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]
Ontology for biomedical investigations experiments OBI obi.owl   [Tracker]
Chemical entities of biological interest biochemistry CHEBI chebi.obo   [Tracker]
PRotein Ontology (PRO) proteins PR pro.obo   [Tracker]
Plant Ontology anatomy and development PO plant_ontology.obo?view=co   [Tracker]
Phenotypic quality phenotype PATO quality.obo   [Tracker]
Biological process biological process GO go.obo   [Tracker]
Cellular component anatomy GO go.obo   [Tracker]
Molecular function biological function GO go.obo   [Tracker]
Zebrafish anatomy and development anatomy ZFA zfa.obo   [Tracker]
OBO Foundry candidate ontologies and other ontologies of interest
Title Domain Prefix File Last changed
NCBI organismal classification taxonomy NCBITaxon taxonomy.dat
NCI Thesaurus health ncithesaurus EVS/
Systems Biology biochemistry SBO SBO_OBO.obo   [Tracker]
Protein modification proteins MOD PSI-MOD.obo
NIF Cell neuroscience NIF_Cell NIF-Cell.owl
BRENDA tissue / enzyme source anatomy BTO BrendaTissueOBO
Mass spectrometry experiments MS psi-ms.obo
Microarray experimental conditions experiments MO MGEDOntology.owl
Ontology for MIRNA Target Prediction OMIT OMIT.owl
NIF Dysfunction neuroscience NIF_Dysfunction NIF-Dysfunction.owl
Protein-protein interaction experiments MI psi-mi25.obo
NMR-instrument specific component of metabolomics investigations experiments NMR NMR.owl
Pathway ontology biological process PW pathway.obo
Mammalian phenotype phenotype MP MPheno_OBO.ontology   [Tracker]
Sample processing and separation techniques provenance SEP sep.obo
Platynereis stage ontology anatomy PD_ST Pdu_Stages.obo
Protein covalent bond proteins RESID RESIDUES.XML
Physico-chemical process REX rex.obo
Information Artifact Ontology information IAO iao.owl   [Tracker]
Basic Formal Ontology upper BFO 1.1
Comparative Data Analysis Ontology CDAO cdao.owl
Ontology for Parasite LifeCycle OPL opl.owl   [Tracker]
Cell Line Ontology CLO clo.owl
MIAPA Ontology MIAPA miapa.owl   [Tracker]
Ontology for General Medical Science medicine OGMS ogms.owl   [Tracker]
eagle-i resource ontology resources ERO ero.owl   [Tracker]
Influenza Ontology health FLU flu.owl   [Tracker]
Infectious disease health IDO ido.owl   [Tracker]
Physico-chemical methods and properties FIX fix.obo
Mouse gross anatomy and development, timed anatomy EMAP EMAP_combined.obo
Mouse gross anatomy and development, abstract anatomy EMAPA EMAPA.obo
Neuro Behavior Ontology behavior NBO behavior.owl   [Tracker]
homology_ontology HOM homology_ontology.obo
verteberate Homologous Organ Groups anatomy vHOG vHOG.obo
Kinetic Simulation Algorithm Ontology algorithms KISAO KISAO   [Tracker]
human phenotype ontology phenotype HP human-phenotype-ontology.obo   [Tracker]
Exposure ontology health ExO CTD_exposure_ontology.obo
Zebrafish developmental stages anatomy ZFS zfs.obo
Evidence codes experiments ECO eco.obo
Pathogen transmission health TRANS transmission_process.obo   [Tracker]
Symptom Ontology health SYMP gemina_symptom.obo
microRNA Ontology miRNAO mirnao.owl
Mouse pathology health MPATH mpath.obo
Anatomical Entity Ontology anatomy AEO aeo.obo 2012/06/01
Common Anatomy Reference Ontology anatomy CARO caro.obo   [Tracker] 2011/12/14
Medaka fish anatomy and development anatomy MFO medaka_ontology.obo 2005/11/08
Spider Ontology anatomy SPD spider_comparative_biology.obo   [Tracker]
Dictyostelium discoideum anatomy anatomy DDANAT dictyostelium_anatomy.obo   [Tracker] 2013/01/19
Fungal gross anatomy anatomy FAO fungal_anatomy.obo
