Representing the Immune Epitope Database in OWL

Bjoern Peters

La Jolla Institute of Allergy and Immunology

Vast amounts of biomedical information are stored in relational databases. Several of these use ontologies to better communicate the meaning and context of their data. However, most often ontology terms are only used to represent in a limited number of fields in a database. An ontology, in this context, essentially functions as a controlled vocabulary and few formal relations are used between database fields. We argue that a full representation of biomedical database content using a principled approach to ontology, encoded using a formal language such as OWL provides significant benefits. These include data consistency checks, the ability to formulate highly expressive queries, and the potential for seamless interoperability with other data resources. We report on our efforts to make such a representation available for the Immune Epitope Database.