title: IMGT, a system and an ontology that bridge biological and computational spheres in bioinformatics.
abstract: IMGT, the international ImMunoGeneTics information system (http://imgt.cines.fr), is the reference in immunogenetics and immunoinformatics. IMGT standardizes and manages the complex immunogenetic data that include the immunoglobulins (IG) or antibodies, the T cell receptors (TR), the major histocompatibility complex (MHC) and the related proteins of the immune system (RPI), which belong to the immunoglobulin superfamily (IgSF) and the MHC superfamily (MhcSF). The accuracy and consistency of IMGT data and the coherence between the different IMGT components (databases, tools and Web resources) are based on IMGT-ONTOLOGY, the first ontology for immunogenetics and immunoinformatics. IMGT-ONTOLOGY manages the immunogenetics knowledge through diverse facets relying on seven axioms, 'IDENTIFICATION', 'DESCRIPTION', 'CLASSIFICATION', 'NUMEROTATION', 'LOCALIZATION', 'ORIENTATION' and 'OBTENTION', that postulate that objects, processes and relations have to be identified, described, classified, numerotated, localized, orientated, and that the way they are obtained has to be determined. These axioms constitute the Formal IMGT-ONTOLOGY, also designated as IMGT-Kaleidoscope. These axioms have been essential for the conceptualization of the molecular immunogenetics knowledge and for the creation of IMGT. Indeed all the components of the IMGT integrated system have been developed, based on standardized concepts and relations, thus allowing IMGT to bridge biological and computational spheres in bioinformatics. The same axioms can be used to generate concepts for multi-scale level approaches at the molecule, cell, tissue, organ, organism or population level, emphasizing the generalization of the application domain. In that way the Formal IMGT-ONTOLOGY represents a paradigm for the elaboration of ontologies in system biology.
authors.affiliation: IMGT, Laboratoire d'ImmunoGénétique Moléculaire, LIGM, UPR CNRS 1142, IGH, 141 rue de la Cardonille, 34396 Montpellier Cedex 5, France. Marie-Paule.Lefranc@igh.cnrs.fr
authors.forename: Marie-Paule
authors.initials: MP
authors.lastname: Lefranc
authors.forename: Véronique
authors.initials: V
authors.lastname: Giudicelli
authors.forename: Laetitia
authors.initials: L
authors.lastname: Regnier
authors.forename: Patrice
authors.initials: P
authors.lastname: Duroux
mesh_terms: D019295:Computational Biology / Q000639:trends*; D003628:Database Management Systems; D030541:Databases, Genetic; D007125:Immunogenetics / Q000379:methods*; D016247:Information Storage and Retrieval / Q000379:methods*; D038622:Internationality; D020407:Internet; D049490:Systems Biology / Q000379:methods*; D018511:Systems Integration