Introduction ®  1 2 Marie-Paule Lefranc Laboratoire d'ImmunoGénétique Moléculaire (LIGM) immunoglobulins (IG) T cell receptors (TR) MHC RPI immunoglobulin superfamily (IgSF) MHC superfamily (MhcSF) 3 13 IG TR 12  molecular synthesis FactsBooks 3 4 6 14 19 15 17 20 22 18 23 24 ® 1 2 1 2 1 1 2 1 2 IMGT-ONTOLOGY 5 2 25 3 13 IMGT Scientific chart 2 IMGT-ML 26 Figure 1 ®    IMGT-ONTOLOGY concepts and IMGT Scientific chart rules IMGT Scientific chart 2 IDENTIFICATION CLASSIFICATION DESCRIPTION NUMEROTATION ORIENTATION OBTENTION 2 5 1 IMGT Marie-Paule page 1 Table 1 IMGT-ONTOLOGY concepts, IMGT Scientific chart rules and examples of IMGT expertised data concepts. IMGT-ONTOLOGY IMGT Scientific chart Examples of IMGT expertised data concepts [2] IDENTIFICATION keywords Species molecule type receptor type chain type gene type structure functionality specificity CLASSIFICATION Reference sequences  nomenclature group subgroup gene allele  Alignment of alleles  DESCRIPTION labels annotations Core Prototypes   2D and 3D structures NUMEROTATION IMGT unique numbering V- and V-LIKE-DOMAINs  C- and C-LIKE-DOMAINs  G- and G-LIKE-DOMAINs Protein displays  IMGT Colliers de Perles  FR-IMGT CDR-IMGT  ORIENTATION Orientation of genomic instances relative to each other Chromosome orientation  Locus orientation  Gene orientation  DNA strand orientation OBTENTION   5 2 1 7 13 IMGT sequence databases, tools and Web resources 2 14 18 Table 2 The IMGT sequence databases, sequence analysis tools and Web resources IMGT sequence databases IMGT sequence analysis tools IMGT Repertoire "Proteins and alleles" IMGT/LIGM-DB  IMGT/PRIMER-DB  IMGT/MHC-DB IMGT/V-QUEST  IMGT/JunctionAnalysis  IMGT/Allele-Align  IMGT/PhyloGene  IG and TR  RPI  IG and TR  MHC  RPI  IG and TR  RPI  Allotypes Isotypes (1) IMGT/Automat [29, 30] is an integrated internal IMGT Java tool which automatically performs the annotation of rearranged cDNA sequences that represent the half of the IMGT/LIGM-DB content. So far 7,418 human and mouse IG and TR cDNA sequences have been automatically annotated by the IMGT/Automat tool, with annotations being as reliable and accurate as those provided by a human annotator.  IMGT sequence databases IMGT/LIGM-DB IMGT/LIGM-DB 7 6 7    IMGT/PRIMER-DB IMGT/PRIMER-DB 1 IMGT/MHC-DB IMGT/MHC-DB 28 IMGT sequence analysis tools IMGT/V-QUEST 10 IMGT/JunctionAnalysis 11 IMGT/Allele-Align IMGT/PhyloGene 12 IMGT/V-QUEST IMGT/V-QUEST 10 IMGT reference directory 10 IMGT/V-QUEST Documentation IMGT/JunctionAnalysis IMGT/JunctionAnalysis 11 11 IMGT/JunctionAnalysis Documentation IMGT/Allele-Align IMGT/Allele-Align IMGT/PhyloGene IMGT/PhyloGene 12 12 IMGT/PhyloGene Documentation IMGT sequence Web resources 2 31 IMGT gene databases, tools and Web resources 2 3 Table 3 The IMGT gene database, genome analysis tools and Web resources IMGT genome database [1] IMGT genome analysis tools IMGT Repertoire "Locus and genes" IMGT/GENE-DB IMGT/LocusView  IMGT/GeneView  IMGT/GeneSearch  IMGT/CloneSearch  IMGT/GeneInfo Chromosomal localizations  Locus representations  Locus description  Gene exon/intron organization  Gene exon/intron splicing sites  Gene tables  Potential germline repertoires  Lists of genes  Correspondence between nomenclatures IMGT Index IMGT Education IMGT Lexique Aide-mémoire Tutorials Questions and answers The IMGT Medical page The IMGT Veterinary page The IMGT Biotechnology page The IMGT Immunoinformatics page IMGT Bloc-notes Interesting links  IMGT/GENE-DB, the IMGT gene database IMGT/GENE-DB 8 Homo sapiens Mus musculus Mus cookii Mus pahari Mus spretus Mus saxicola Mus minutoïdes 3 4 27 8 32 33 34 35 2 7 IMGT gene analysis tools IMGT/LocusView IMGT/GeneView IMGT/GeneSearch IMGT/CloneSearch IMGT/GeneInfo IMGT/LocusView IMGT/GeneView IMGT/GeneSearch IMGT/CloneSearch IMGT/GeneInfo 13 IMGT gene Web resources 3 4 3 IMGT structure database, tool and Web resources 4 14 18 Table 4 IMGT structure database, analysis tool and Web resources IMGT structural database [1] IMGT structural analysis tool [1] IMGT Repertoire "2D and 3D structures" IMGT/3D structure-DB IMGT/StructuralQuery IG and TR  MHC  RPI  IMGT classes for amino acid characteristics   3D representations  3 4 14 16 2 20 15 16 21 2B 17 3 18 Figure 2   Figure 3 IMGT Colliers de Perles of the two G-DOMAINs of MHC class I (A) and of MHC class II (B) proteins (codes PDB 1bd2 and 1aqd, respectively, in IMGT/3Dstructure-DB [9]). The IMGT Collier de Perles of a G-DOMAIN is based on the IMGT unique numbering for G-DOMAIN and G-LIKE-DOMAIN [18]. (A) The two MHC-I G-DOMAINs, G-ALPHA1 (top) and G-ALPHA2 (bottom), form the groove of the MHC class I chain (I-ALPHA). (B) The two MHC-II G-DOMAINs, G-ALPHA (top) of the MHC class II alpha chain (II-ALPHA) and G-BETA (bottom) of the MHC class II beta chain (II-BETA), form the groove of the MHC class II protein [36]. Amino acids are shown in the one-letter abbreviation. Hatched circles correspond to missing positions according to the IMGT unique numbering [18]. Positions in colour correspond to the IMGT contact sites provided, for each peptide/MHC 3D structure, in IMGT/3Dstructure-DB [36].  IMGT/3Dstructure-DB, the IMGT 3D structure database IMGT/3Dstructure-DB 9 9 36 37 38 16 18 16 19 IMGT/3Dstructure-DB Domain contacts IMGT/3Dstructure-DB Residue@Position contacts 37 IMGT/3Dstructure-DB Documentation IMGT/StructuralQuery tool IMGT/StructuralQuery 9 37 IMGT structure Web resources 16 19 16 31 eleven IMGT classes 31 Conclusion  2 2 25 3 4 39 42  Citing IMGT 1