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] 2012/01/28
Cellular component anatomy GO gene_ontology_edit.obo   [Tracker] 2012/01/28
Chemical entities of biological interest biochemistry CHEBI chebi.obo   [Tracker] 2012/01/10
Molecular function biological function GO gene_ontology_edit.obo   [Tracker] 2012/01/28
Phenotypic quality phenotype PATO quality.obo   [Tracker]
PRotein Ontology (PRO) proteins PR pro.obo   [Tracker]
Xenopus anatomy and development anatomy XAO xenopus_anatomy.obo 2011/10/07
Zebrafish anatomy and development anatomy ZFA zebrafish_anatomy.obo   [Tracker] 2011/12/15
OBO Foundry candidate ontologies and other ontologies of interest
Title Domain Prefix File Last changed
Adverse Event Reporting Ontology health AERO
Amphibian gross anatomy anatomy AAO AAO_v2_edit.obo
Amphibian taxonomy anatomy ATO amphibian_taxonomy.obo
Anatomical Entity Ontology anatomy AEO aeo.obo 2011/12/15
Ascomycete phenotype ontology phenotype APO ascomycete_phenotype.obo 2011/09/30
Basic Formal Ontology upper BFO 1.1
Bilateria anatomy anatomy BILA bilateria_mrca.obo
Biological imaging methods experiments FBbi image.obo 2011/05/24
BRENDA tissue / enzyme source anatomy BTO BrendaTissueOBO
C. elegans development anatomy WBls worm_development.obo
C. elegans gross anatomy anatomy WBbt WBbt.obo   [Tracker]
C. elegans phenotype phenotype WBPhenotype worm_phenotype.obo 2012/01/28
Cell type anatomy CL cl.obo   [Tracker]
Chemical Information Ontology biochemistry CHEMINF cheminf.owl
Common Anatomy Reference Ontology anatomy CARO caro.obo   [Tracker] 2011/12/14
Comparative Data Analysis Ontology CDAO cdao.owl
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] 2011/07/04
Environment Ontology environment ENVO envo.obo   [Tracker] 2011/03/24
Event (INOH pathway ontology) biological process IEV Event Ontology Download
Evidence codes experiments ECO evidence_code.obo 2011/12/14
eVOC (Expressed Sequence Annotation for Humans) experiments EV evoc_v2.7_obo.tar.gz
Exposure ontology health ExO CTD_exposure_ontology.obo
Fission Yeast Phenotype Ontology phenotype FYPO fypo_edit.obo   [Tracker]
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 2011/06/10
Gene Regulation Ontology genomic BOOTStrep GRO_latest
homology_ontology HOM homology_ontology.obo
Human developmental anatomy, abstract version, v2 anatomy EHDAA2 human-dev-anat-abstract2.obo 2012/01/23
Human developmental anatomy, timed version anatomy EHDA human-dev-anat-staged.obo 2007/06/17
Human disease ontology health DOID HumanDO.obo   [Tracker]
human phenotype ontology phenotype HP human-phenotype-ontology.obo   [Tracker]
Hymenoptera Anatomy Ontology anatomy HAO hao.owl
Infectious disease health IDO ido.owl   [Tracker]
Influenza Ontology health FLU flu.owl   [Tracker]
Information Artifact Ontology information IAO iao.owl   [Tracker]
Kinetic Simulation Algorithm Ontology algorithms KISAO KISAO   [Tracker]
Lipid Ontology lipids LiPrO LipidOntology
Malaria Ontology health IDOMAL IDOMAL.obo
Mammalian phenotype phenotype MP mammalian_phenotype.obo   [Tracker] 2012/01/26
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 2011/09/15
Mosquito insecticide resistance environment MIRO mosquito_insecticide_resistance.obo 2012/01/28
Mouse adult gross anatomy anatomy MA adult_mouse_anatomy.obo   [Tracker] 2011/07/21
Mouse gross anatomy and development anatomy EMAP EMAP.obo 2007/06/17
Mouse pathology health MPATH mouse_pathology.obo 2011/10/26
NCBI organismal classification taxonomy NCBITaxon taxonomy.dat
NCI Thesaurus health ncithesaurus EVS/
Neuro Behavior Ontology behavior NBO behavior.obo   [Tracker]
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 (legacy) 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]
Ontology of Adverse Events adverse events, health OAE oae.owl
Ontology of Medically Related Social Entities medicine OMRSE omrse.owl
Pathogen transmission health TRANS transmission_process.obo   [Tracker]
Pathway ontology biological process PW pathway.obo
Physico-chemical process REX rex.obo 2007/03/08
Plant Environmental Conditions environment EO environment_ontology.obo 2009/01/09
Plant Ontology anatomy and development PO plant_ontology.obo?view=co   [Tracker]
Plant Trait Ontology phenotype TO plant_trait.obo   [Tracker] 2011/12/10
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
Relation ontology all RO ro.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] 2012/01/18
Software ontology SWO swo_merged.owl
Spatial Ontology anatomy BSPO spatial.obo   [Tracker] 2011/07/13
Spider Ontology anatomy SPD spider_comparative_biology.obo   [Tracker] 2011/11/24
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] 2011/10/04
Teleost taxonomy taxonomy TTO teleost_taxonomy.obo   [Tracker] 2011/12/14
Terminology of Anatomy of Human Embryology anatomy TAHE
Terminology of Anatomy of Human Histology anatomy TAHH
Tick gross anatomy anatomy TADS tick_anatomy.obo 2007/12/13
Uber anatomy ontology anatomy UBERON uberon.owl   [Tracker]
Units of measurement phenotype UO
Vaccine ontology health VO vo   [Tracker]
verteberate Homologous Organ Groups anatomy vHOG vHOG.obo
Vertebrate Musculoskeletal Anatomy Ontology anatomy VAO vertebrate_anatomy.obo   [Tracker]

Last updated Sat Jan 28 01:00:08 2012