IMGT Index
Ontology (IMGT-ONTOLOGY)
An ontology is a concise and non ambiguous description of the more significant and
relevant concepts in a application domain.
IMGT-ONTOLOGY [1], is the first ontology which allows the management of the immunogenetics
knowledge for all vertebrate species.
- Giudicelli, V. and Lefranc, M.-P. "Ontology for Immunogenetics: IMGT-ONTOLOGY",
Bioinformatics, 15, 1047-1054 (1999)
PMID: 10745995, LIGM:221,
- Lefranc, M.-P. et al. "IMGT-ONTOLOGY for Immunogenetics and Immunoinformatics, http://www.imgt.org", In Silico Biology, 2004, 4, 17-29. Epub 2003, 4, 0004, LIGM:278, PMID: 15089751
- Lefranc, M.-P. et al. "IMGT-Choreography for Immunogenetics and Immunoinformatics", In Silico Biology, 2005, 5, 45-60, Epub 2005, 5, 0006, 24 Dec 2004, LIGM:294, PMID: 15972004
- Duroux, P. et al., "IMGT-Kaleidoscope, the Formal IMGT-ONTOLOGY paradigm", Biochimie, 90, 570-583 (2008). Epub 2007 Sep11. PMID: 17949886
Introduction
The molecular synthesis and genetics of the immunoglobulin (IG) and T cell receptor (TR) chains and the polymorphism of the MHC are particularly complex, and therefore one of the first tasks of IMGT-ONTOLOGY comprises a formal specification of the terms to be used in the domain of immunogenetics and bioinformatics [2-8].
IMGT-ONTOLOGY includes a controlled vocabulary and annotation rules which are indispensable to ensure accuracy, consistency and coherence in IMGT® [5]. IMGT-ONTOLOGY allows scientists and clinicians to use identical terms with the same meaning. This provides a semantic repository to be included in more general molecular biology ontologies, and will be therefore of a great help to increase interoperability between specialist and generalist databases.
IMGT-ONTOLOGY axioms and concepts
Seven IMGT-ONTOLOGY axioms have been defined [1,6-8]: 'IDENTIFICATION', 'DESCRIPTION', 'CLASSIFICATION', 'NUMEROTATION', 'LOCALIZATION', 'ORIENTATION', and 'OBTENTION'. They constitute the Formal IMGT-ONTOLOGY or IMGT-Kaleidoscope [9,10].
The IMGT-ONTOLOGY concepts of identification, description, classification, numerotation, localization, orientation and obtention were generated from these axioms and described in ref. [1,2,6-8].
Concepts of interaction that are necessary to define interactions between entities were defined based on these concepts.
- Figures illustrating some of the IMGT-ONTOLOGY axioms and concepts (IMGT Education).
- Correspondence between the IMGT-ONTOLOGY axioms and the IMGT Scientific chart rules (IMGT Scientific chart).
- IMGT-ONTOLOGY and IMGT Scientific chart rules and examples in ImmunoGrid
- ImmunoGrid, The European Virtual Human Immune System Project (IST-2004-028069)
- D1.2 Scientific chart rules
and ontologies report
Marie-Paule Lefranc, François Ehrenmann, Patrice Duroux and Véronique Giudicelli
Describes the IMGT-ONTOLOGY concepts of identification, description and classification at the molecular level, generated from the IDENTIFICATION, DESCRIPTION and CLASSIFICATION axioms of the Formal IMGT-ONTOLOGY (IMGT-Kaleidoscope). - D1.3 IMGT unique numbering and
controlled vocabularies report
Marie-Paule Lefranc, François Ehrenmann, Patrice Duroux and Véronique Giudicelli
Describes the IMGT-ONTOLOGY concepts of numerotation at the molecular level, generated from the NUMEROTATION axiom of the Formal IMGT-ONTOLOGY (IMGT-Kaleidoscope). Two major concepts of numerotation, IMGT unique numbering and IMGT Collier de Perles, are used to define the V, C and G type domains. - D1.4 New concepts of "INTERACTION"
and "LOCALIZATION" and deduced IMGT Scientific chart rules report
Marie-Paule Lefranc, François Ehrenmann, Véronique Giudicelli and Patrice Duroux
Describes IMGT-ONTOLOGY concepts of interaction for the characterization of antigen/receptor and domain interactions. Two major concepts of interaction, pMHC contact site and IMGT Residue@Position, are used, respectively, to define peptide/MHC interactions, and more generally antigen/receptor and domain interactions.
