Journal Article

An ontology for major histocompatibility restriction

Sidney, John, Kaufman, Jim, Ellis, Shirley, Tallmadge, Rebecca L., Peters, Bjoern, Vita, Randi, Seymour, Emily, Butcher, Geoff W., Overton, James A., Sette, Alessandro, Hammond, John

2016

Overview

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.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V
• Subject: Algorithms / Analysis / Animals / Antigenic determinants / Bioinformatics / Combinatorial Libraries / Computational Biology/Bioinformatics / Computer Appl. in Life Sciences / Data Mining and Knowledge Discovery / Databases, Protein / Epitopes - genetics / Gene Ontology / Histocompatibility Antigens - genetics / Histocompatibility Antigens - immunology / HLA Antigens - genetics / HLA Antigens - immunology / Humans / Major Histocompatibility Complex - genetics / Mathematics / Mathematics and Statistics / Software