Communication between database developers, researchers, analysis tool developers, and team members is crucial, and can be performed in harmony only when a common vocabulary is established. An ontology, which is an explicit formal specification of the terms in the domain and relationships among them, is an effective way to share the knowledge contained in that domain. Accordingly, since the IEDB's domain is epitope-related data, we have created an ontology that captures detailed conceptual structure related to these data.