IMGT-ontology for immunogenetics and immunoinformatics

In Silico Biology

Volumn 4, Issue 1, 2004, Pages 17-29

  Lefranc, Marie Paule ^a   Giudicelli, Véronique ^a   Ginestoux, Chantal ^a   Bosc, Nathalie ^a   Folch, Géraldine ^a   Guiraudou, Delphine ^a   Jabado Michaloud, Joumana ^a   Magris, Séverine ^a   Scaviner, Dominique ^a   Thouvenin, Valérie ^a   Combres, Kora ^a   Girod, David ^a   Jeanjean, Stéphanie ^a   Protat, Céline ^a   Monod, Mehdi Yousfi ^a   Duprat, Elodie ^a   Kaas, Quentin ^a   Pommié, Christelle ^a   Chaume, Denys ^a   Lefranc, Gérard ^a  

^a CNRS and University Montpellier II   (France)

Author keywords

Antibody; Collier de Perles; Database; HLA; IMGT; Immunogenetics; Immunoglobulin; Immunoglobulin superfamily; Immunoinformatics; Information system; Knowledge resource; Leukemia; Lymphoma; MHC; Ontology; Polymorphism; Primer; T cell receptor; Three dimensional (3D) structure

Indexed keywords

IMMUNOGLOBULIN; OLIGONUCLEOTIDE; T LYMPHOCYTE RECEPTOR;

ACCESS TO INFORMATION; ACQUIRED IMMUNE DEFICIENCY SYNDROME; AMINO ACID SEQUENCE; ANTIBODY ENGINEERING; ARTICLE; AUTOIMMUNE DISEASE; BIOINFORMATICS; BIOTECHNOLOGY; GENE MAPPING; GENETIC DATABASE; GENETIC POLYMORPHISM; GENETIC VARIABILITY; HUMAN; IMMUNE RESPONSE; IMMUNE SYSTEM; IMMUNOGENETICS; IMMUNOTHERAPY; INFORMATION PROCESSING; INFORMATION SYSTEM; INTERNET; LEUKEMIA; LYMPHOMA; MAJOR HISTOCOMPATIBILITY COMPLEX; MEDICAL INFORMATION SYSTEM; MEDICAL RESEARCH; MOLECULAR EVOLUTION; MYELOMA; NUCLEOTIDE SEQUENCE; PHAGE DISPLAY; QUALITY CONTROL; SEQUENCE ANALYSIS; SEQUENCE DATABASE; STANDARDIZATION; THREE DIMENSIONAL IMAGING; VERTEBRATE;

ANIMALS; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; GENES, IMMUNOGLOBULIN; GENES, T-CELL RECEPTOR; HUMANS; IMMUNOGENETICS;

EID: 2642551345     PISSN: 13866338     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (58)

