title: An ontology for major histocompatibility restriction.
abstract: BACKGROUND
  MHC molecules are a highly diverse family of proteins that play a key role in cellular immune recognition. Over time, different techniques and terminologies have been developed to identify the specific type(s) of MHC molecule involved in a specific immune recognition context. No consistent nomenclature exists across different vertebrate species.
  
  
  OBJECTIVE
  To correctly represent MHC related data in The Immune Epitope Database (IEDB), we built upon a previously established MHC ontology and created an ontology to represent MHC molecules as they relate to immunological experiments.
  
  
  METHODS
  This ontology models MHC protein chains from 16 species, deals with different approaches used to identify MHC, such as direct sequencing verses serotyping, relates engineered MHC molecules to naturally occurring ones, connects genetic loci, alleles, protein chains and multi-chain proteins, and establishes evidence codes for MHC restriction. Where available, this work is based on existing ontologies from the OBO foundry.
  
  
  CONCLUSIONS
  Overall, representing MHC molecules provides a challenging and practically important test case for ontology building, and could serve as an example of how to integrate other ontology building efforts into web resources.
authors.affiliation: La Jolla Institute for Allergy and Immunology, 9420 Athena Circle La Jolla, San Diego, California 92037 USA.
authors.forename: Randi
authors.identifier: 0000-0001-8957-7612
authors.initials: R
authors.lastname: Vita
authors.affiliation: La Jolla Institute for Allergy and Immunology, 9420 Athena Circle La Jolla, San Diego, California 92037 USA.
authors.forename: James A
authors.initials: JA
authors.lastname: Overton
authors.affiliation: La Jolla Institute for Allergy and Immunology, 9420 Athena Circle La Jolla, San Diego, California 92037 USA.
authors.forename: Emily
authors.initials: E
authors.lastname: Seymour
authors.affiliation: La Jolla Institute for Allergy and Immunology, 9420 Athena Circle La Jolla, San Diego, California 92037 USA.
authors.forename: John
authors.initials: J
authors.lastname: Sidney
authors.affiliation: University of Cambridge, Trinity Ln, Cambridge, CB2 1TN UK.
authors.forename: Jim
authors.initials: J
authors.lastname: Kaufman
authors.affiliation: Cornell University College of Veterinary Medicine, Ithaca, New York 14853-6401 USA.
authors.forename: Rebecca L
authors.initials: RL
authors.lastname: Tallmadge
authors.affiliation: The Pirbright Institute, Ash Rd, Woking, GU24 0NF UK.
authors.forename: Shirley
authors.initials: S
authors.lastname: Ellis
authors.affiliation: The Pirbright Institute, Ash Rd, Woking, GU24 0NF UK.
authors.forename: John
authors.initials: J
authors.lastname: Hammond
authors.affiliation: The Babraham Institute, Cambridge, CB22 3AT UK.
authors.forename: Geoff W
authors.initials: GW
authors.lastname: Butcher
authors.affiliation: La Jolla Institute for Allergy and Immunology, 9420 Athena Circle La Jolla, San Diego, California 92037 USA.
authors.forename: Alessandro
authors.initials: A
authors.lastname: Sette
authors.affiliation: La Jolla Institute for Allergy and Immunology, 9420 Athena Circle La Jolla, San Diego, California 92037 USA.
authors.forename: Bjoern
authors.initials: B
authors.lastname: Peters
mesh_terms: D000818:Animals; D030562:Databases, Protein; D000939:Epitopes / Q000235:genetics; D063990:Gene Ontology; D006680:HLA Antigens / Q000235:genetics / Q000276:immunology; D006649:Histocompatibility Antigens / Q000235:genetics / Q000276:immunology; D006801:Humans; D008285:Major Histocompatibility Complex / Q000235:genetics*; D012984:Software
chemical_list: D000939:Epitopes; D006680:HLA Antigens; D006649:Histocompatibility Antigens
keywords: Immune epitope; MHC; Major histocompatibility complex; Ontology