In summary, intermediate to high-quality draft sequencing of target genomes, combined with low-quality draft sequencing of close phylogenetic relatives, is sufficient for the prediction of DNA diagnostic signatures. Prediction of peptide/ protein signature candidates, in contrast, requires finished sequencing to avoid substantial underestimation of conserved peptide regions. An ontology for immune epitopes: application to the design of a broad scope database of immune reactivities BACKGROUND: Epitopes can be defined as the molecular structures bound by specific receptors, which are recognized during immune responses. The Immune Epitope Database and Analysis Resource (IEDB) project will catalog and organize information regarding antibody and T cell epitopes from infectious pathogens, experimental antigens and self-antigens, with a priority on NIAID Category A-C pathogens () and emerging/re-emerging infectious diseases. Both intrinsic structural and phylogenetic features, as well as information relating to the interactions of the epitopes with the host's immune system will be catalogued. DESCRIPTION: To effectively represent and communicate the information related to immune epitopes, a formal ontology was developed. The semantics of the epitope domain and related concepts were captured as a hierarchy of classes, which represent the general and specialized relationships between the various concepts. A complete listing of classes and their properties can be found at . CONCLUSION: The IEDB's ontology is the first ontology specifically designed to capture both intrinsic chemical and biochemical information relating to immune epitopes with information relating to the interaction of these structures with molecules derived from the host immune system. We anticipate that the development of this type of ontology and associated databases will facilitate rigorous description of data related to immune epitopes, and might ultimately lead to completely new methods for describing and modeling immune responses. An epitope can be defined as the molecular structure recognized by the products of immune responses. According to this definition, epitopes are the specific molecular entities engaged in binding to antibody molecules or specific T cell receptors. An extended definition also includes the specific molecules binding in the peptide binding sites of MHC receptors. We have previously described [1] the general design of the Immune Epitope Database and Analysis Resource (IEDB), a broad program recently initiated by National Institute of Allergy and Infectious Diseases (NIAID). The overall goal of the IEDB is to catalog and organize a large body of information regarding antibody and T cell epitopes from infectious pathogens and other sources [2] . Priority will be placed on NIAID Category A-C pathogens (http://www2.niaid.nih.gov/Biodefense/ bandc_priority.htm) and emerging/re-emerging infectious diseases. Epitopes of human and non-human primates, rodents, and other species for which detailed information is available will be included. It is envisioned that this new effort will catalyze the development of new methods to predict and model immune responses, will aid in the discovery and development of new vaccines and diagnostics, and will assist in basic immunological investigations.