1. Barbié, V. and Lefranc, M.-P. (1998). The human immunoglobulin kappa variable (IGKV) genes and joining (IGKJ) segments. Exp. Clin. Immunogenet. 15, 171-183.
2. Benson, D. A., Karsch-Mizrachi, I., Lipman, D. J., Ostell, J. and Wheeler, D. L. (2003). GenBank. Nucleic Acids Res. 31, 23-27.
3. Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N. and Bourne, P. E. (2000). The Protein Data Bank. Nucleic Acids Res. 28, 235-242.
4. Bosc, N. and Lefranc, M.-P. (2003). IMGT Locus in Focus: The mouse (Mus musculus) T cell receptor alpha (TRA) and delta (TRD) variable genes. Dev. Comp. Immunol. 27, 465-497.
5. Chardes, T., Chapal, N., Bresson, D., Bes, C., Giudicelli, V., Lefranc, M.-P. and Peraldi-Roux, S. (2002). The human anti-thyroid peroxidase autoantibody repertoire in Graves and Hashimoto's autoimmune thyroid diseases. Immunogenetics 54, 141-157.
6. Chaume, D., Giudicelli, V. and Lefranc, M.-P. (2001). IMGT-XML 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, pp. 71-75.
7. Chaume, D., Giudicelli, V., Combres, K. and Lefranc, M.-P. (2003). IMGT-ONTOLOGY and IMGT-ML for Immunogenetics and immunoinformatics. European Congress in Computational Biology ECCB'2003, Sequence databases and Ontologies satellite event, Paris.
8. Chothia, C. and Lesk, A. M. (1987). Canonical structures for the hypervariable regions of immunoglobulins. J. Mol. Biol. 196, 901-917.
9. Duprat, E. and Lefranc, M.-P. (2003). IMGT standardization and analysis of V-LIKE, C-LIKE and G-LIKE-DOMAINS. European Congress in Computational Biology ECCB'2003, Paris.
10. Elemento, O. and Lefranc, M.-P. (2003). IMGT/PhyloGene: an online software package for phylogenetic analysis of immunoglobulin and T cell receptor genes. Dev. Comp. Immunol. 27, 763-779.
11. Folch, G. and Lefranc, M.-P. (2000a). The human T cell receptor beta variable (TRBV) genes. Exp. Clin. Immunogenet. 17, 42-54.
12. Folch, G. and Lefranc M.-P. (2000b). The human T cell receptor beta diversity (TRBD) and beta joining (TRBJ) genes. Exp. Clin. Immunogenet. 17, 107-114.
13. Folch, G., Scaviner, D., Contet, V. and Lefranc, M.-P. (2000). Protein displays of the human T cell receptor alpha, beta, gamma and delta variable and joining regions. Exp. Clin. Immunogenet. 17, 205-215.
14. Giudicelli, V. and Lefranc, M.-P. (1999). Ontology for Immunogenetics: IMGT-ONTOLOGY. Bioinformatics 12, 1047-1054.
15. Giudicelli, V., Chaume, D., Bodmer, J., Müller, W., Busin, C., Marsh, S., Bontrop, R., Lemaitre, M.; Malik, A. and Lefranc, M.-P. (1997). IMGT, the international ImMunoGeneTics database. Nucleic Acids Res. 25, 206-211.
16. Giudicelli, V., Chaume, D. and Lefranc, M.-P. (1998a). IMGT/LIGM-DB: A systematized approach for ImMunoGeneTics database coherence and data distribution improvement. Proceedings of the Sixth International Conference on Intelligent Systems for Molecular Biology. ISBM'98, pp. 59-68.
17. Giudicelli, V., Chaume, D., Mennessier, G., Althaus, H. H., Müller, W., Bodmer, J., Malik, A. and Lefranc, M.-P. (1998b). IMGT, the international ImMunoGeneTics database: a new Design for Immnnogenetics Data Access. In: B.Cesnik et al. (Eds.). Proceedings of the Ninth World Congress on Medical Informatics, MEDINFO' 98, IOS Press, Amsterdam. pp. 351-355.
18. Giudicelli, V., Protat, C. and Lefranc, M.-P. (2003). The IMGT strategy for the automatic annotation of IG and TR cDNA sequences: IMGT/Automat. European Congress in Computational Biology ECCB'2003, Paris.
