Open Biological and Biomedical Ontology (OBO) Foundry

obo-foundryCreated on Feb 9th, 2020

The Open Biological and Biomedical Ontology (OBO) Foundry is a collective of ontology developers that are committed to collaboration and adherence to shared principles. The mission of the OBO Foundry is to develop a family of interoperable ontologies that are both logically well-formed and scientifically accurate. To achieve this, OBO Foundry participants voluntarily adhere to and contribute to the development of an evolving set of principles including open use, collaborative development, non-overlapping and strictly-scoped content, and common syntax and relations, based on ontology models that work well, such as the Gene Ontology (GO).

The OBO Foundry is overseen by an Operations Committee with Editorial, Technical and Outreach working groups. The processes of the Editorial working group are modelled on the journal refereeing process. A complete treatment of the OBO Foundry is given in "The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration".

On this site you will find a table of ontologies, available in several formats, with details for each, and documentation on OBO Principles.

You can contribute to this site using GitHub OBOFoundry/OBOFoundry.github.io or get in touch with us by joining our mail list https://groups.google.com/forum/#!forum/obo-discuss.

Members

The Cell Ontology is designed as a structured controlled vocabulary for cell types. This ontology was constructed for use by the model organism and other bioinformatics databases, where there is a need for a controlled vocabulary of cell types. This ontology is not organism specific it covers cell types from prokaryotes to mammals. However, it excludes plant cell types, which are covered by PO.

Integration with other ontologies

Cell types in CL are linked to uberon via part-of relationships. The cl.owl product imports a subset of the entire uberon ontology. To see all cell types in the context of all anatomical structures, use the uberon ext release.

Cell types are linked to GO biological processes via the capable-of relationship type. CL also links to other ontologies such as ChEBI, pr and pato.

In turn, CL is linked to from a variety of ontologies such as GO, Uberon and various phenotype ontologies.