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J Biomed Semantics. 2016 Jan 11;7:1. doi: 10.1186/s13326-016-0045-5. eCollection 2016.

An ontology for major histocompatibility restriction.

Author information

1
La Jolla Institute for Allergy and Immunology, 9420 Athena Circle La Jolla, San Diego, California 92037 USA.
2
University of Cambridge, Trinity Ln, Cambridge, CB2 1TN UK.
3
Cornell University College of Veterinary Medicine, Ithaca, New York 14853-6401 USA.
4
The Pirbright Institute, Ash Rd, Woking, GU24 0NF UK.
5
The Babraham Institute, Cambridge, CB22 3AT UK.

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.

PURPOSE:

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.

DESCRIPTION:

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.

KEYWORDS:

Immune epitope; MHC; Major histocompatibility complex; Ontology

PMID:
26759709
PMCID:
PMC4709943
DOI:
10.1186/s13326-016-0045-5
[Indexed for MEDLINE]
Free PMC Article

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