IMGT-ONTOLOGY, IMGT Databases, Tools, and Web Resources for Immunoinformatics - Immunoinformatics - page 4

Veterinary page, The IMGT Biotechnology page, IMGT Index], and external
links [IMGT Bloc-notes (The IMGT Immunoinformatics page, Interesting links), and
Other accesses (SRS, BLAST)]. Despite the heterogeneity of these different compo-
nents, all data in the IMGT ® information system are expertly annotated. The accu-
racy, the consistency, and the integration of the IMGT ® data, as well as the coher-
ence between the different IMGT ® components (databases, tools, and Web
resources) are based on IMGT-ONTOLOGY (Giudicelli and Lefranc 1999), the first
ontology in the domain, which provides a semantic specification of the terms to be
used in immunogenetics and immunoinformatics, and thus allows the management of
immunogenetic knowledge for all vertebrate species. IMGT-ONTOLOGY comprises
seven main concepts: IDENTIFICATION, CLASSIFICATION, DESCRIPTION,
NUMEROTATION, LOCALIZATION, ORIENTATION, and OBTENTION (Giu-
dicelli and Lefranc 1999; Lefranc et al. 2004a; Lefranc et al. 2004b; Lefranc et al.
2005a). Standardized keywords, standardized IG and TR gene nomenclature, stan-
dardized labels, the IMGT unique numbering, annotation rules, and standardized
origin/methodology were defined, respectively, based on these seven main concepts.
IMGT-ONTOLOGY concepts are available for biologists and IMGT ® users in
the IMGT Scientific chart and formalized for computer scientists in IMGT-ML using
XML (Extensible Markup Language) Schema. The IMGT Scientific chart (Lefranc,
Giudicelli, Ginestoux, Bodmer, Müller, Bontrop, Lemaitre, Malik, Barbié, and
Chaume 1999) comprises controlled vocabulary and annotation rules for data and
knowledge management of the IG, TR, and MHC of vertebrate species, and of the
RPI of any species, that belong to IgSF and MhcSF. All IMGT ® data are expertly
annotated according to the IMGT Scientific chart rules. The IMGT Scientific chart is
available as a section of the IMGT Web resources (IMGT Marie-Paule page). These
HTML pages are devoted to biologists, IMGT users, and IMGT annotators. Exam-
ples of IMGT expert data concepts, derived from the IMGT Scientific chart rules,
correspond to section titles and subtitles in IMGT Repertoire (Lefranc et al. 2004a;
Lefranc et al. 2004b).
IMGT-ML (Chaume, Giudicelli, and Lefranc 2001; Chaume, Giudicelli, Combres,
and Lefranc 2003; Chaume, Giudicelli, Combres, Ginestoux, and Lefranc 2005) is the
formalization of IMGT-ONTOLOGY using XML Schema for interoperability with other
information systems. IMGT ® components (databases, tools, and IMGT Repertoire Web
resources) have been developed according to three main biological approaches. The
IMGT ® genomic approach is gene-centered focusing on the study of the genes within
their loci and on the chromosomes. The IMGT ® genetic approach refers to the study of
the genes in relation to sequence polymorphisms and mutations and their expression,
specificity, and evolution. The IMGT ® structural approach refers to the study of 2D and
3D structures of the IG, TR, MHC, and RPI, and to the antigen or ligand binding charac-
teristics in relation to protein functions, polymorphisms, and evolution. IMGT-
Choreography, based on the Web service architecture paradigm, will enable significant
biological and clinical requests addressing the entire IMGT ® information system.