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carried out by the T cell receptor complex (TcR), a multisubunit transmembrane sur-
face complex made up of a T cell receptor (TR) and of the CD3 chains, that is associ-
ated, in the immunological synapse, to the CD4 or CD8 coreceptors, to the CD28 and
CTLA-4 costimulatory proteins, to the CD2 adhesion molecule, and to intracellular
kinases (Lefranc and Lefranc 2001). The TR directly binds the peptide/MHC complex
(pMHC), and activates the T cell through interactions with the CD3 and other compo-
nents of the TcR (Vasmatzis, Cornette, Sezerman, and DeLisi 1996a; Sim, Zerva,
Greene, and Gascoigne 1996; Kjer-Nielsen, Clements, Purcell, Brooks, Whisstock,
Burrows, McCluskey, and Rossjohn 2003). Three-dimensional (3D) structures of the
TR, pMHC, and TR/pMHC complexes provide an atomic description of their interac-
tions (Kaas, Ruiz, and Lefranc 2004; Kaas and Lefranc 2005).
Since 1989, IMGT
®
, the international ImMunoGeneTics information system
®
(Lefranc, Giudicelli, Kaas, Duprat, Jabado-Michaloud, Scaviner, Ginestoux,
Clément, Chaume, and Lefranc 2005c), http://imgt.cines.fr, has offered standardized
genetic and structural data on immunoglobulins (IG), TR, and MHC, and on related
proteins of the immune system (RPI) that belong to the immunoglobulin superfamily
(IgSF) and to the MHC superfamily (MhcSF). In order to facilitate data comparison
and cross-referencing between experiments from different laboratories whatever the
receptor, the chain type, the domain, or the species, IMGT
®
has developed IMGT-
ONTOLOGY (Giudicelli and Lefranc 1999), the first ontology in immunogenetics
and immunoinformatics.
Based on the IMGT-ONTOLOGY concepts, the IMGT Scientific chart
provides the controlled vocabulary and the annotation rules necessary for the iden-
tification, the description, the classification, and the numbering of the IG, TR,
MHC, and RPI (Lefranc 2004a; Lefranc, Giudicelli, Ginestoux, Bosc, Folch,
Guiraudou, Jabado-Michaloud, Magris, Scaviner, Thouvenin, Combres, Girod,
Jeanjean, Protat, Monod, Duprat, Kaas, Pommié, Chaume, and Lefranc 2004b;
Lefranc, Clément, Kaas, Duprat, Chastellan, Coelho, Combres, Ginestoux, Giudi-
celli, Chaume, and Lefranc 2005a). The IDENTIFICATION concept refers to the
IMGT standardized keywords that are essential for the sequence and 3D structure
assignments. The DESCRIPTION concept provides the IMGT standardized labels
used to describe structural and functional regions that compose IG, TR, MHC, and
RPI sequences and 3D structures. Standardized labels have also been defined to
characterize the three-dimensional assembly of domains and chains. The
CLASSIFICATION concept provides immunologists and geneticists with a stan-
dardized nomenclature per locus and per species. The human IG and TR gene
nomenclature elaborated by IMGT was approved by the Human Genome Organisa-
tion (HUGO) Nomenclature Committee, HGNC (Wain, Bruford, Lovering, Lush,
Wright, and Povey 2002), in 1999. The mouse IG and TR gene names with IMGT
reference sequences were provided by IMGT to HGNC and to the Mouse Genome
Database (MGD; Blake, Richardson, Bult, Kadin, and Eppig 2003) in July 2002.
The NUMEROTATION concept provides the IMGT unique numbering for the IG
and TR V-DOMAIN and the V-LIKE-DOMAIN of the IgSF proteins other than IG
or TR (Lefranc, Pommié, Ruiz, Giudicelli, Foulquier, Truong, Thouvenin-Contet,
and Lefranc 2003b), and for the IG and TR C-DOMAIN and the C-LIKE-DOMAIN
of the IgSF proteins other than IG or TR (Lefranc, Pommié, Kaas, Duprat, Bosc,