Drosophila development anatomy FBdv fly_development.obo   [Tracker] 2010/07/01
Biological imaging methods experiments FBbi image.obo 2013/11/05
OBO relationship types (legacy) all OBO_REL ro.obo   [Tracker] 2010/06/07
Ascomycete phenotype ontology phenotype APO ascomycete_phenotype.obo 2014/06/30
Fly taxonomy taxonomy FBsp fly_taxonomy.obo   [Tracker] 2007/04/10
Teleost taxonomy taxonomy TTO teleost_taxonomy.obo   [Tracker] 2012/07/19
Ontology of Vaccine Adverse Events OVAE ovae.owl
Plant Trait Ontology phenotype TO trait.obo?view=co   [Tracker]
Plant Environmental Conditions environment EO environment_ontology.obo
Vertebrate Skeletal Anatomy Ontology anatomy VSAO vsao.obo   [Tracker]
Ontology of Biological Attributes phenotype OBA oba.owl
Adverse Event Reporting Ontology health AERO aero.owl
Beta Cell Genomics Ontology BCGO bcgo.owl   [Tracker]
Biological Collections Ontology BCO bco.owl   [Tracker]
Chemical Methods Ontology health CHMO chmo.owl   [Tracker]
Cell type anatomy CL cl.owl   [Tracker]
Cardiovascular Disease Ontology health CVDO cvdo.owl   [Tracker]
Human disease ontology health DOID doid.obo   [Tracker]
The Drug Ontology health DRON dron.owl   [Tracker]
Environment Ontology environment ENVO envo-basic.obo   [Tracker]
Epidemiology Ontology EPO epo.owl
Drosophila gross anatomy anatomy FBbt fbbt.obo   [Tracker]
Drosophila Phenotype Ontology FBcv dpo.owl
Foundational Model of Anatomy (subset) anatomy FMA fma.obo   [Tracker]
Geographical Entity Ontology GEO geo.owl   [Tracker]
Hymenoptera Anatomy Ontology anatomy HAO hao.owl
Malaria Ontology health IDOMAL idomal.obo
Mouse adult gross anatomy anatomy MA ma.obo   [Tracker]
Mental Functioning Ontology MF mf.owl   [Tracker]
Emotion Ontology health MFOEM mfoem.owl   [Tracker]
Mosquito insecticide resistance environment MIRO miro.obo
The Ontology of Genes and Genomes OGG ogg.owl   [Tracker]
Ontology for genetic interval OGI ogi.owl   [Tracker]
Ontology of Genetic Susceptibility Factor OGSF ogsf.owl   [Tracker]
Ontology of Medically Related Social Entities medicine OMRSE omrse.owl
Population and Community Ontology PCO pco.owl   [Tracker]
Porifera Ontology anatomy PORO poro.owl   [Tracker]
Relation ontology all RO ro.owl
Tick gross anatomy anatomy TADS tads.obo
Teleost Anatomy Ontology anatomy TAO tao.obo   [Tracker]
Mosquito gross anatomy anatomy TGMA tgma.obo
Uber anatomy ontology, basic version anatomy uberon-basic basic.obo
Uber anatomy ontology anatomy UBERON ext.owl   [Tracker]
Vertebrate Taxonomy Ontology VTO vto.owl   [Tracker]
C. elegans gross anatomy anatomy WBbt wbbt.obo   [Tracker]
C. elegans phenotype phenotype WBPhenotype wbphenotype.obo
RNA ontology molecular structure RNAO rnao.obo
Chemical Information Ontology biochemistry CHEMINF cheminf.owl
Mathematical modeling ontology MAMO mamo-xml.owl   [Tracker]
Ontology of Adverse Events adverse events, health OAE oae.owl
Software ontology SWO swo_merged.owl
Units of measurement phenotype UO unit.obo
Variation Ontology VariO vario.obo
Lipid Ontology lipids LiPrO LipidOntology
Vaccine ontology health VO vo   [Tracker]
Biological Spatial Ontology anatomy BSPO bspo.obo   [Tracker]
C. elegans development anatomy WBls worm_development.obo
Taxonomic rank vocabulary taxonomy TAXRANK taxrank.obo
Human developmental anatomy, abstract version, v2 anatomy EHDAA2 ehdaa2.obo
Fission Yeast Phenotype Ontology phenotype FYPO fypo.obo?format=raw   [Tracker]
Sequence types and features biological sequence SO so-xp.obo?format=raw   [Tracker]
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 Oct 17 23:59:10 2014