Advertisement

Molecular Biotechnology

, Volume 40, Issue 1, pp 101–111 | Cite as

IMGT®, the International ImMunoGeneTics Information System® for Immunoinformatics

Methods for Querying IMGT® Databases, Tools, and Web Resources in the Context of Immunoinformatics
  • Marie-Paule Lefranc
Review

Abstract

IMGT®, the International ImMunoGeneTics information system® (http://imgt.cines.fr), was created in 1989 by the Laboratoire d’ImmunoGénétique Moléculaire (LIGM) (Université Montpellier 2 and CNRS) at Montpellier, France, in order to standardize and manage the complexity of immunogenetics data. IMGT® is recognized as the international reference in immunogenetics and immunoinformatics. IMGT® is a high quality integrated knowledge resource, specialized in (i) the immunoglobulins (IG), T cell receptors (TR), major histocompatibility complex (MHC) of human and other vertebrates; (ii) proteins that belong to the immunoglobulin superfamily (IgSF) and to the MHC superfamily (MhcSF); and (iii) related proteins of the immune systems (RPI) of any species. IMGT® provides a common access to standardized data from genome, proteome, genetics, and three-dimensional (3D) structures for the IG, TR, MHC, IgSF, MhcSF, and RPI. IMGT® interactive on-line tools are provided for genome, sequence, and 3D structure analysis. IMGT® Web resources comprise 10,000 HTML pages of synthesis and knowledge (IMGT Scientific chart, IMGT Repertoire, IMGT Education, etc.) and external links (IMGT Bloc-notes and IMGT other accesses).

Keywords

IMGT Ontology Immunoglobulin T cell receptor MHC IgSF MhcSF 

Notes

Acknowledgments

I thank Véronique Giudicelli, Patrice Duroux, Quentin Kaas, Joumana Jabado-Michaloud, Géraldine Folch, Chantal Ginestoux, Denys Chaume, and Gérard Lefranc for helpful discussions. I am deeply grateful to the IMGT® team for its expertise and constant motivation. IMGT® is a registered mark of the Centre National de la Recherche Scientifique (CNRS). IMGT® has received the National Bioinformatics Platform RIO label since 2001 (CNRS, INSERM, CEA, and INRA). IMGT® was funded in part by the BIOMED1 (BIOCT930038), Biotechnology BIOTECH2 (BIO4CT960037) and 5th PCRDT Quality of Life and Management of Living Resources (QLG2-200001287) programmes of the European Union (EU). IMGT® is currently supported by the CNRS, the Ministère de l’Education Nationale, de l’Enseignement Supérieur et de la Recherche (MENESR) (Université Montpellier 2 Plan Pluri-Formation, Institut Universitaire de France), Réseau National des Génopoles, the Région Languedoc-Roussillon, the Agence Nationale de la Recherche ANR (BIOSYS06_135457, FLAVORES), and the EU ImmunoGrid (IST-028069).

