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Ontology (IMGT-ONTOLOGY)

An ontology is a concise and non ambiguous description of the more significant and relevant concepts in an application domain.
IMGT-ONTOLOGY [1-23], is the first ontology which allows the management of the immunogenetics knowledge for all vertebrate species with jaws (gnathostomata) [24, 25].

The IMGT-ONTOLOGY axioms and concepts led to a new science, immunoinformatics, created in 1989 by IMGT® at the interface between immunogenetics and bioinformatics, for the study of the antigen receptors of the adaptive immune response, the immunoglobulins (IG) or antibodies and the T cell receptors (TR) [24].

Citing IMGT-ONTOLOGY
Giudicelli, V. and Lefranc, M.-P. Ontology for Immunogenetics: IMGT-ONTOLOGY. Bioinformatics, 15, 1047-1054 (1999) PMID: 10745995, LIGM:221 pdficon
Giudicelli, V. and Lefranc, M.-P., IMGT-ONTOLOGY 2012. Online access Front Genet. 3:79. doi: 10.3389/fgene.2012.00079. Epub 2012 May 23 (2012) PMID:22654892
Lefranc, M-P. Immunoglobulin (IG) and T cell receptor genes (TR): IMGT®, and the birth and rise of immunoinformatics. Front Immunol. Feb 05;5:22 (2014). doi: 10.3389/fimmu.2014.00022. Open access. PMID: 24600447 LIGM: 429

Introduction

The molecular synthesis and genetics of the immunoglobulin (IG) and T cell receptor (TR) chains and the polymorphism of the MH 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, of the rules for IMGT gene nomenclature and for the numbering of amino acids and codons [2-5,17-23].

IMGT-ONTOLOGY includes a controlled vocabulary and annotation rules which are indispensable to ensure accuracy, consistency and coherence of immunogenetics data with scientific knowledge [6-14,16] in IMGT®, the international ImMunoGeneTics information system® [24,25]. 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: 'IDENTIFICATION' [18], 'DESCRIPTION' [19], 'CLASSIFICATION' [20], 'NUMEROTATION' [21,22], 'LOCALIZATION', 'ORIENTATION', and 'OBTENTION'. They constitute the Formal IMGT-ONTOLOGY or IMGT-Kaleidoscope [15].

The IMGT-ONTOLOGY concepts of identification, description, classification, numerotation, localization, orientation and obtention were generated from these axioms and described in the references [1-21].

The concepts of interaction that are necessary to define interactions between entities were defined based on these concepts.

Other IMGT Web resources:

IMGT-ONTOLOGY in Encyclopedia of Systems Biology

Encyclopedia of Systems Biology, New York: Springer Science+Business Media, LLC, 2013, Dubitzky W., Wolkenhauer O., Cho K.-H. and H. Yokota H. (eds.). 4 chapters (titles in bold) and 41 essays on IMGT-ONTOLOGY

