Factor OGSF ogsf.owl   [Tracker]
Software ontology SWO swo_merged.owl
Geographical Entity Ontology GEO geo.owl   [Tracker]
microRNA Ontology miRNAO mirnao.owl
Molecular Process Ontology MOP mop.obo   [Tracker]
Comparative Data Analysis Ontology CDAO cdao.owl
MIAPA Ontology MIAPA miapa.owl   [Tracker]
homology_ontology HOM hom.obo
The Ontology of Genes and Genomes DINTO dinto.owl   [Tracker]
Biological Collections Ontology BCO bco.owl   [Tracker]
Ontology of Vaccine Adverse Events OVAE ovae.owl   [Tracker]
Physico-chemical methods and properties FIX fix.obo
Variation Ontology VariO vario.obo
Vertebrate Taxonomy Ontology VTO vto.owl   [Tracker]
Ontology for genetic interval OGI ogi.owl   [Tracker]
Ontology for Parasite LifeCycle OPL opl.owl   [Tracker]
Physico-chemical process REX rex.obo
Drosophila Phenotype Ontology FBcv dpo.owl
Name Reaction Ontology RXNO rxno.obo   [Tracker]
Mathematical modeling ontology MAMO mamo-xml.owl   [Tracker]
Mental Functioning Ontology MF mf.owl   [Tracker]
Ontology for MIRNA Target Prediction OMIT OMIT.owl
The Ontology of Genes and Genomes OGG ogg.owl   [Tracker]
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
Zebrafish developmental stages anatomy ZFS zfs.obo
Uber anatomy ontology anatomy UBERON ext.owl   [Tracker]
Human developmental anatomy, abstract version, v2 anatomy EHDAA2 ehdaa2.obo
Uber anatomy ontology, basic version anatomy uberon-basic basic.obo
BRENDA tissue / enzyme source anatomy BTO BrendaTissueOBO
Medaka fish anatomy and development anatomy MFO medaka_ontology.obo 2005/11/08
Dictyostelium discoideum anatomy anatomy DDANAT dictyostelium_anatomy.obo   [Tracker] 2013/01/19
C. elegans development anatomy WBls worm_development.obo
Platynereis stage ontology anatomy PD_ST Pdu_Stages.obo
Mosquito gross anatomy anatomy TGMA tgma.obo
Spider Ontology anatomy SPD spider_comparative_biology.obo   [Tracker] 2014/01/09
Common Anatomy Reference Ontology anatomy CARO caro.obo   [Tracker] 2011/12/14
Anatomical Entity Ontology anatomy AEO aeo.obo 2012/06/01
C. elegans gross anatomy anatomy WBbt wbbt.obo   [Tracker]
Teleost Anatomy Ontology anatomy TAO tao.obo   [Tracker]
Vertebrate Skeletal Anatomy Ontology anatomy VSAO vsao.obo   [Tracker]
Drosophila gross anatomy anatomy FBbt fbbt.obo   [Tracker]
Mouse adult gross anatomy anatomy MA ma.obo   [Tracker]
Porifera Ontology anatomy PORO poro.owl   [Tracker]
Mouse gross anatomy and development, abstract anatomy EMAPA EMAPA.obo
Drosophila development anatomy FBdv fly_development.obo   [Tracker] 2010/07/01
Biological Spatial Ontology anatomy BSPO bspo.obo   [Tracker]
Hymenoptera Anatomy Ontology anatomy HAO hao.owl
Mouse gross anatomy and development, timed anatomy EMAP EMAP_combined.obo
Fungal gross anatomy anatomy FAO fungal_anatomy.obo 2014/02/07
verteberate Homologous Organ Groups anatomy vHOG vHOG.obo
Cell type anatomy CL cl.owl   [Tracker]
Foundational Model of Anatomy (subset) anatomy FMA fma.obo   [Tracker]
Tick gross anatomy anatomy TADS tads.obo
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
Microarray experimental conditions experiments MO MGEDOntology.owl
Beta Cell Genomics Ontology experiments BCGO bcgo.owl   [Tracker]
Protein-protein interaction experiments MI psi-mi25.obo
Evidence codes experiments ECO eco.obo
Mass spectrometry experiments MS psi-ms.obo
NMR-instrument specific component of metabolomics investigations experiments NMR NMR.owl
Adverse Event Reporting Ontology health AERO aero.owl
CranioMaxilloFacial ontology health CMF cmf.owl   [Tracker]
Vaccine ontology health VO vo   [Tracker]
The Drug Ontology health DRON dron.owl   [Tracker]
NCI Thesaurus health ncithesaurus EVS/
Chemical Methods Ontology health CHMO chmo.owl   [Tracker]
Emotion Ontology health MFOEM mfoem.owl   [Tracker]
Exposure ontology health ExO CTD_exposure_ontology.obo
Pathogen transmission health TRANS transmission_process.obo   [Tracker]
Malaria Ontology health IDOMAL idomal.obo
Influenza Ontology health FLU flu.owl   [Tracker]
Human disease ontology health DOID doid.obo   [Tracker]
Ontology for Biobanking health OBIB obib.owl   [Tracker]
Informed Consent Ontology health ICO ico.owl   [Tracker]
Infectious disease health IDO ido.owl   [Tracker]
Mental Disease Ontology health MFOMD mfomd.owl   [Tracker]
Mouse pathology health MPATH mpath.obo
Symptom Ontology health SYMP gemina_symptom.obo
Cardiovascular Disease Ontology health CVDO cvdo.owl   [Tracker]
Information Artifact Ontology information IAO iao.owl   [Tracker]
Lipid Ontology lipids LiPrO LipidOntology
Ontology for General Medical Science medicine OGMS ogms.owl   [Tracker]
Ontology of Medically Related Social Entities medicine OMRSE omrse.owl
RNA ontology molecular structure RNAO rnao.obo
NIF Dysfunction neuroscience NIF_Dysfunction NIF-Dysfunction.owl
NIF Cell neuroscience NIF_Cell NIF-Cell.owl
human phenotype ontology phenotype HP human-phenotype-ontology.obo   [Tracker]
C. elegans phenotype phenotype WBPhenotype wbphenotype.obo
Ontology of Biological Attributes phenotype OBA oba.owl
Mammalian phenotype phenotype MP MPheno_OBO.ontology   [Tracker]
Plant Trait Ontology phenotype TO trait.obo?view=co   [Tracker]
Units of measurement phenotype UO unit.obo
Fission Yeast Phenotype Ontology phenotype FYPO fypo.obo?format=raw   [Tracker]
Ascomycete phenotype ontology phenotype APO ascomycete_phenotype.obo 2014/06/30
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]
Fly taxonomy taxonomy FBsp fly_taxonomy.obo   [Tracker] 2007/04/10
Teleost taxonomy taxonomy TTO teleost_taxonomy.obo   [Tracker] 2012/07/19
NCBI organismal classification taxonomy NCBITaxon taxonomy.dat
Taxonomic rank vocabulary taxonomy TAXRANK taxrank.obo
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 Sat Jan 17 00:00:29 2015