IMGT-Choreography for Immunogenetics and Immunoinformatics

Issue title: ONTOLOGY WORKSHOP GÖTTINGEN 2004

Article type: Research Article

Authors: Lefranc, Marie-Paule | Clément, Oliver | Kaas, Quentin | Duprat, Elodie | Chastellan, Patrick | Coelho, Isabelle | Combres, Kora | Ginestoux, Chantal | Giudicelli, Véronique | Chaume, Denys | Lefranc, Gérard

Affiliations: IMGT, the international ImMunoGeneTics information system®, Université Montpellier II, Laboratoire d'ImmunoGénétique Moléculaire LIGM, UPR CNRS 1142, Institut de Génétique Humaine IGH, 141 rue de la Cardonille, 34396 Montpellier Cedex 5, France. Tel.: +33 4 99 61 99 65; Fax: +33 4 99 61 99 01

Note: [] Corresponding author. Institut Universitaire de France. E-mail: [email protected]

Abstract: IMGT, the international ImMunoGeneTics information system® (http://imgt.cines.fr), was created in 1989 at Montpellier, France. IMGT is a high quality integrated knowledge resource specialized in immunoglobulins (IG), T cell receptors (TR), major histocompatibility complex (MHC) of human and other vertebrates, and related proteins of the immune system (RPI) which belong to the immunoglobulin superfamily (IgSF) and MHC superfamily (MhcSF). IMGT provides a common access to standardized data from genome, proteome, genetics and three-dimensional structures. The accuracy and the consistency of IMGT data are based on IMGT-ONTOLOGY, a semantic specification of terms to be used in immunogenetics and immunoinformatics. IMGT-ONTOLOGY has been formalized using XML Schema (IMGT-ML) for interoperability with other information systems. We are developing Web services to automatically query IMGT databases and tools. This is the first step towards IMGT-Choreography which will trigger and coordinate dynamic interactions between IMGT Web services to process complex significant biological and clinical requests. IMGT-Choreography will further increase the IMGT leadership in immunogenetics and immunoinformatics for medical research (repertoire analysis of the IG antibody recognition sites and of the TR recognition sites in autoimmune and infectious diseases, AIDS, leukemias, lymphomas, myelomas), veterinary research (IG and TR repertoires in farm and wild life species), genome diversity and genome evolution studies of the adaptive immune responses, biotechnology related to antibody engineering (single chain Fragment variable (scFv), phage displays, combinatorial libraries, chimeric, humanized and human antibodies), diagnostics (detection and follow-up of residual diseases) and therapeutical approaches (grafts, immunotherapy, vaccinology). IMGT is freely available at http://imgt.cines.fr.

Keywords: IMGT, ontology, database, information system, knowledge resource, immunoinformatics, immunogenetics, antibody, immunoglobulin, T cell receptor, superfamily, MHC, HLA, Collier de Perles, three-dimensional, 3D structure, polymorphism, choreography, Web service, annotation

Journal: In Silico Biology, vol. 5, no. 1, pp. 45-60, 2005