IMGT EC FP5 project (European Commission Fifth Framework programme)

Quality of Life and Management of Living Resources (QLG2-2000-01287) implemented in the Fifth Framework programme (1999-2002)

Integrated system to manage the enormous complexity of the genome and proteome of the specific immune response: IMGT, the international ImMunoGeneTics information system®

• IMGT Home page
• IMGT coordinator
• IMGT EC FP5 partners
• Overall objectives of the project
• Progress to date
• IMGT creations and updates
• Workpackages and milestones

IMGT Home page

IMGT, the international ImMunoGeneTics information system® http://www.imgt.org

IMGT coordinator

IMGT initiator and coordinator: Marie-Paule Lefranc (Marie-Paule.Lefranc@igh.cnrs.fr)
Senior member of the Institut Universitaire de France
Chair of Immunogenetics and Immunoinformatics
Professor Université Montpellier II
CNRS Délégation Languedoc-Roussillon, LIGM, IGH, Montpellier (France)

IMGT EC FP5 partners

LIGM Laboratoire d'ImmunoGénétique Moléculaire, IGH, CNRS, Université Montpellier II, Montpellier, France EMBL-EBI European Molecular Biology Laboratory-European Bioinformatic Institute, Hinxton, UK CR Cancer Research UK, London, UK EUROGENTEC Seraing, Belgium BPRC Biomedical Primate Research Centre, Rijswijk, The Netherlands

Overall objectives of the project

IMGT, the international ImMunoGeneTIcs information system® http://www.imgt.org is one of the most successful and integrated European project. The workplan of the 5th PCRDT focused on the genome and proteome (genes, proteins, polymorphisms and structures) of the immunoglobulins (IG), T cell receptors (TR) and major histocompatibility complex (MHC) of human and other vertebrates. The IMGT consortium managed to go beyond the expected deliverables and milestones with the creation of additional new databases (IMGT/3Dstructure-DB, IMGT/GENE-DB) and tools (IMGT/JunctionAnalysis, IMGT/PhyloGene, IMGT/Allele-Align, IMGT/GeneView, IMGT/GeneSearch, IMGT/LocusView), in addition to those expected in the workplan. Moreover, the IMGT Repertoire (the IMGT major Web resource on IG, TR and MHC) has been extended to related proteins of the immune system (RPI), particularly those with V-like, C-like and G-like domains, opening new insights in the evolution of these proteins.

Progress to date

The IMGT Home page is at Montpellier at http://www.imgt.org and provides a common access to a high-quality integrated information system® specializing in IG, TR, MHC and RPI of human and other vertebrate species. It comprises:

Author: Marie-Paule Lefranc Marie-Paule.Lefranc@igh.cnrs.fr
1. the IMGT databases
• Sequence databases:
• IMGT/LIGM-DB (IG and TR, 105 species, 69 621 sequences in April 2003). By comparison SWISS-PROT has 125 236 entries)
• IMGT/MHC-DB (HLA, MHC-NHP) hosted at EBI
• IMGT/PRIMER-DB (IG, TR)
• Genome database:
• IMGT/GENE-DB (IG, TR)
• 3D structure database:
• IMGT/3Dstructure-DB (IG, TR, MHC, RPI)
2. IMGT Web resources (8000 pages)
• IMGT Repertoire (IG, TR, MHC, RPI)
• IMGT Scientific chart (IG, TR, MHC, RPI)
• IMGT Bloc-notes (IMGT Immunoinformatics page,..)
• IMGT Index
• IMGT Education
3. and IMGT interactive tools
• IMGT/V-QUEST (IG, TR)
• IMGT/JunctionAnalysis (IG, TR)
• IMGT/Allele-Align (IG, TR)
• IMGT/PhyloGene (IG, TR)
• IMGT/LocusView (IG, TR, MHC)
• IMGT/GeneSearch (IG, TR, MHC)
• IMGT/LocusView (IG, TR, MHC)

The unique common access to IMGT is the IMGT Home page http://www.imgt.org. The IMGT MHC sequence databases (human: IMGT/HLA and nonhuman primates: IMGT/MHC-NHP) are hosted on the EBI server. All the other IMGT databases, resources and tools on IG, TR, MHC and RPI are localized at Montpellier on the CINES and IGH servers.

