title: An ontology for immune epitopes: application to the design of a broad scope database of immune reactivities.
abstract: 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 (http://www2.niaid.nih.gov/Biodefense/bandc_priority.htm) 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.
  
  
  METHODS
  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 http://www.immuneepitope.org/ontology/index.html.
  
  
  CONCLUSIONS
  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.
authors.affiliation: La Jolla Institute of Allergy and Immunology, 3030 Bunker Hill Street, Suite 326, San Diego, California, 92109, USA. muthu@liai.org
authors.forename: Muthuraman
authors.initials: M
authors.lastname: Sathiamurthy
authors.forename: Bjoern
authors.initials: B
authors.lastname: Peters
authors.forename: Huynh-Hoa
authors.initials: HH
authors.lastname: Bui
authors.forename: John
authors.initials: J
authors.lastname: Sidney
authors.forename: John
authors.initials: J
authors.lastname: Mokili
authors.forename: Stephen S
authors.initials: SS
authors.lastname: Wilson
authors.forename: Ward
authors.initials: W
authors.lastname: Fleri
authors.forename: Deborah L
authors.initials: DL
authors.lastname: McGuinness
authors.forename: Philip E
authors.initials: PE
authors.lastname: Bourne
authors.forename: Alessandro
authors.initials: A
authors.lastname: Sette