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
Zebrafish anatomy and development anatomy ZFA zfa.obo   [Tracker]
Xenopus anatomy and development anatomy XAO xenopus_anatomy.obo   [Tracker]
Cellular component anatomy GO go.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
The Ontology of Genes and Genomes OGG ogg.owl   [Tracker]
MIAPA Ontology MIAPA miapa.owl   [Tracker]
Cell Line Ontology CLO clo.owl
Beta Cell Genomics Ontology BCGO bcgo.owl   [Tracker]
Ontology for MIRNA Target Prediction OMIT OMIT.owl
Variation Ontology VariO vario.obo
microRNA Ontology miRNAO mirnao.owl
Geographical Entity Ontology GEO geo.owl   [Tracker]
Ontology for Parasite LifeCycle OPL opl.owl   [Tracker]
Ontology for genetic interval OGI ogi.owl   [Tracker]
Ontology of Genetic Susceptibility Factor OGSF ogsf.owl   [Tracker]
Physico-chemical process REX rex.obo
Vertebrate Taxonomy Ontology VTO vto.owl   [Tracker]
Biological Collections Ontology BCO bco.owl   [Tracker]
Drosophila Phenotype Ontology FBcv dpo.owl
Population and Community Ontology PCO pco.owl   [Tracker]
Epidemiology Ontology EPO epo.owl
Comparative Data Analysis Ontology CDAO cdao.owl
Ontology of Vaccine Adverse Events OVAE ovae.owl   [Tracker]
Mental Functioning Ontology MF mf.owl   [Tracker]
Physico-chemical methods and properties FIX fix.obo
homology_ontology HOM homology_ontology.obo
Mathematical modeling ontology MAMO mamo-xml.owl   [Tracker]
Software ontology SWO swo_merged.owl
Ontology of Adverse Events adverse events, health OAE oae.owl
Kinetic Simulation Algorithm Ontology algorithms KISAO KISAO   [Tracker]
OBO relationship types (legacy) all OBO_REL ro.obo   [Tracker] 2010/06/07
Relation ontology all RO ro.owl
Zebrafish developmental stages anatomy ZFS zfs.obo
Mouse gross anatomy and development, timed anatomy EMAP EMAP_combined.obo
C. elegans development anatomy WBls worm_development.obo
Foundational Model of Anatomy (subset) anatomy FMA fma.obo   [Tracker]
Mosquito gross anatomy anatomy TGMA tgma.obo
C. elegans gross anatomy anatomy WBbt wbbt.obo   [Tracker]
Porifera Ontology anatomy PORO poro.owl   [Tracker]
BRENDA tissue / enzyme source anatomy BTO BrendaTissueOBO
Drosophila gross anatomy anatomy FBbt fbbt.obo   [Tracker]
Common Anatomy Reference Ontology anatomy CARO caro.obo   [Tracker] 2011/12/14
Uber anatomy ontology anatomy UBERON ext.owl   [Tracker]
Vertebrate Skeletal Anatomy Ontology anatomy VSAO vsao.obo   [Tracker]
Anatomical Entity Ontology anatomy AEO aeo.obo 2012/06/01
Fungal gross anatomy anatomy FAO fungal_anatomy.obo 2014/02/07
Teleost Anatomy Ontology anatomy TAO tao.obo   [Tracker]
Uber anatomy ontology, basic version anatomy uberon-basic basic.obo
verteberate Homologous Organ Groups anatomy vHOG vHOG.obo
Spider Ontology anatomy SPD spider_comparative_biology.obo   [Tracker] 2014/01/09
Biological Spatial Ontology anatomy BSPO bspo.obo   [Tracker]
Hymenoptera Anatomy Ontology anatomy HAO hao.owl
Medaka fish anatomy and development anatomy MFO medaka_ontology.obo 2005/11/08
Tick gross anatomy anatomy TADS tads.obo
Mouse gross anatomy and development, abstract anatomy EMAPA EMAPA.obo
Drosophila development anatomy FBdv fly_development.obo   [Tracker] 2010/07/01
Platynereis stage ontology anatomy PD_ST Pdu_Stages.obo
Cell type anatomy CL cl.owl   [Tracker]
Human developmental anatomy, abstract version, v2 anatomy EHDAA2 ehdaa2.obo
Mouse adult gross anatomy anatomy MA ma.obo   [Tracker]
Dictyostelium discoideum anatomy anatomy DDANAT dictyostelium_anatomy.obo   [Tracker] 2013/01/19
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]
Mosquito insecticide resistance environment MIRO miro.obo
Plant Environmental Conditions environment EO environment_ontology.obo
Environment Ontology environment ENVO envo-basic.obo   [Tracker]
Protein-protein interaction experiments MI psi-mi25.obo
Mass spectrometry experiments MS psi-ms.obo
NMR-instrument specific component of metabolomics investigations experiments NMR NMR.owl
Evidence codes experiments ECO eco.obo
Microarray experimental conditions experiments MO MGEDOntology.owl
Biological imaging methods experiments FBbi image.obo 2013/11/05
Infectious disease health IDO ido.owl   [Tracker]
Vaccine ontology health VO vo   [Tracker]
Chemical Methods Ontology health CHMO chmo.owl   [Tracker]
Pathogen transmission health TRANS transmission_process.obo   [Tracker]
Symptom Ontology health SYMP gemina_symptom.obo
Influenza Ontology health FLU flu.owl   [Tracker]
NCI Thesaurus health ncithesaurus EVS/
Malaria Ontology health IDOMAL idomal.obo
Mouse pathology health MPATH mpath.obo
Emotion Ontology health MFOEM mfoem.owl   [Tracker]
Cardiovascular Disease Ontology health CVDO cvdo.owl   [Tracker]
Exposure ontology health ExO CTD_exposure_ontology.obo
Adverse Event Reporting Ontology health AERO aero.owl
Human disease ontology health DOID doid.obo   [Tracker]
The Drug Ontology health DRON dron.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]
Plant Trait Ontology phenotype TO trait.obo?view=co   [Tracker]
Fission Yeast Phenotype Ontology phenotype FYPO fypo.obo?format=raw   [Tracker]
Units of measurement phenotype UO unit.obo
Mammalian phenotype phenotype MP MPheno_OBO.ontology   [Tracker]
C. elegans phenotype phenotype WBPhenotype wbphenotype.obo
Ascomycete phenotype ontology phenotype APO ascomycete_phenotype.obo 2014/06/30
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]
Taxonomic rank vocabulary taxonomy TAXRANK taxrank.obo
Fly taxonomy taxonomy FBsp fly_taxonomy.obo   [Tracker] 2007/04/10
NCBI organismal classification taxonomy NCBITaxon taxonomy.dat
Teleost taxonomy taxonomy TTO teleost_taxonomy.obo   [Tracker] 2012/07/19
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 Mon Dec 1 00:00:18 2014