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
Biological process biological process GO gene_ontology_edit.obo   [Tracker] 2010/08/29
Cellular component anatomy GO gene_ontology_edit.obo   [Tracker] 2010/08/29
Chemical entities of biological interest biochemistry CHEBI chebi.obo   [Tracker] 2010/08/03
Molecular function biological function GO gene_ontology_edit.obo   [Tracker] 2010/08/29
Phenotypic quality phenotype PATO quality.obo   [Tracker] 2010/08/19
PRotein Ontology (PRO) proteins PRO pro.obo   [Tracker] 2010/08/20
Xenopus anatomy and development anatomy XAO xenopus_anatomy.obo 2009/12/02
Zebrafish anatomy and development anatomy ZFA zebrafish_anatomy.obo   [Tracker] 2010/08/06
OBO Foundry candidate ontologies and other ontologies of interest
Title Domain Prefix File Last changed
Amphibian gross anatomy anatomy AAO amphibian_anatomy.obo 2008/06/19
Amphibian taxonomy anatomy ATO amphibian_taxonomy.obo
Ascomycete phenotype ontology phenotype APO ascomycete_phenotype.obo 2010/05/12
Basic Formal Ontology upper BFO 1.1
Bilateria anatomy anatomy BILA bilateria_mrca.obo
Biological imaging methods experiments FBbi image.obo 2010/05/05
BRENDA tissue / enzyme source anatomy BTO BrendaTissueOBO
C. elegans development anatomy WBls worm_development.obo 2008/01/31
C. elegans gross anatomy anatomy WBbt WBbt.obo   [Tracker] 2010/08/26
C. elegans phenotype phenotype WBPhenotype worm_phenotype.obo 2010/08/27
Cell type anatomy CL cell.obo   [Tracker] 2010/08/19
Cereal plant trait phenotype TO plant_trait.obo   [Tracker] 2010/08/29
Chemical Information Ontology biochemistry CHEMINF cheminf.owl
Common Anatomy Reference Ontology anatomy CARO caro.obo   [Tracker] 2010/06/24
Dendritic cell anatomy,immunology DC_CL DC-CL_deployed.obo 2009/06/30
Dictyostelium discoideum anatomy anatomy DDANAT dictyostelium_anatomy.obo   [Tracker] 2010/04/06
Drosophila development anatomy FBdv fly_development.obo   [Tracker] 2010/07/01
Drosophila gross anatomy anatomy FBbt fly_anatomy.obo   [Tracker] 2010/08/25
Environment Ontology environment ENVO envo.obo   [Tracker] 2010/02/03
Event (INOH pathway ontology) biological process IEV Event Ontology Download
Evidence codes experiments ECO evidence_code.obo 2010/03/18
eVOC (Expressed Sequence Annotation for Humans) experiments EV evoc_v2.7_obo.tar.gz
Fly taxonomy taxonomy FBsp fly_taxonomy.obo   [Tracker] 2007/04/10
Foundational Model of Anatomy (subset) anatomy FMA fma2_obo.obo   [Tracker]
Fungal gross anatomy anatomy FAO fungal_anatomy.obo 2009/11/17
Gene Regulation Ontology genomic BOOTStrep GRO_latest
homology_ontology HOM homology_ontology.obo
Human developmental anatomy, abstract version anatomy EHDAA human-dev-anat-abstract.obo 2007/06/17
Human developmental anatomy, abstract version, v2 anatomy EHDAA2 human-dev-anat-abstract2.obo 2010/07/03
Human developmental anatomy, timed version anatomy EHDA human-dev-anat-staged.obo 2007/06/17
Human disease health DOID human_disease.obo   [Tracker] 2010/08/28
human phenotype ontology phenotype HP human-phenotype-ontology.obo   [Tracker]
Hymenoptera Anatomy Ontology anatomy HAO hao.obo
Infectious disease health IDO ido.owl   [Tracker]
Influenza Ontology health FLU flu.owl   [Tracker]
Information Artifact Ontology information IAO iao.owl   [Tracker]
Lipid Ontology lipids LiPrO LipidOntology