C
IMGT-ONTOLOGY, ChainType (Lefranc M.-P., p. 972-973)
IMGT-ONTOLOGY, CLASSIFICATION axiom (Lefranc M.-P., p. 973-974)
Complementarity determining region (CDR-IMGT) (Lefranc M.-P., p. 451-453)
IMGT-ONTOLOGY, ConfigurationType (Lefranc M.-P., p. 974-975)
Constant (C) domain (Lefranc M.-P., p. 487-489)
Constant (C) gene (Lefranc M.-P., p. 489-490)
Conventional gene (Lefranc M.-P., p. 499-500)
D
IMGT-ONTOLOGY, DESCRIPTION axiom (p. 975-976)
Diversity (D) gene (Lefranc M.-P., p. 606-607)
IMGT-ONTOLOGY, DomainType (M-P Lefranc, p. 976-977)
E
Epitope (Lefranc M.-P., p. 672-673)
F
Framework region (FR-IMGT) (Lefranc M.-P., p. 758-759)
Functional (Lefranc M.-P., p. 771-772)
FunctionalityType (Lefranc M.-P., p. 777-778)
IMGT-ONTOLOGY, FunctionType (Lefranc M.-P., p. 977-978)
G
Gene and allele nomenclature (Lefranc M.-P., p. 787-788)
IMGT-ONTOLOGY, GeneType (Lefranc M.-P., p. 978-979)
Groove (G) domain (Lefranc M.-P., p. 872-873)
H
IMGT-ONTOLOGY, Highconcept (Lefranc M.-P., p. 979-980)
I
IMGT-ONTOLOGY, IDENTIFICATION axiom (Lefranc M.-P., p. 980-981)
IMGT Collier de Perles (chapter: Lefranc M.-P., p. 944-952 (3 fig))
IMGT unique numbering, (chapter: Lefranc M.-P., p. 952-959 (3 fig.))
IMGT-ONTOLOGY (chapter: Giudicelli V. and Lefranc M.-P., p. 964-972)
IMGT® information system (chapter: Lefranc M.-P., p. 959-964 (2 fig.))
Immunogenetics (Lefranc M.-P., p. 998)
Immunoglobulin superfamily (IgSF) (Lefranc M.-P., p. 998-999)
Immunoglobulin synthesis (Lefranc M.-P., p. 999-1002 (2 fig.))
Immunoinformatics (Lefranc M.-P., p. 1002)
Information system (Lefranc M.-P., p. 1027-1028)
J
Joining (J) gene (Lefranc M.-P., p. 1062)
L
Labels and relations (Lefranc M.-P., p. 1091-1092)
IMGT-ONTOLOGY, Leafconcept (Lefranc M.-P., p. 981)
IMGT-ONTOLOGY, LOCALIZATION axiom (M-P Lefranc, p. 981-982)
IMGT-ONTOLOGY, LocationType (Lefranc M.-P., p. 982-983)
M
MH superfamily (MhSF) (Lefranc M.-P., p. 1302-1303)
MoleculeType (Lefranc M.-P., p. 1455-1456)
IMGT-ONTOLOGY, Molecule_EntityType (Lefranc M.-P., p. 983-984)
N
IMGT-ONTOLOGY, NUMEROTATION axiom (Lefranc M.-P., p. 984-985)
O
IMGT-ONTOLOGY, OBTENTION axiom (Lefranc M.-P., p. 985-986)
ORF (open reading frame) (Lefranc M.-P., p. 1566-1567)
IMGT-ONTOLOGY, ORIENTATION axiom (Lefranc M.-P., 986-987)
P
Paratope (Lefranc M.-P., p. 1632-1633)
Productive (Lefranc M.-P., p. 1756)
Pseudogene (Lefranc M.-P., p. 1800-1801)
R
Recombination signal (RS) (Lefranc M.-P., p. 1823-1824)
S
IMGT-ONTOLOGY, SpecificityType (Lefranc M.-P., p. 987-988)
IMGT-ONTOLOGY, StructureType (Lefranc M.-P., p. 988)
T
TaxonRank (Lefranc M.-P., p. 2145-2146)
U
IMGT-ONTOLOGY, Unproductive (Lefranc M.-P., p. 988-989)
V
Variable (V) domain (Lefranc M.-P., p. 2336-2337)
Variable (V) gene (Lefranc M.-P., p. 2338)

IMGT-ONTOLOGY mapping with GO and SO

How is IMGT-ONTOLOGY related to Gene Ontology (GO) ?

IMGT-ONTOLOGY:

  • is specialized on immunoglobulins (IG), T cell receptors (TR), 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).
  • is complementary to GO for these proteins, the IMGT-ONTOLOGY concepts starting, for the IG, TR and MH, at the following GO concepts:
IMGT-ONTOLOGY GO
Immunoglobulin (IG) GO:0019814
T cell receptor (TR) GO:0042101
Major histocompatibility (MH) GO:0042611

and their children:

IMGT-ONTOLOGY GO
T cell receptor (TR) alpha_beta GO:0042105
T cell receptor (TR) gamma_delta GO:0042106
Major histocompatibility 1 (MH1) GO:0042612
Major histocompatibility 2 (MH2) GO:0042613

These seven 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.

How is IMGT-ONTOLOGY related to Sequence Ontology (SO) ?


