OBOPedia: An Encyclopaedia of Biology Using OBO Ontologies

Ontologies contain knowledge about a domain for use by tools or hu-mans. A source of knowledge should be usable by a human to ‘find out about’or learn about the entities of a domain and their relationship to each other. Thecorpus of biomedical ontologies now contains ‘encyclopaedic’ knowledge aboutbiology and should be capable of being used by humans to learn about entitiesin molecular biology. Yet multiple separate ontologies and the typical style ofpresentation of the knowledge in the ontologies mean that their use as a learn-ing resource is sub-optimal. To address this issue we have created OBOPedia, aweb based encyclopaedia of biology as seen by the Open Biomedical Ontologies(OBO) Consortium. OBOPedia exploits the OBO’s use of standard representa-tions and meaningful human readable terms and natural language definitions tocreate a basic OBOPedia encyclopaedia entry. An entry is supplemented with anontology’s synonyms and uses the ontology’s taxonomic links to provide ‘seealso’ cross-references within the alphabetical list of entries. Currently, OBOPe-dia has access to ten OBO ontologies, including all the OBO Foundry ontolo-gies, which have a total of over 210,000 entries. Our evaluations indicate that anOBOPedia style of presentation has a role as an alternative way of presentingknowledge of a domain collected as an ontology or ontologies. OBOPedia offersanother view into a field of interest that is based on a collection of ontologies asa reference resource, but one in which a user need not know it is an ontology.OBOPedia may be used viahttp://www.obopedia.org.uk. The sourcecode and documentation for OBOPedia are available viahttps://bitbucket.org/adam944/ontologyencyclopaedia