Imgt-ontology 2012

IMGT® the international ImMunoGenetics information system® Université Montpellier 2, Laboratoire d'ImmunoGénétique Moléculaire, Institut de Génétique Humaine, UPR CNRS Montpellier, France.
Frontiers in Genetics 05/2012; 3:79. DOI: 10.3389/fgene.2012.00079
Source: PubMed

ABSTRACT Immunogenetics is the science that studies the genetics of the immune system and immune responses. Owing to the complexity and diversity of the immune repertoire, immunogenetics represents one of the greatest challenges for data interpretation: a large biological expertise, a considerable effort of standardization and the elaboration of an efficient system for the management of the related knowledge were required. IMGT®, the international ImMunoGeneTics information system® ( has reached that goal through the building of a unique ontology, IMGT-ONTOLOGY, which represents the first ontology for the formal representation of knowledge in immunogenetics and immunoinformatics. IMGT-ONTOLOGY manages the immunogenetics knowledge through diverse facets that rely on the seven axioms of the Formal IMGT-ONTOLOGY or IMGT-Kaleidoscope: "IDENTIFICATION," "DESCRIPTION," "CLASSIFICATION," "NUMEROTATION," "LOCALIZATION," "ORIENTATION," and "OBTENTION." The concepts of identification, description, classification, and numerotation generated from the axioms led to the elaboration of the IMGT(®) standards that constitute the IMGT Scientific chart: IMGT®standardized keywords (concepts of identification), IMGT® standardized labels (concepts of description), IMGT® standardized gene and allele nomenclature (concepts of classification) and IMGT unique numbering and IMGT Collier de Perles (concepts of numerotation). IMGT-ONTOLOGY has become the global reference in immunogenetics and immunoinformatics for the knowledge representation of immunoglobulins (IG) or antibodies, T cell receptors (TR), and major histocompatibility (MH) proteins of humans and other vertebrates, proteins of the immunoglobulin superfamily (IgSF) and MH superfamily (MhSF), related proteins of the immune system (RPI) of vertebrates and invertebrates, therapeutic monoclonal antibodies (mAbs), fusion proteins for immune applications (FPIA), and composite proteins for clinical applications (CPCA).

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    • "A high throughput version, IMGT/HighV-QUEST [17,21,22], analyzes up to 500,000 IG or T cell receptors (TR) sequences. High quality results are based on the standardized concepts of IMGT-ONTOLOGY [23], that are generated from the axioms of CLASSIFICATION (standardized nomenclature) [24], DESCRIPTION (standardized labels) [25], NUMEROTATION (IMGT unique numbering [26-28], IMGT Collier de Perles [29]). IMGT/HighV-QUEST results are identical to those obtained by IMGT/V-QUEST online, except for the IMGT Collier de Perles. "
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    ABSTRACT: Background Immunoglobulin (IG) complementarity determining region (CDR) includes VH CDR1, VH CDR2, VH CDR3, VL CDR1, VL CDR2 and VL CDR3. Of these, VH CDR3 plays a dominant role in recognizing and binding antigens. Three major mechanisms are involved in the formation of the VH repertoire: germline gene rearrangement, junctional diversity and somatic hypermutation. Features of the generation mechanisms of VH repertoire in humans and mice share similarities while VH CDR3 amino acid (AA) composition differs. Previous studies have mainly focused on germline gene rearrangement and the composition and structure of the CDR3 AA in humans and mice. However the number of AA changes due to somatic hypermutation and analysis of the junctional mechanism have been ignored. Methods Here we analyzed 9,340 human and 6,657 murine unique productive sequences of immunoglobulin (IG) variable heavy (VH) domains derived from IMGT/LIGM-DB database to understand how VH CDR3 AA compositions significantly differed between human and mouse. These sequences were identified and analyzed by IMGT/HighV-QUEST (, including gene usage, number of AA changes due to somatic hypermutation, AA length distribution of VH CDR3, AA composition, and junctional diversity. Results Analyses of human and murine IG repertoires showed significant differences. A higher number of AA changes due to somatic hypermutation and more abundant N-region addition were found in human compared to mouse, which might be an important factor leading to differences in VH CDR3 amino acid composition. Conclusions These findings are a benchmark for understanding VH repertoires and can be used to characterize the VH repertoire during immune responses. The study will allow standardized comparison for high throughput results obtained by IMGT/HighV-QUEST, the reference portal for NGS repertoire.
    Theoretical Biology and Medical Modelling 07/2014; 11(1):30. DOI:10.1186/1742-4682-11-30 · 0.95 Impact Factor
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    • "Amongst others things, this allows linkage of anatomical structures across species, allowing inferences of homology and comparison of features such as gene and protein expression across species. Another cross-species ontology, and one that complements work on anatomy, is described by Giudicelli and Lefranc (2012). They provide an update on the IMGT-Ontology which is an ontology of immunogenetics and immunoinformatics used in the international ImMunoGeneTics information system® ( "
    Frontiers in Genetics 02/2014; 5:18. DOI:10.3389/fgene.2014.00018
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    ABSTRACT: T and B cell repertoires are collections of lymphocytes, each characterised by its antigen-specific receptor. We review here classical technologies and analysis strategies developed to assess Immunoglobulin (IG) and T cell receptor (TR) repertoire diversity, and describe recent advances in the field. First, we describe the broad range of available methodological tools developed in the past decades, each of which answering different questions and showing complementarity for progressive identification of the level of repertoire alterations: global overview of the diversity by flow cytometry, IG repertoire descriptions at the protein level for the identification of IG reactivities, IG/TR CDR3 spectratyping strategies, and related molecular quantification or dynamics of T/B cell differentiation. Additionally, we introduce the recent technological advances in molecular biology tools allowing deeper analysis of IG/TR diversity by next-generation sequencing (NGS), offering systematic and comprehensive sequencing of IG/TR transcripts in a short amount of time. NGS provides several angles of analysis such as clonotype frequency, CDR3 diversity, CDR3 sequence analysis, V allele identification with a quantitative dimension, therefore requiring high-throughput analysis tools development. In this line, we discuss the recent efforts made for nomenclature standardisation and ontology development. We then present the variety of available statistical analysis and modelling approaches developed with regards to the various levels of diversity analysis, and reveal the increasing sophistication of modelling approaches. To conclude, we provide some examples of recent mathematical modelling strategies and perspectives that illustrate the active rise of a ìnext-generationî of repertoire analysis.
    Frontiers in Immunology 11/2013; 4. DOI:10.3389/fimmu.2013.00413
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