IMGT creations and updates

Workpackages and milestones

• WP1 - Genome and proteome of the immunoglobulins and T cell receptors of non-mammalian vertebrates: phylogeny and evolution
• M1.1 - Enhancement of the IMGT repertoire on the genes and alleles of IG and TR of non-mammalian vertebrates for phylogeny and evolution
• M1.2 - Update and enhancement of the IMGT-ONTOLOGY
• M1.3 - Curation of 1 500 IG and TR sequence entries in IMGT/LIGM-DB
• WP2 - Genome and proteome of the immunoglobulins and T cell receptors of mammals: comparative genomics
• M2.1 - Enhancement of the IMGT repertoire on the genes and alleles of IG and TR of mammals for comparative genomics
• M2.2 - Educational resource information for comparative genomics
• M2.3 - Curation of 2 000 IG and TR sequences in IMGT/LIGM-DB
• WP3 - Genome and proteome of the immunoglobulins and T cell receptors of rodents: towards functional genomics
• M3.1 - Enhancement of the IMGT repertoire on the genes and alleles of rodents, for functional genomics
• M3.2 - IMGT/Colliers de Perles tool in the IMGT interface (tool for IMGT annotators)
• M3.3 - Curation of the sequences in IMGT/LIGM-DB (section rodents)
• WP4 - Genome and proteome of the immunoglobulins and T cell receptors of human: for therapeutic approaches
• M4.1 - Enhancement of the IMGT repertoire on the human genes and alleles, and structural data for therapeutic approaches
• M4.2 - IMGT/PROTEIN-DB, a novel database containing protein specific annotations of IG and TR
• M4.3 - Enhancement of IMGT/LIGM-DB interoperability with genome and structural databases (in development)
• WP5 - Genome and proteome of the HLA (human MHC)
• M5.1 - Completion of a usable and user-friendly relational database and its various interfaces
• M5.2 - Major re-analysis of a large body of world-wide HLA population genetics data
• WP6 - Genome and proteome of the MHC of non-human primates and other mammals
• M6.1 - Completion of the non-human primate MHC database
• M6.2 - Setting up of a Web page for MHC of mammals
• WP7 - Development of IMGT/PRIMER-DB, the database for oligonucleotides of immunoglobulins, T cell receptors and MHC of all vertebrates
• M7.1 - Completion of the IMGT/PRIMER database
• M7.2 - Setting up of the IMGT/PRIMER-DB data coherence module for data integrity and coherence
• WP8 - Enhancement of IMGT data acquisition, annotation procedure, common data access and data distribution
• M8.1 - Enhancement of IMGT data acquisition and direct submission by authors
• M8.2 - Improvement in the automation of the annotation procedure
• M8.3 - Interoperability of IMGT with other databases and analysis tools

Created: 09/05/2003
Last updated: Monday, 11-Jul-2011 12:56:52 CEST
Editor: Chantal Ginestoux
Contact: Marie-Paule Lefranc

IMGT Home page | IMGT Repertoire (IG and TR) | IMGT Repertoire (MH) | IMGT Repertoire (RPI) | IMGT Index | IMGT Scientific chart | IMGT Education | IMGT Latest news

Software material and data coming from IMGT server may be used for academic research only, provided that it is referred to IMGT®, and cited as "IMGT®, the international ImMunoGeneTics information system® http://www.imgt.org (founder and director: Marie-Paule Lefranc, Montpellier, France)." References to cite: Lefranc, M.-P. et al., Nucleic Acids Research, 27, 209-212 (1999) Cover of NAR; Ruiz, M. et al., Nucleic Acids Research, 28, 219-221 (2000); Lefranc, M.-P., Nucleic Acids Research, 29, 207-209 (2001); Lefranc, M.-P., Nucleic Acids Res., 31, 307-310 (2003); Lefranc, M.-P. et al., In Silico Biol., 5, 0006 (2004) [Epub], 5, 45-60 (2005); Lefranc, M.-P. et al., Nucleic Acids Res., 33, D593-D597 (2005) Full text; Lefranc, M.-P. et al., Nucleic Acids Research 2009 37: D1006-D1012; doi:10.1093/nar/gkn838 Full text.

IMGT founder and director: Marie-Paule Lefranc Marie-Paule.Lefranc@igh.cnrs.fr Bioinformatics manager: Véronique Giudicelli Veronique.Giudicelli@igh.cnrs.fr Computer manager: Patrice Duroux Patrice.Duroux@igh.cnrs.fr Webmaster: Chantal Ginestoux Chantal.Ginestoux@igh.cnrs.fr
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