For these reasons, it was apparent at the outset of the project that it was crucial to develop a rigorous conceptual framework to represent the knowledge related to the epitopes. Such a framework was key to sharing information and ideas among developers, scientists, and potential users, and to allowing the design of an effective logical structure of the database itself. Accordingly, we decided to develop a formal ontology. Over the years, the term "ontology" has been defined and utilized in many ways by the knowledge engineering community [4] . We will adopt the definition of "ontology" as "the explicit formal specifications of the terms in a domain and the relationships among them" [5] . According to Noy and McGuinness [6] , "ontology defines a common vocabulary for researchers who need to share information in a domain and helps separate domain knowledge from operational knowledge". Thus, availability of a formal ontology is relevant in designing a database, in cataloging the information, in communicating the database structure to researchers, developers and users, and in integrating multiple database schema designs and applications.