References

  1. 1.
    Lefranc, M.-P., & Lefranc, G. (2001). The Immunoglobulin FactsBook. London, UK: Academic Press, 458 p. ISBN:012441351X.Google Scholar
  2. 2.
    Lefranc, M.-P., & Lefranc, G. (2001). The T cell Receptor FactsBook. London, UK: Academic Press, 398 p. ISBN:0124413528.Google Scholar
  3. 3.
    Lefranc, M.-P., Giudicelli, V., Kaas, Q., Duprat, E., Jabado-Michaloud, J., Scaviner, D., Ginestoux, C., Clément, O., Chaume, D., & Lefranc G. (2005). IMGT, the International ImMunoGeneTics information system. Nucleic Acids Research, 33, D593–D597.CrossRefGoogle Scholar
  4. 4.
    Lefranc, M.-P., Clément, O., Kaas, Q., Duprat, E., Chastellan, P., Coelho, I., Combres, K., Ginestoux, C., Giudicelli, V., Chaume, D., & Lefranc, G. (2005). IMGT-Choreography for immunogenetics and immunoinformatics. Epub In Silico Biology 5 0006, http://www.bioinfo.de/isb/2004/05/0006/24 December 2004. In Silico Biology, 5, 45–60.
  5. 5.
    Giudicelli, V., & Lefranc, M.-P. (1999). Ontology for immunogenetics: The IMGTONTOLOGY. Bioinformatics, 12, 1047–1054.CrossRefGoogle Scholar
  6. 6.
    Chaume, D., Giudicelli, V., & Lefranc, M.-P. (2001). IMGT-ML a language for IMGT-ONTOLOGY and IMGT/LIGM-DB data. In: CORBA and XML: Towards a Bioinformatics Integrated Network Environment, Proceedings of NETTAB 2001, Network tools and Applications in Biology, May 17–18, Gchoa, Italy, pp. 71–75.Google Scholar
  7. 7.
    Chaume, D., Giudicelli, V., Combres, K., & Lefranc, M.-P. (2003) IMGTONTOLOGY and IMGT-ML for Immunogenetics and immunoinformatics. In: Abstract book of the Sequence Databases and Ontologies Satellite Event, European Congress in Computational Biology ECCB’2003, September 27–30, Paris, France, pp. 22–23.Google Scholar
  8. 8.
    Letovsky, S. I., Cottingham, R. W., Porter, C. J., & Li, P. W. (1998). GDB: The human genome database. Nucleic Acids Research, 26, 94–99.CrossRefGoogle Scholar
  9. 9.
    Wain, H. M., Bruford, E. A., Lovering, R. C., Lush, M. J., Wright, M. W., & Povey, S. (2002). Guidelines for human gene nomenclature. Genomics, 79, 464–470.CrossRefGoogle Scholar
  10. 10.
    Lefranc, M.-P., Pommié, C., Ruiz, M., Giudicelli, V., Foulquier, E., Truong, L., Thouvenin-Contet, V., & Lefranc, G. (2003). IMGT unique numbering for immunoglobulin and T cell receptor variable domains and Ig superfamily V-like domains. Development and Comparative Immunology, 27, 55–77.CrossRefGoogle Scholar
  11. 11.
    Lefranc, M.-P., Pommié, C., Kaas, Q., Duprat, E., Bosc, N., Guiraudou, D., Jean C., Ruiz, M., Da Piedade, I., Rouard, M., Foulquier, E., Thouvenin, V., & Lefranc, G. (2005). IMGT unique numbering for immunoglobulin and T cell receptor constant domains and Ig superfamily C-like domains. Development and Comparative Immunology, 29, 185–203.CrossRefGoogle Scholar
  12. 12.
    Lefranc, M.-P., Duprat, E., Kaas, Q., Tranne, M., Thiriot, A., & Lefranc, G. (2005). IMGT unique numbering for MHC groove G-DOMAIN and MHC superfamily (MhcSF) G-LIKE-DOMAIN. Development and Comparative Immunology, 29, 917–938.CrossRefGoogle Scholar
  13. 13.
    Ruiz, M., & Lefranc, M.-P. (2002). IMGT gene identification and Colliers de Perles of human immunoglobulins with known 3D structures. Immunogenetics, 53, 857–883.CrossRefGoogle Scholar
  14. 14.
    Cochrane, G., Aldebert, P., Althorpe, N., Andersson, M., Baker, W., Baldwin, A., Bates, K., Bhattacharyya, S., Browne, P., van den Broek, A., Castro, M., Duggan, K., Eberhardt, R., Faruque, N., Gamble, J., Kanz, C., Kulikova, T., Lee, C., Leinonen, R., Lin, Q., Lombard, V., Lopez, R., McHale, M., McWilliam, H., Mukherjee, G., Nardone, F., Garcia Pastor, M. P., Sobhany, S., Stoehr, P., Tzouvara, K., Vaughan, R., Wu, D., Zhu, W., & Apweiler, R. (2006). EMBL nucleotide sequence database: developments in 2005. Nucleic Acids Research, 34, D10–D15.CrossRefGoogle Scholar
