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

Last updated Mon Aug 30 01:00:01 2010