Abstract
IMGT®, the international ImMunoGeneTics information system® (CNRS and Montpellier University) is the global reference in immunogenetics and immunoinformatics. By its creation in 1989, IMGT® marked the advent of immunoinformatics, which emerged at the interface between immunogenetics and bioinformatics. IMGT® is specialized in the immunoglobulins (IG) or antibodies, T cell receptors (TR), major histocompatibility (MH), and IgSF and MhSF superfamilies. IMGT® has been built on the IMGT-ONTOLOGY axioms and concepts, which bridged the gap between genes, sequences and three-dimensional (3D) structures. The concepts include the IMGT® standardized keywords (identification), IMGT® standardized labels (description), IMGT® standardized nomenclature (classification), IMGT unique numbering and IMGT Colliers de Perles (numerotation). IMGT® comprises seven databases, 15,000 pages of web resources and 17 tools. IMGT® tools and databases provide a high-quality analysis of the IG from fish to humans, for basic, veterinary and medical research, and for antibody engineering and humanization. They include, as examples: IMGT/V-QUEST and IMGT/JunctionAnalysis for nucleotide sequence analysis and their high-throughput version IMGT/HighV-QUEST for next generation sequencing, IMGT/DomainGapAlign for amino acid sequence analysis of IG domains, IMGT/3Dstructure-DB for 3D structures, contact analysis and paratope/epitope interactions of IG/antigen complexes, and the IMGT/mAb-DB interface for therapeutic antibodies and fusion proteins for immunological applications (FPIA).
Highlights
IMGT-ONTOLOGY and the IMGT® information system, which are at the origin of immunoinformatics [45], have provided the concepts, the knowledge environment and the informatics frame for a standardized and integrated analysis of the IG, from gene to structure and function
IMGT/V-QUEST is frequently used by clinicians for the analysis of IG somatic hypermutations in leukemia, lymphoma and myeloma, and more in chronic lymphocytic leukemia (CLL) [16,72,73,74,75] in which the percentage of mutations of the rearranged IGHV gene in the VH of the leukemic clone has a prognostic value for the patients
IMGT/V-QUEST is the standard recommended by the European Research Initiative on CLL (ERIC) for comparative analysis between laboratories [72]
Summary
More than 325 IMGT® standardized keywords (189 for sequences and 137 for 3D structures) were precisely defined [57]. They represent the controlled vocabulary assigned during the annotation process and allow standardized search criteria for querying the IMGT® databases and for the extraction of sequences and 3D structures They have been entered in BioPortal [87] at the National Center for Biomedical Ontology (NCBO) in 2010. Standardized keywords are assigned at each step of the molecular synthesis of an IG Those assigned to a nucleotide sequence are found in the “DE” (definition) and “KW” (keyword) lines of the IMGT/LIGM-DB files [7]. They characterize, for instance, the gene type, the configuration type and the functionality type [57]. Four types of AA changes are identified in IMGT®: very similar (+ + +), similar (+ + , + +), dissimilar ( +, + , + ), and very dissimilar ( )
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
