OBO Foundry

The OBO Foundry effort makes it easier to integrate biomedical results and carry out analysis in bioinformatics.

The formalization of concepts in the biomedical domain is especially known via the work of the Gene Ontology Consortium, a part of the OBO Foundry.

[3] OBO forms part of the resources of the U.S. National Center for Biomedical Ontology (NCBIO) and a central element of the NCBO's BioPortal.

[5] An integration into OBO of the OntoClean's theory of rigidity has been proposed as a step to standardize candidate ontologies.

[6] The OBO Foundry community is also dedicated to developing tools to facilitate creating and maintaining ontologies.

ROBOT aggregates functions for routine tasks in ontology development, is open source, and can be used either via the command line or as a library for any language on the Java Virtual Machine.

As a community effort, standard common mappings have been created for lossless roundtrip transformations between Open Biomedical Ontologies (OBO) format and OWL.

For example, the integration of the Human Disease Ontology[20] to Wikidata has enabled its link to the description of cell-lines from the resource Cellosaurus.

[21] One of the goals of the integration of OBO Foundry to Wikidata has been to lower the barriers for non-ontologists to contribute to and use ontologies.

Wikidata is arguably easier to understand and use than the traditional ontology models (which require a high degree of specific expertise).

[27] The choice of a numerical ID was made in order to improve maintenance and evolution of the resources.

[29] Ontologies evolve in time, refining concepts and descriptions according to advances in the knowledge of their specific domains.

Examples of use include linking to terms by other ontologies, use in semantic web projects, use in annotations or other research applications.

The OBO Foundry defines scientific consensus as "multiple publications by independent labs over a year come to the same conclusion, and there is no or limited (<10%) dissenting opinions published in the same time frame.