From IMGT-ONTOLOGY DESCRIPTION Axiom to IMGT Standardized Labels: For Immunoglobulin (IG) and T Cell Receptor (TR) Sequences and Structures

Abstract

INTRODUCTIONMore than 560 IMGT standardized labels have been defined for the description of immunoglobulin (IG) and T cell receptor (TR) sequences and structures. These labels, as detailed here, are based on the concepts of description (generated from the DESCRIPTION axiom) of IMGT-ONTOLOGY, the global reference in immunogenetics and immunoinformatics, built by IMGT, the international ImMunoGeneTics information system. IMGT labels for nucleotide sequences correspond to the “Molecule_EntityPrototype” concept with its leafconcepts (a leafconcept is the finest level of granularity), its associated concepts of description, and its prototypes or graphical representations. These labels have been essential for the IG and TR description in the IMGT sequence and gene databases (IMGT/LIGM-DB, IMGT/GENE-DB) and tools (IMGT/V-QUEST, IMGT/JunctionAnalysis, IMGT/HighV-QUEST, IMGT/LIGMotif). IMGT labels for amino acid sequences and structures correspond to the “RECEPTOR,” “CHAIN,” and “DOMAIN” concepts. These labels have been crucial for the IG and TR description in the IMGT two-dimensional (2D) and three-dimensional (3D) databases (IMGT/2Dstructure-DB, IMGT/3Dstructure-DB) and tools (IMGT/DomainDisplay, IMGT/DomainGapAlign). As all leafconcepts of description are directly translated into IMGT standardized labels for use in the IMGT databases and tools, IMGT-ONTOLOGY concepts of description contribute to data coherence and consistency and facilitate the interoperability between the different components of IMGT, bridging the description of sequences and structures.