19. Kabat, E. A., Wu, T. T., Perry, H. M., Gottesman, K. S. and Foeller, C. (1991). Sequences of proteins of immunological interest. National Institute of Health Publications, Washington D.C., USA. pp. 91-3242.
20. Kaas, Q. and Lefranc, M.-P. (2002). IMGT/3DStructure-DB for immnnoglobulin, T cell receptor and MHC structural data. European Congress in Computational Biology ECCB'2002, P72.
21. Kaas, Q. and Lefranc, M.-P. (2003). IMGT/StructuralQuery: a tool for structural data analysis of immunoglobulin and T cell receptor variable domains (http://imgt.cines.fr). European Congress in Computational Biology ECCB'2003, Paris.
22. Lefranc, M.-P. (1997). Unique database numbering system for immunogenetic analysis. Immunology Today 18, 509.
23. Lefranc, M.-P. (1998). IMGT (ImMunoGeneTics) Locus on Focus. A new section of Experimental and Clinical Immunogenetics. Exp. Clin. Immunogenet. 15, 1-7.
24. Lefranc, M.-P. (1999). The IMGT unique numbering for Immnnoglobulins, T cell receptors and Ig-like domains. The Immunologist 7, 132-136.
25. Lefranc, M.-P. (2000a). Nomenclature of the human immunoglobulin genes. Current Protocols in Immunology. Wiley J. and Sons, New York, USA. Supplement 40, A.1P.1-A.1P.37.
26. Lefranc, M.-P. (2000b). Nomenclature of the human T cell Receptor genes. Current Protocols in Immunology. Wiley J. and Sons, New York, USA. Supplement 40, A.1O.1-A.1O.23.
27. Lefranc, M.-P. (2000c). Locus maps and genomic repertoire of the human Ig genes. The Immunologist 8, 80-87.
28. Lefranc, M.-P. (2000d). Locus maps and genomic repertoire of the human T-cell receptor genes. The Immunologist 8, 72-79.
29. Lefranc, M.-P. (2000e). Web sites of Interest to Immunologists. Current Protocols in Immunology. Wiley J. and Sons, New York, USA. A.1J.1-A.1J.33.
30. Lefranc, M.-P. (2001a). IMGT, the international ImMunoGeneTics database. Nucleic Acids Res. 29, 207-209.
31. Lefranc, M.-P. (2001b). Nomenclature of the human immunoglobulin heavy (IGH) genes. Exp. Clin. Immunogenet. 18, 100-116.
32. Lefranc, M.-P. (2001c). Nomenclature of the human immunoglobulin kappa (IGK) genes. Exp. Clin. Immunogenet. 18, 161-174.
33. Lefranc, M.-P. (2001d). Nomenclature of the human immunoglobulin lambda (IGL) genes. Exp. Clin. Immunogenet. 18, 242-254.
34. Lefranc, M.-P. (2002). IMGT, the international ImMunoGeneTics database: a high-quality information system for comparative immunogenetics and immunology. Dev. Comp. Immunol. 26, 697-705.
35. Lefranc, M.-P. (2003a). IMGT, the international ImMunoGeneTics database® (http://imgt.cines.fr). Nucleic Acids Res. 31, 307-310.
36. Lefranc, M.-P. (2003b). IMGT® databases, web resources and tools for immunoglobulin and T cell receptor sequence analysis (http://imgt.cines.fr). Leukemia. 17, 260-266.
37. Lefranc, M.-P. and Lefranc G. (2001a). The Immunoglobulin FactsBook. Academic Press, London, UK, 458 pages, ISBN:012441351X.
38. Lefranc, M.-P., Lefranc, G. (2001b). The T cell receptor FactsBook. Academic Press, London, UK, 398 pages, ISBN:0124413528.
39. Lefranc, M.-P., Giudicelli, V., Busin, C., Bodmer, J., Müller, W., Bontrop, R., Lemaitre, M., Malik, A. and Chaume, D. (1998). IMGT, the international ImMunoGeneTics database. Nucleic Acids Res. 26, 297-303.
40. Lefranc, M.-P., Giudicelli, V., Ginestoux, C., Bodmer, J., Müller, W., Bontrop, R., Lemaitre, M., Malik, A., Barbié, V. and Chaume, D. (1999). IMGT, the international ImMunoGeneTics database. Nucleic Acids Res. 27, 209-212.