Malaria Ontology health IDOMAL IDOMAL.obo
Mammalian phenotype phenotype MP mammalian_phenotype.obo   [Tracker] 2010/08/29
Mass spectrometry experiments MS psi-ms.obo
Medaka fish anatomy and development anatomy MFO medaka_ontology.obo 2005/11/08
Microarray experimental conditions experiments MO MGEDOntology.owl
Minimal anatomical terminology anatomy MAT minimal_anatomical_terminology.obo 2009/01/24
Molecule role (INOH Protein name/family name ontology) proteins IMR molecule_role.obo
Mosquito gross anatomy anatomy TGMA mosquito_anatomy.obo 2009/02/05
Mosquito insecticide resistance environment MIRO mosquito_insecticide_resistance.obo 2010/08/29
Mouse adult gross anatomy anatomy MA adult_mouse_anatomy.obo   [Tracker] 2010/04/04
Mouse gross anatomy and development anatomy EMAP EMAP.obo 2007/06/17
Mouse pathology health MPATH mouse_pathology.obo 2010/01/14
NCBI organismal classification taxonomy NCBITaxon taxonomy.dat
NCI Thesaurus health ncithesaurus EVS/
NIF Cell neuroscience NIF_Cell NIF-Cell.owl
NIF Dysfunction neuroscience NIF_Dysfunction NIF-Dysfunction.owl
NIF Gross Anatomy neuroscience NIF_GrossAnatomy NIF-GrossAnatomy.owl
NMR-instrument specific component of metabolomics investigations experiments NMR NMR.owl
OBO relationship types all OBO_REL ro.obo   [Tracker] 2010/06/07
Ontology for biomedical investigations experiments OBI obi.owl   [Tracker]
Ontology for General Medical Science medicine OGMS ogms.owl   [Tracker]
Pathogen transmission health TRANS transmission_process.obo   [Tracker] 2009/05/28
Pathway ontology biological process PW pathway.obo
Physico-chemical methods and properties FIX fix.obo
Physico-chemical process REX rex.obo 2007/03/08
Plant environmental conditions environment EO environment_ontology.obo 2009/01/09
Plant growth and developmental stage anatomy PO po_temporal.obo?view=co   [Tracker]
Plant structure anatomy PO po_anatomy.obo?view=co   [Tracker]
Platynereis stage ontology anatomy PD_ST Pdu_Stages.obo
Protein covalent bond proteins RESID RESIDUES.XML
Protein Domains proteins IPR InterPro FTP directory
Protein modification proteins MOD PSI-MOD.obo
Protein-protein interaction experiments MI psi-mi25.obo
Proteomics data and process provenance proteins ProPreO ProPreO-060506.owl
RNA ontology molecular structure RNAO rnao.obo
Sample processing and separation techniques provenance SEP sep.obo
Sequence types and features biological sequence SO so.obo   [Tracker] 2010/08/27
Software ontology SWO softwareontology.owl
Spatial Ontology anatomy BSPO spatial.obo   [Tracker] 2010/05/18
Spider Ontology anatomy SPD spider_comparative_biology.obo   [Tracker] 2010/03/17
Subcellular anatomy ontology anatomy SAO SAO.owl
Suggested Ontology for Pharmacogenomics health SOPHARM sopharm
Symptom Ontology health SYMP gemina_symptom.obo
Systems Biology biochemistry SBO SBO_OBO.obo   [Tracker]
Taxonomic rank vocabulary taxonomy TAXRANK taxonomic_rank.obo
Teleost Anatomy Ontology anatomy TAO teleost_anatomy.obo   [Tracker] 2010/08/27
Teleost taxonomy taxonomy TTO teleost_taxonomy.obo   [Tracker] 2010/08/24
Tick gross anatomy anatomy TADS tick_anatomy.obo 2007/12/13
Uber anatomy ontology anatomy UBERON uberon.obo   [Tracker]
Units of measurement phenotype UO unit.obo 2010/08/26
Vaccine ontology health VO vo   [Tracker]

Last updated Mon Aug 30 01:00:01 2010