  15. 15.
    Benson, D. A., Karsch-Mizrachi, I., Lipman, D. J., Ostell, J., & Wheeler, D. L. (2006). GenBank. Nucleic Acids Research, 34, D16–D20.CrossRefGoogle Scholar
  16. 16.
    Okubo, K., Sugawara, H., Gojobori, T., & Tateno, Y. (2006). DDBJ in preparation for overview of research activities behind data submissions. Nucleic Acids Research, 34, D6–D9.CrossRefGoogle Scholar
  17. 17.
    Eilbeck, K., Lewis, S. E., Mungall, C. J., Yandell, M., Stein, L., Durbin, R., & Ashburner, M. (2005). The sequence ontology: A tool for the unification of genome annotations. Genome Biology, 6(5), R44. Epub 29 Apr 2005.CrossRefGoogle Scholar
  18. 18.
    Lefranc, M.-P. (2000). Nomenclature of the human immunoglobulin genes. In J. E. Coligan, B. E. Bierer, D. E. Margulies, E. M. Shevach, & W. Strober (Eds.), Current protocols in immunology (pp. A.1P.1–A.1P.37). Hoboken, NJ: Wiley and Sons.Google Scholar
  19. 19.
    Lefranc, M.-P. (2000). Nomenclature of the human T cell receptor genes. In J. E. Coligan, B. E. Bierer, D. E. Margulies, E. M. Shevach, & W. Strober (Eds.), Current protocols in immunology (pp. A.1O.1–A.1O.23). Hoboken, N.J.: Wiley and Sons.Google Scholar
  20. 20.
    Giudicelli, V., Chaume, D., & Lefranc, M.-P. (2005). IMGT/GENE-DB: A comprehensive database for human and mouse immunoglobulin and T cell receptor genes. Nucleic Acids Research, 33, D256–D261.CrossRefGoogle Scholar
  21. 21.
    Lefranc, M.-P. (1997). Unique database numbering system for immunogenetic analysis. Immunology Today, 18, 509.CrossRefGoogle Scholar
  22. 22.
    Lefranc, M.-P. (1999). The IMGT unique numbering for immunoglobulins, T cell receptors and Ig-like domains. The Immunologist, 7, 132–136.Google Scholar
  23. 23.
    Kabat, E. A., Wu, T. T., Perry, H. M., Gottesman, K. S., & Foeller, C. (1991). Sequences of proteins of immunological interest. Washington, DC, USA: National Institute of Health Publications Publication no. 91-3242.Google Scholar
  24. 24.
    Satow, Y., Cohen, G. H., Padlan, E. A., & Davies, D. R. (1986). Phosphocholine binding immunoglobulin Fab McPC603. Journal of Molecular Biology, 190, 593–604.CrossRefGoogle Scholar
  25. 25.
    Chothia, C., & Lesk, A. M. (1987). Canonical structures for the hypervariable regions of immunoglobulins. Journal of Molecular Biology, 196, 901–917.CrossRefGoogle Scholar
  26. 26.
    Duprat, E., Kaas, Q., Garelle, V., Lefranc, G., & Lefranc, M.-P. (2004). IMGT standardization for alleles and mutations of the V-LIKE-DOMAINs and C-LIKE-DOMAINs of the immunoglobulin superfamily. In: Pandalai, S. G. (Ed.), Recent research developments in human genetics (Vol. 2, pp. 111–136). Research Signpost: Trivandrum, Kerala, India, .Google Scholar
  27. 27.
    Bertrand, G., Duprat, E., Lefranc, M.-P., Marti, J., & Coste, J. (2004). Characterization of human FCGR3B*02 (HNA-1b, NA2) cDNAs and IMGT standardized description of FCGR3B alleles. Tissue Antigens, 64, 119–131.CrossRefGoogle Scholar
  28. 28.
    Frigoul, A., & Lefranc, M.-P. (2005) MICA: Standardized IMGT allele nomenclature, polymorphisms and diseases. In Pandalai, S. G., (Ed.), Recent research developments in human genetics (Vol. 3, pp. 95–145). Research Signpost: Trivandrum, Kerala, India.Google Scholar
  29. 29.
    Baum, T. P., Pasqual, N., Thuderoz, F., Hierle, V., Chaume, D., Lefranc, M.-P., Jouvin-Marche, E., Marche, P. N., & Demongeot, J. (2004). IMGT/GeneInfo: Enhancing V(D)J recombination database accessibility. Nucleic Acids Research, 32, D51–D54.CrossRefGoogle Scholar
  30. 30.
    Giudicelli, V., Duroux, P., Ginestoux, C., Folch, G., Jabado-Michaloud, J., Chaume, D., & Lefranc, M.-P. (2006). IMGT/LIGM-DB, the IMGT® comprehensive database of immunoglobulin and T cell receptor nucleotide sequences. Nucleic Acids Research, 34, D781–D784.CrossRefGoogle Scholar
  31. 31.
