OBO

OBO, short for Open Biological and Biomedical Ontologies, refers to a family of ontologies used to describe biological and biomedical concepts in a computable, interoperable way. The term also designates the community and governance framework known as the OBO Foundry, which coordinates the development and sharing of these ontologies to promote data integration and reuse across research domains.

The OBO Foundry establishes design principles to ensure interoperability, openness, and reusability. Ontologies in this ecosystem are developed with common naming conventions, stable identifiers, and clear documentation. They are typically represented in the OBO format or in OWL, and they emphasize logical consistency, cross-referencing, and alignment with shared relations such as is_a, part_of, and regulates. Ontologies are published under open licenses and maintained with versioning to support reproducible use in databases and analysis pipelines.

Notable ontologies in the OBO ecosystem include the Gene Ontology (GO), which covers gene product functions; CHEBI (Chemical Entities of Biological Interest); the Sequence Ontology (SO); the Phenotype and Trait Ontology (PATO); and OBO ontologies for biomedical investigations (OBI) and diseases (DOID). These resources are widely used for annotating genes, proteins, phenotypes, and diseases, enabling cross-database queries, semantic search, and integrative analyses across diverse data sets.

Access and governance are provided through the OBO Foundry and related repositories. Ontologies are openly available, versioned, and maintained by a community of researchers and curators, with contributions coordinated through platforms such as GitHub and the OBO Foundry portal. The ecosystem supports international collaboration and ongoing refinement of terms and relationships.