List of the 64 IMGT Labels used in SO
IMGT-ONTOLOGY
DESCRIPTION concept
IMGT Labels		 Sequence Ontology (SO)
terms
J-RS SO:0000302
J-HEPTAMER SO:0000515
J-NONAMER SO:0000514
J-SPACER SO:0000517
V-RS SO:0000538
V-HEPTAMER SO:0000533
V-NONAMER SO:0000536
V-SPACER SO:0000537
5'D-HEPTAMER SO:0000496
5'D-NONAMER SO:0000497
5'D-RS SO:0000556
5'D-SPACER SO:0000498
3'D-HEPTAMER SO:0000493
3'D-NONAMER SO:0000494
3'D-RS SO:0000570
3'D-SPACER SO:0000495
C-CLUSTER SO:0000558
C-GENE SO:0000478
(DJ)-C-CLUSTER SO:0000539
(DJ)-J-C-CLUSTER SO:0000540
(DJ)-J-CLUSTER SO:0000485
D-J-GENE SO:0000572
D-(DJ)-C-CLUSTER SO:0000504
D-(DJ)-J-C-CLUSTER SO:0000506
D-(DJ)-J-CLUSTER SO:0000508
D-(DJ)-CLUSTER SO:0000505
D-J-C-CLUSTER SO:0000509
D-J-CLUSTER SO:0000560
D-CLUSTER SO:0000559
D-GENE SO:0000458
J-C-CLUSTER SO:0000511
J-CLUSTER SO:0000513
J-GENE SO:0000470
(VDJ)-C-CLUSTER SO:0000541
(VDJ)-J-C-CLUSTER SO:0000487
(VDJ)-J-CLUSTER SO:0000488
V-D-J-GENE SO:0000574
V-D-GENE SO:0000510
(VJ)-C-CLUSTER SO:0000489
(VJ)-J-C-CLUSTER SO:0000490
(VJ)-J-CLUSTER SO:0000491
V-J-GENE SO:0000576
V-(DJ)-C-CLUSTER SO:0000542
V-(DJ)-J-C-CLUSTER SO:0000564
V-(DJ)-J-CLUSTER SO:0000519
V-(DJ)-CLUSTER SO:0000518
V-D-(DJ)-C-CLUSTER SO:0000527
V-D-(DJ)-J-C-CLUSTER SO:0000529
V-D-(DJ)-J-CLUSTER SO:0000530
V-D-(DJ)-CLUSTER SO:0000528
V-D-J-C-CLUSTER SO:0000531
V-D-J-CLUSTER SO:0000532
V-J-C-CLUSTER SO:0000535
V-J-CLUSTER SO:0000534
V-(VDJ)-C-CLUSTER SO:0000520
V-(VDJ)-J-C-CLUSTER SO:0000565
V-(VDJ)-J-CLUSTER SO:0000522
V-(VDJ)-CLUSTER SO:0000521
V-(VJ)-C-CLUSTER SO:0000523
V-(VJ)-J-C-CLUSTER SO:0000566
V-(VJ)-J-CLUSTER SO:0000525
V-(VJ)-CLUSTER SO:0000524
V-CLUSTER SO:0000526
V-GENE SO:0000466

Conferences and workshops

European and ANR projects

References:

