Information Technology Reference
In-Depth Information
1.3 IMGT-ONTOLOGY Concepts and IMGT
®
Components
for Genomics
1.3.1 IMGT
®
Genome Database
The IMGT
®
genomic approach refers to the study of the genes within their loci and
on the chromosomes. Genomic data are managed in IMGT/GENE-DB, which is the
comprehensive IMGT
®
genome database, created by LIGM, Montpellier, France, on
the Web since January 2003 (Giudicelli, Chaume,
and Lefranc
2005).
In March 2007, IMGT/GENE-DB contained 1512 genes and 2461 alleles (673 IG
and TR genes and 1215 alleles from
Homo sapiens
, and 839 IG and TR genes and
1,246 alleles from
Mus musculus, Mus cookii, Mus pahari, Mus spretus, Mus saxi-
cola, Mus minutoïdes
). All human and mouse IG and TR genes are available in
IMGT/GENE-DB. Based on the IMGT
®
CLASSIFICATION concept, all the human
IMGT
®
gene names (Lefranc and Lefranc 2001a; Lefranc and Lefranc 2001b;
Lefranc 2000a; Lefranc 2000b; Lefranc 2000c; Lefranc 2000d) were approved by the
HUman Genome Organisation (HUGO) Nomenclature Committee HGNC in 1999
(Wain, Bruford, Lovering, Lush, Wright, and Povey 2002), and entered in
IMGT/GENE-DB (Giudicelli et al. 2005), Genome DataBase GDB, Canada
(Letovsky, Cottingham, Porter, and Li 1998), LocusLink at NCBI, USA (Pruitt and
Maglott 2001), and GeneCards (Safran, Chalifa-Caspi, Shmueli, Olender, Lapidot,
Rosen, Shmoish, Peter, Glusman, Feldmesser, Adato, Peter, Khen, Atarot, Groner,
and Lancet 2003). Reciprocal links exist between IMGT/GENE-DB and the general-
ist nomenclature (HGNC) and genome databases (GDB, Entrez Gene at NCBI, and
GeneCards). The mouse IG and TR gene names (Martinez and Lefranc 1998; Bosc
and Lefranc 2000; Bosc, Contet, and Lefranc 2001; Martinez, Folch, and Lefranc
2001; Bosc and Lefranc 2003) with IMGT reference sequences were provided by
IMGT
®
to HGNC and to the Mouse Genome Database MGD (Blake, Richardson,
Bult, Kadin, Eppig, and Mouse Genome Database Group 2003) in July 2002. Que-
ries in IMGT/GENE-DB can be performed according to IG and TR gene classifica-
tion criteria, and IMGT reference sequences have been defined for each allele of
each gene based on one or, whenever possible, several of the following criteria:
germline sequence, first sequence published, longest sequence, mapped sequence
(Lefranc et al. 1999). IMGT/GENE-DB interacts dynamically with IMGT/LIGM-DB
(Giudicelli, Ginestoux, Folch, Jabado-Michaloud, Chaume, and Lefranc 2006) to
download and display gene-related sequence data. This is the first example of an
interaction between IMGT
®
databases using the CLASSIFICATION concept.
1.3.2 IMGT
®
Genome Analysis Tools
The IMGT
®
genome analysis on-line tools comprise IMGT/LocusView,
IMGT/GeneView, IMGT/GeneSearch, IMGT/CloneSearch, IMGT/GeneInfo, and
IMGT/GeneFrequency. IMGT/LocusView and IMGT/GeneView manage the locus
organization and the gene location and provide display of physical maps for the human
IG, TR, and MHC loci and for the mouse TRA/TRD locus. IMGT/LocusView allows
