We have previously described some of the general concepts relating to the IEDB design [1, 2] . More information relating to various aspects of the project can be accessed at http://www.immuneepitope.org/. Herein, we report a detailed description of the novel aspects of the IEDB ontology. In designing our application architecture, we have followed the common system engineering practice of first determining the scope and nature of the data involved. A first essential step is to understand the semantics of the domain and to capture that knowledge in an agreed-upon format. Arranging the domain concepts in a taxonomy is one of the initial organizing steps in the ontology design process. The class hierarchy represents the generalization and specialization relationships between the various classes of objects in a domain [6] . Briefly, classes describe concepts in the domain. Subclasses represent concepts (classes) that are more specific than the superclass and these subclasses can have their own unique properties. Slots represent properties of the classes. For example, in Figure 1 , we see that there is a class named Reference and three more specific subclasses of Reference: Journal Article, Patent Application, and Direct Submission. Figure 1 also shows that the class Epitope has a number of properties (slots) associated with it such as "has Epitope Structure" and "has Epitope Source".