41. Lefranc, M.-P., Lefranc, G., Pommié, C., Ruiz, M., Giudicelli, V., Foulquier, E., Truong, L. and Thouvenin-Contet, V. (2003). IMGT, unique numbering for immunoglobulin and T cell receptor variable domains and Ig superfamily V-Like domains. Dev. Comp. Immunol. 27, 55-77.
42. Martinez-Jean, C., Folch, G. and Lefranc, M.-P. (2001). Nomenclature and Overview of the Mouse (Mus musculus and Mus sp.) Immunoglobulin Kappa (IGK) Genes. Exp. Clin. Immunogenet. 18, 255-279.
43. Miyazaki, S., Sugawara, H., Gojobori, T. and Tateno, Y. (2003). DNA Data Bank of Japan (DDBJ) in XML. Nucleic Acids Res. 31, 13-16.
44. Pallarès, N., Frippiat, J.P., Giudicelli, V. and Lefranc, M.-P. (1998). The human immunoglobulin lambda variable (IGLV) genes and joining (IGLJ) segments. Exp. Clin. Immunogenet. 15, 8-18.
45. Pallarès, N., Lefebvre, S., Contet, V., Matsuda, F. and Lefranc, M.-P. (1999). The human immunoglobulin heavy variable (IGHV) genes. Exp. Clin. Immunogenet. 16, 36-60.
46. Pommié, C, Levadoux, S., Sabatier, R., Lefranc, G. and Lefranc, M.-P. (2003). IMGT standardized criteria for statistical analysis of immunoglobulin V-REGION amino acid properties. European Congress in Computational Biology ECCB'2003, Paris.
47. Robinson, J., Malik, A., Parham, P., Bodmer, J. G. and Marsh, S. G. (2000). IMGT/HLA Database - a sequence database for the human major histocompatibility complex. Tissue Antigens 55, 280-287.
48. Robinson, J., Waller, M. J., Parham, P., de Groot, N., Bontrop, R., Kennedy, L. J., Stoehr, P. and Marsh, S. G. (2003). IMGT/HLA and IMGT/MHC: sequence databases for the study of the major histocompatibility complex. Nucleic Acids Res. 31, 311-314.
49. Ruiz, M., Pallarès, N., Contet, V., Barbié, V. and Lefranc, M.-P. (1999). The human immunoglobulin heavy diversity (IGHD) and joining (IGHJ) segments. Exp. Clin. Immunogenet. 16, 173-184.
50. Ruiz, M., Giudicelli, V., Ginestoux, C., Stoehr, P., Robinson, J., Bodmer, J., Marsh, S. G., Bontrop, R., Lemaitre, M., Lefranc, G., Chaume, D. and Lefranc, M.-P. (2000). IMGT, the international ImmunoGeneTics database. Nucleic Acids Res. 28, 219-221.
51. Ruiz, M and Lefranc, M.-P. (2002). IMGT gene identification and Colliers de Perles of human immunoglobulin with known 3D structures. Immunogenet. 53, 857-883.
52. Satow, Y., Cohen, G.H., Padlan, E.A., Davies, D.R. (1986). Phosphocholine binding immunoglobulin Fab. McPC603. J. Mol. Biol. 190, 593-604.
53. Scaviner, D., Barbié, V., Ruiz, M. and Lefranc, M.-P. (1999). Protein displays of the human immunoglobulin heavy, kappa and lambda variable and joining regions. Exp. Clin. Immunogenet. 16, 234-240.
54. Scaviner, D. and Lefranc, M.-P. (2000a). The human T cell receptor alpha variable (TRAV) genes. Exp. Clin. Immunogenet. 17, 83-96.
55. Scaviner, D. and Lefranc, M.-P. (2000b). The human T cell receptor alpha joining (TRAJ) genes. Exp. Clin. Immunogenet. 17, 97-106.
56. Stoesser, G., Baker, W., Van den Broek; A., Garcia-Pastor, M., Kanz, C., Kulikova, T., Leinonen, R., Lin, Q., Lombard, V., Lopez, R., Mancuso, R., Nardone, F., Stoehr, P., Tuli, M. A., Tzouvara, K. and Vaughan, R. (2003). The EMBL nucleotide sequence database: major new developments. Nucleic Acids Res. 31, 17-22.
57. Wain, H. M., Bruford, E. A., Lovering, R. C., Lush, M. J., Wright, M. W. and Povey, S. (2002). Guidelines for human gene nomenclature. Genomics 79, 464-470.
58. Williams, A. F. and Barclay, A. N. (1988). The immunoglobulin superfamily-domains for cell surface recognition. Annu. Rev. Immunol. 6, 381-405.