OBO Foundry
Overview
The OBO Foundry is an international consortium of ontology developers committed to developing a suite of interoperable, open biomedical ontologies. Founded in 2001 and formalised in 2007 with the publication of the OBO Foundry principles (Nature Biotechnology, Ashburner et al.), it provides the governance framework and quality standards for a coordinated family of ontologies that form the semantic backbone of modern biomedical data integration. OBO Foundry occupies the same role for biomedical ontologies that INCF occupies for neuroscience data standards and GA4GH occupies for genomics standards: it is the governing body that sets principles, reviews candidate ontologies, and coordinates interoperability across member ontologies.
Foundry Principles
OBO ontologies must adhere to a set of shared principles ensuring quality and interoperability:
- Ontologies are freely available under CC BY 3.0 or equivalent.
- All ontologies use OWL2 and/or OBO flat file format.
- Term identifiers are globally unique and stable (e.g.
HP:0001250,GO:0007268). - Ontologies are versioned with dated releases and stable identifiers across versions.
- Each ontology has a defined, non-overlapping scope.
- All terms have human-readable textual definitions.
- Ontologies reuse terms from other OBO Foundry members rather than duplicating them.
Key OBO Foundry Ontologies in This Vault
The following OBO Foundry member ontologies have dedicated nodes:
| Ontology | Node | Domain |
|---|---|---|
| GO | GO | Gene function (biological process, molecular function, cellular component) |
| HPO | HPO | Human phenotypes for rare disease genomics |
| UBERON | UBERON | Cross-species anatomy |
| MONDO | MONDO | Unified disease ontology (harmonises ICD, OMIM, ORDO) |
| ORDO | ORDO | Orphanet rare disease classification |
| OBI | OBI | Biomedical investigation protocols and assays |
| Cell Ontology | Cell Ontology | Cell type classification |
| ChEBI | ChEBI | Chemical entities of biological interest |
| MeSH | MeSH | Medical subject headings (NLM; OBO aligned) |
Tools and Infrastructure
OntoBee (https://www.ontobee.org) is the OBO ontology browser. The EBI Ontology Lookup Service (https://www.ebi.ac.uk/ols) is the EMBL-EBI ontology browser supporting all OBO Foundry members. BioPortal (https://bioportal.bioontology.org) is the NCBO ontology portal hosting OBO and non-OBO ontologies. Protégé (https://protege.stanford.edu) is the primary ontology editing tool used by OBO Foundry curators. ROBOT (https://robot.obolibrary.org) is a command-line tool for OBO ontology manipulation and quality control.
Connections
Resources
- https://obofoundry.org (OBO Foundry portal — full ontology list)
- https://www.ebi.ac.uk/ols (EBI Ontology Lookup Service)
- https://obofoundry.org/principles/fp-000-summary.html (OBO Foundry Principles)
- https://github.com/OBOFoundry (GitHub organisation)