IMGT-ONTOLOGY concepts and data are described with XML Schema in IMGT-ML.
| [1] |
Giudicelli, V. and Lefranc, M.-P., Bioinformatics, 15, 1047-1054 (1999)
PMID: 10745995,
|
| [2] | Guidicelli, V. Ph D thesis, Université Montpellier II (11 December 1998) Conception d'une ontologie en Immunogénétique et développement d'un module de cohérence pour le contrôle de qualité de IMGT/LIGM-DB. |
| [3] | Guidicelli, V. et al., MEDINFO 98, Cesnik, B. et al (Eds), Amsterdam, IOS Press, 351-355 (1998) PMID: 10384476 |
| [4] | Giudicelli, V., et al., Proceedings of the Sixth International Conference on Intelligent Systems for Molecular Biology, ISBM-98, 59-68 (1998) PMID: 9783210 |
| [5] | Giudicelli, V. and Lefranc, M.-P., "IMGT-ONTOLOGY: gestion et découverte de connaissances au sein d'IMGT", In: Extraction et gestion des connaissances EGC 2003, Extraction des connaissances et apprentissage, Revue des Sciences et Technologies de l'Information RSTI, Ed. Lavoisier, Series RIA-ECA, 17, 13-23 (2003) |
| [6] | Lefranc, M.-P., et al., In Silico Biology, 2004, 4, 17-29. Epub 2003, 4, 0004. PMID: 15089751 |
| [7] | Lefranc, M.-P. et al., In Silico Biology, 2005, 5, 45-60, Epub 2005, 5, 0006, 24 Dec 2004. PMID: 15972004 |
| [8] | Lefranc, M.-P. et al., Immunome Res., 2005, 1, 3, 20 September 2005, doi:10.1186/1745-7580-1-3, PMID: 16305737 |
| [9] | Giudicelli, V. and Lefranc, M.-P., Le Paradigme IMGT-ONTOLOGY. Chap. 6, In: Standards pour la Biologie Systémique, ECRIN-OMNISCIENCE (in press) |
| [10] | Giudicelli, V. et al., IMGT-Kaleidoscope, the Formal IMGT-ONTOLOGY paradigm. |
- The second Workshop on Ontology and Genome
Workshop on Ontology and Data Integration for Biology - May 20-22, 2003, Tokyo, Japan
IMGT Posters and diaporama
FAQ: How is IMGT-ONTOLOGY related to Gene Ontology (GO) ?
IMGT-ONTOLOGY:
- is specialized on immunoglobulins (IG), T cell receptors (TR), major histocompatibility complex (MHC), immunoglobulin superfamily (IgSF), MHC superfamily (MhcSF), and related proteins of the immune system (RPI).
- is complementary to GO for these proteins, the IMGT-ONTOLOGY concepts starting, for the IG, TR and MHC, at the following GO concepts:
| IMGT-ONTOLOGY | GO |
|---|---|
| Immunoglobulin | GO:0019814 |
| T cell receptor | GO:0042101 |
| Major histocompatibility complex | GO:0042611 |
and their children:
| IMGT-ONTOLOGY | GO |
|---|---|
| alpha-beta T cell receptor | GO:0042105 |
| MHC class I | GO:0042612 |
| MHC class II | GO:0042613 |
These six entries are the only ones that are shared by IMGT-ONTOLOGY and GO, emphasizing the complementarity of the two ontologies. Note that the GO definitions (immunoglobulin complex, T cell receptor complex, MHC protein complex, respectively) are misleading owing to the use of the word "complex" and therefore not used by IMGT.
FAQ: How is IMGT-ONTOLOGY related to Sequence Ontology (SO) ?
- Sixty-four of the IMGT/LIGM-DB standardized labels for nucleotide sequences are used in Sequence Ontology (SO).
- IMGT Labels are part of the IMGT-ONTOLOGY DESCRIPTION axiom. They also include IMGT/PROTEIN-DB and IMGT/3Dstructure-DB labels which are not dealt within SO.
Last updated: Friday, 15-Jan-2010 17:12:50 CET
Authors: Véronique Giudicelli and Marie-Paule Lefranc
Editors: Manuel Ruiz and Chantal Ginestoux
Contact: Marie-Paule Lefranc
Software material and data coming from IMGT server may be used for academic research only,
provided that it is referred to IMGT®, and cited as "IMGT®, the international ImMunoGeneTics
information system® http://www.imgt.org
(founder and director: Marie-Paule Lefranc, Montpellier, France)."
References to cite:
Lefranc, M.-P. et al.,
Nucleic Acids Research, 27, 209-212 (1999)
Cover of NAR;
Ruiz, M. et al.,
Nucleic Acids Research, 28, 219-221 (2000);
Lefranc, M.-P.,
Nucleic Acids Research, 29, 207-209 (2001);
Lefranc, M.-P.,
Nucleic Acids Res., 31, 307-310 (2003);
Lefranc, M.-P. et al.,
In Silico Biol., 5, 0006 (2004) [Epub],
5, 45-60 (2005);
Lefranc, M.-P. et al.,
Nucleic Acids Res., 33, D593-D597 (2005)
Full text;
Lefranc, M.-P. et al.,
Nucleic Acids Research 2009 37: D1006-D1012; doi:10.1093/nar/gkn838
Full text.
For any other use please contact Marie-Paule Lefranc
Marie-Paule.Lefranc@igh.cnrs.fr.
IMGT founder and director: Marie-Paule Lefranc
Marie-Paule.Lefranc@igh.cnrs.fr
Bioinformatics manager: Véronique Giudicelli
Veronique.Giudicelli@igh.cnrs.fr
Computer manager: Patrice Duroux
Patrice.Duroux@igh.cnrs.fr
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