OBOPedia: An Encyclopaedia of Biology Using OBO Ontologies

Ontologies contain knowledge about a domain for use by tools or humans. 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. The corpus of biomedical ontologies now contains ‘encyclopaedic’ knowledge about biology and should be capable of being used by humans to learn about entities in molecular biology. Yet multiple separate ontologies and the typical style of presentation of the knowledge in the ontologies mean that their use as a learning resource is sub-optimal. To address this issue we have created OBOPedia, a web based encyclopaedia of biology as seen by the Open Biomedical Ontologies (OBO) Consortium. OBOPedia exploits the OBO’s use of standard representations and meaningful human readable terms and natural language definitions to create a basic OBOPedia encyclopaedia entry. An entry is supplemented with an ontology’s synonyms and uses the ontology’s taxonomic links to provide ‘see also’ cross-references within the alphabetical list of entries. Currently, OBOPedia has access to ten OBO ontologies, including all the OBO Foundry ontologies, which have a total of over 210,000 entries. Our evaluations indicate that an OBOPedia style of presentation has a role as an alternative way of presenting knowledge of a domain collected as an ontology or ontologies. OBOPedia offers another view into a field of interest that is based on a collection of ontologies as a reference resource, but one in which a user need not know it is an ontology. OBOPedia may be used via http://www.obopedia.org.uk. The source code and documentation for OBOPedia are available via https://bitbucket. org/adam944/ontologyencyclopaedia.