IMGT-ONTOLOGY, IMGT Databases, Tools, and Web Resources for Immunoinformatics - Immunoinformatics - page 1

Chapter 1
IMGT-ONTOLOGY, IMGT ® Databases, Tools,
and Web Resources for Immunoinformatics
Marie-Paule Lefranc
IMGT ® , the International ImMunoGeneTics Information System ® , Université Montpellier II,
Institut Universitaire de France, Laboratoire d'ImmunoGénétique Moléculaire LIGM, UPR
CNRS 1142, Institut de Génétique Humaine IGH, 141 rue de la Cardonille, 34396 Montpellier
Cedex 5, France, [e-mail]
Abstract. IMGT ® , the international ImMunoGeneTics information system ® , was created in 1989
as a high-quality integrated knowledge resource specialized in immunoglobulins (IG), T cell
receptors (TR), major histocompatibility complexes (MHC) of human and other vertebrates, and
related proteins of the immune system (RPI) which belong to the immunoglobulin superfamily
(IgSF) and to the MHC superfamily (MhcSF). IMGT ® is the international reference in immuno-
genetics and immunoinformatics. IMGT ® combines sequence databases (IMGT/LIGM-DB,
IMGT/PRIMER-DB, IMGT/PROTEIN-DB, IMGT/MHC-DB), a genome database (IMGT/
GENE-DB), and a three-dimensional (3D) structure database (IMGT/ 3Dstructure-DB) with
interactive analysis tools (IMGT/V-QUEST, IMGT/JunctionAnalysis) and Web resources com-
prising 8000 HTML pages (IMGT Repertoire). The accuracy and consistency of IMGT data are
based on IMGT-ONTOLOGY, available for biologists and IMGT users in the IMGT Scientific
chart and for computer scientists in IMGT-ML, in XML format. IMGT ® components (databases,
tools, and Web resources) have been developed according to three main biological approaches:
the genomic approach that is gene centered, the genetic approach that refers to genes in relation
to their polymorphisms, expression, specificity, and evolution, and the structural approach that
analyses 3D structures in relation to protein function and recognition sites. We are implementing
Web services for the IMGT databases and tools. This is the first step toward IMGT-
Choreography that will trigger and coordinate dynamic interactions between IMGT Web services
in order to process complex significant biological and clinical requests. IMGT ® is widely used in
fundamental and medical research (repertoire analysis of the IG antibody sites and of the TR
recognition sites in autoimmune diseases, infectious diseases, AIDS, leukemias, lymphomas,
myelomas), veterinary research situations (IG and TR repertoires in farm and wildlife species),
genome diversity and genome evolution studies of the adaptive immune responses, biotechnol-
ogy related to antibody engineering (single chain Fragment variable (scFv), phage displays,
combinatorial libraries, chimeric, humanized, and human antibodies), diagnostics (clonalities,
detection and follow-up of residual diseases), and therapeutical approaches (graft, immunother-
apy, vaccinology). IMGT ® is freely available at http://imgt.cines.fr.
1.1 Introduction
Genome and proteome analysis interpretation represents the current great challenge,
as a huge quantity of data is produced by many scientific fields, including fundamental,
clinical, veterinary, and pharmaceutical research. In particular, the number of sequences