title: IMGT-Kaleidoscope, the formal IMGT-ONTOLOGY paradigm.
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 which 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. Through the example of the IG molecular synthesis, the concepts generated from the "IDENTIFICATION", "DESCRIPTION", "CLASSIFICATION" and "NUMEROTATION" axioms are detailed with their main instances and semantic relations. The axioms have been essential for the conceptualization of the molecular immunogenetics knowledge and can be used to generate concepts for multi scale 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: the international ImMunoGeneTics information system, Université Montpellier 2, 34396 Montpellier Cedex 5, France.
authors.forename: Patrice
authors.initials: P
authors.lastname: Duroux
authors.forename: Quentin
authors.initials: Q
authors.lastname: Kaas
authors.forename: Xavier
authors.initials: X
authors.lastname: Brochet
authors.forename: Jérôme
authors.initials: J
authors.lastname: Lane
authors.forename: Chantal
authors.initials: C
authors.lastname: Ginestoux
authors.forename: Marie-Paule
authors.initials: MP
authors.lastname: Lefranc
authors.forename: Véronique
authors.initials: V
authors.lastname: Giudicelli
mesh_terms: D000595:Amino Acid Sequence; D000906:Antibodies / Q000737:chemistry / Q000235:genetics; D019295:Computational Biology; D003628:Database Management Systems; D030541:Databases, Genetic; D006801:Humans; D007125:Immunogenetics; D007136:Immunoglobulins / Q000737:chemistry / Q000235:genetics; D008969:Molecular Sequence Data; D011487:Protein Conformation; D012984:Software; D012985:Software Design
chemical_list: D000906:Antibodies; D007136:Immunoglobulins