The ontology developed for IEDB and described herein complements two explicit ontologies that are presently available: the IMGT-Ontology and the Gene Ontology (GO). The IMGT-Ontology [15] was created for the international ImMunoGeneTics Database (IMGT), which is an integrated database specializing in antigen receptors (immunoglobulin and T Cell receptors) and MHC molecules of all vertebrate species. This is, to the best of our knowledge, the first ontology in the domain of immunogenetics and immunoinformatics. The GO project [16] provides structured, controlled vocabularies that cover several domains of molecular and cellular biology. GO provides an excellent framework for genes, gene products, and their sequences, but it does not address the specific epitope substructure of the gene products. The IMGT provides an excellent ontological framework for the immune receptors but lacks information relating to the epitopes themselves. Therefore it was necessary to expand the available ontologies and to create an ontology specifically designed to represent the information of immune receptor interaction with immune epitopes. Wherever possible, the IEDB ontology conforms to standard vocabularies for capturing values for certain fields. For capturing disease names, IEDB uses the International Classification for Diseases (ICD-10) [17]. The NCBI Taxonomy database nomenclature [18, 19] is used to capture species and strain names, and HLA Allele names are consistent with the HLA nomenclature reports [20] .