    Folch, G., Bertrand, J., Lemaitre, M., & Lefranc, M.-P. (2004). IMGT/PRIMER-DB. In M. Y. Galperin (Ed.), Database listing. The Molecular Biology Database Collection: 2004 update. Nucleic Acids Research, 32, D3–D22.Google Scholar
  32. 32.
    Robinson, J., Waller, M. J., Parham, P., de Groot, N., Bontrop, R., Kennedy, L. J., Stoehr, P., & Marsh, S. G. (2003). IMGT/HLA and IMGT/MHC sequence databases for the study of the major histocompatibility complex. Nucleic Acids Research, 31, 311–314.CrossRefGoogle Scholar
  33. 33.
    Giudicelli, V., Chaume, D., & Lefranc, M.-P. (2004). IMGT/V-QUEST, an integrated software program for immunoglobulin and T cell receptor V-J and V-D-J rearrangement analysis. Nucleic Acids Research, 32, W435–W440.CrossRefGoogle Scholar
  34. 34.
    Yousfi Monod, M., Giudicelli, V., Chaume, D., & Lefranc, M.-P. (2004). IMGT/JunctionAnalysis: The first tool for the analysis of the immunoglobulin and T cell receptor complex V-J and V-D-J JUNCTIONs. Bioinformatics, 20, i379–i385.CrossRefGoogle Scholar
  35. 35.
    Elemento, O., & Lefranc, M.-P. (2003). IMGT/PhyloGene: An on-line tool for comparative analysis of immunoglobulin and T cell receptor genes. Development and Comparative Immunology, 27, 763–779.CrossRefGoogle Scholar
  36. 36.
    Kaas, Q., Ruiz, M., & Lefranc, M.-P. (2004). IMGT/3Dstructure-DB and IMGT/StructuralQuery, a database and a tool for immunoglobulin, T cell receptor and MHC structural data. Nucleic Acids Research, 32, D208–D210.CrossRefGoogle Scholar
  37. 37.
    Pommié, C., Sabatier, S., Lefranc, G., & Lefranc, M.-P. (2004). IMGT standardized criteria for statistical analysis of immunoglobulin V-REGION amino acid properties. Journal of Molecular Recognition, 17, 17–32.CrossRefGoogle Scholar
  38. 38.
    Lefranc, M.-P. (2006). Web sites of interest to immunologists. In J. E. Coligan, B. E. Bierer, D. E. Margulies, E. M. Shevach, & W. Strober (Eds.), Current protocols in immunology (pp. A.1J.1–A.1J.74). Hoboken, NJ: Wiley and Sons.Google Scholar
  39. 39.
    Maglott, D., Ostell, J., Pruitt, K. D., & Tatusova, T. (2007). Entrez Gene: Gene-centered information at NCBI. Nucleic Acids Research, 35, D26–D31.CrossRefGoogle Scholar
  40. 40.
    Giudicelli, V., Chaume, D., Jabado-Michaloud, J., & Lefranc, M.-P. (2005). Immunogenetics sequence annotation: The strategy of IMGT based on IMGTONTOLOGY. Studies in Health Technology and Informatics, 116, 3–8.Google Scholar
  41. 41.
    Lefranc, M.-P. (2004). IMGT, The International ImMunoGeneTics Information System®, http://imgt.cines.fr. In B. K. C. Lo (Ed.), Antibody engineering: Methods and protocols. Totowa, NJ: Humana. Methods in Molecular Biology, 248, 27–49.
  42. 42.
    Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N., & Bourne, P. E. (2000). The Protein Data Bank. Nucleic Acids Research, 28, 235–242.CrossRefGoogle Scholar
  43. 43.
    Duprat, E., Lefranc, M.-P., & Gascuel, O. (2006). A simple method to predict protein binding from aligned sequences—Application to MHC superfamily and beta2-microglobulin. Bioinformatics, 22, 453–459.CrossRefGoogle Scholar
  44. 44.
    Kaas, Q., & Lefranc, M.-P. (2005). T cell receptor/peptide/MHC molecular characterization and standardized pMHC contact sites in IMGT/3Dstructure-DB. Epub In Silico Biology 5 0046, 20 October 2005. In Silico Biol. 5, 505–528.Google Scholar
  45. 45.
    Duroux, P., Kaas, Q., Brochet, X., Lane, J., Ginestoux, C., Lefranc, M.-P., & Giudicelli, V. (2008). IMGT-Kaleidoscope, the formal IMGT-ONTOLOGY paradigm. Biochimie, 90, 570–583.CrossRefGoogle Scholar

Copyright information

© Humana Press 2008

Authors and Affiliations

  1. 1.IMGT, The International ImMunoGeneTics Information System, Laboratoire d’ImmunoGénétique MoléculaireUniversité Montpellier 2, Institut de Génétique Humaine, IGH, UPR CNRS 1142Montpellier Cedex 5France

Personalised recommendations