[1] Giudicelli, V. and Lefranc, M.-P. Ontology for Immunogenetics: IMGT-ONTOLOGY. Bioinformatics, 15:1047-1054 (1999) PMID: 10745995, pdf
[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. IMGT-ONTOLOGY for Immunogenetics and Immunoinformatics, http://www.imgt.org. In Silico Biology, 4, 17-29. Epub 2003, 4, 0004 (2004) PMID: 15089751
[7] Lefranc, M.-P. IMGT-ONTOLOGY and IMGT databases, tools and web resources for immunogenetics and immunoinformatics. Mol. Immunol., 40, 647-660 (2004). PMID:14644091
[8] Lefranc, M.-P. et al. IMGT-Choreography for Immunogenetics and Immunoinformatics. In Silico Biology, 5, 45-60, Epub 2005, 5, 0006, 24 Dec 2004 (2005) PMID: 15972004
[9] Lefranc, M.-P. IMGT-ONTOLOGY and IMGT databases, tools and Web resources for Immunoinformatics. From the IMGT genomics, genetics and structural approaches to IMGT-Choreography Interdisciplinary seminar series. Computer Science and IT with/for Biology. Keet C.M. and Franconi E. (eds), Free University of Bozen-Bolzano, Italy, pp. 26-38 (2005)
[10] Giudicelli, V. et al. Immunogenetics sequence annotation: the strategy of IMGT based on IMGT-ONTOLOGY. The XIXth International Congress of the European Federation for Medical Informatics, Geneva, Switzerland, MIE 2005, Geneva, Switzerland, August 28- September 1, 2005. In: Connecting Medical Informatics and Bio-informatics. Proceedings of the Medical Informatics Europe MIE 2005 (Engelbrecht R., Geissbuhler A., Lovis C. and Mihalas G. eds.), IOS Press, Technology and Informatics. Stud. Health Technol. Inform., 116, 3-8 (2005) PMID:16160227
[11] Lefranc, M.-P. et al. IMGT, the international ImMunoGeneTics information system®: a standardized approach for immunogenetics and immunoinformatics. Immunome Res., 1, 3, 20 September 2005, doi:10.1186/1745-7580-1-3 (2005) PMID: 16305737
[12] Giudicelli, V. and Lefranc, M.-P., Le Paradigme IMGT-ONTOLOGY. n: Biologie Systémique Standards et modèles (Roux M. Ed.), Collection Ecrin, Omniscience, Presses Universitaires de France, Paris, Chapitre 6, pp143-164. (2007) ISBN: 978-2-916097-12-1
[13] Lefranc, M.-P. IIMGT-ONTOLOGY, IMGT® databases, tools and Web resources for Immunoinformatics. In: Immunoinformatics (Schoenbach C., Ranganathan S. and Brusic V. eds.), Immunomics Reviews, Series of Springer Science and Business Media LLC, Springer, New York, USA chap. 1, pp.1-18 (2008)
[14] Lefranc, M.-P. et al., IMGT, a system and an ontology that bridge biological and computational spheres in bioinformatics. Brief Bioinform., 9:263-75. doi: 10.1093/bib/bbn014. Epub 2008 Apr 19 (2008) PMID:18424816
[15] Duroux P et al., IMGT-Kaleidoscope, the Formal IMGT-ONTOLOGY paradigm. Biochimie, 90:570-83. Epub 2007 Sep 11 (2008) PMID:17949886
[16] Lane J. et al. From IMGT-ONTOLOGY to IMGT/LIGMotif: the IMGT® standardized approach for immunoglobulin and T cell receptor gene identification and description in large genomic sequences. BMC Bioinformatics, 11:223; doi:10.1186/1471-2105-11-223 (2010) PMID:20433708
[17] Lefranc, M.-P. Antibody nomenclature: From IMGT-ONTOLOGY to INN definition. MAbs., 3(1):1-2. Epub 2011 Jan 1 (2011) PMID: 21099347
[18] Lefranc, M.-P. From IMGT-ONTOLOGY IDENTIFICATION Axiom to IMGT Standardized Keywords: For Immunoglobulins (IG), T Cell Receptors (TR), and Conventional Genes. Cold Spring Harb Protoc., 1;2011(6): 604-613. pii: pdb.ip82. doi: 10.1101/pdb.ip82(2011) PMID:21632792.
IMGT booklet high resolutionpdficon lower resolutionpdficon 'With generous provision from Cold Spring Harbor (CSH) Protocols'
[19] Lefranc, M.-P. From IMGT-ONTOLOGY DESCRIPTION Axiom to IMGT Standardized Labels: For Immunoglobulin (IG) and T Cell Receptor (TR) Sequences and Structures. Cold Spring Harb Protoc., 1;2011(6): 614-626. pii: pdb.ip83. doi: 10.1101/pdb.ip83 (2011) PMID:21632791.
IMGT booklet high resolutionpdficon lower resolutionpdficon 'With generous provision from Cold Spring Harbor (CSH) Protocols'.
[20] Lefranc, M.-P. From IMGT-ONTOLOGY CLASSIFICATION Axiom to IMGT Standardized Gene and Allele Nomenclature: For Immunoglobulins (IG) and T Cell Receptors (TR). Cold Spring Harb Protoc., 1;2011(6): 627-632. pii: pdb.ip84. doi: 10.1101/pdb.ip84 (2011) PMID:21632790.
IMGT booklet high resolutionpdficon lower resolutionpdficon 'With generous provision from Cold Spring Harbor (CSH) Protocols'.
[21] Lefranc, M.-P. "IMGT Collier de Perles for the Variable (V), Constant (C), and Groove (G) Domains of IG, TR, MH, IgSF, and MhSF" Cold Spring Harb Protoc. 2011 Jun 1;2011(6). pii: pdb.ip86. doi: 10.1101/pdb.ip86. PMID: 21632788
IMGT booklet high resolutionpdficon lower resolutionpdficon 'With generous provision from Cold Spring Harbor (CSH) Protocols'.
[22] Lefranc, M.-P. IMGT Unique Numbering for the Variable (V), Constant (C), and Groove (G) Domains of IG, TR, MH, IgSF, and MhSF. Cold Spring Harb Protoc., 1;2011(6). pii: pdb.ip85. doi: 10.1101/pdb.ip85 (2011) PMID: 21632789
IMGT booklet high resolutionpdficon lower resolutionpdficon 'With generous provision from Cold Spring Harbor (CSH) Protocols'.
[23] Giudicelli, V. and Lefranc, M.-P., IMGT-ONTOLOGY 2012. Front Genet., 3:79. doi: 10.3389/fgene.2012.00079. Epub 2012 May 23 (2012)PMID:22654892
[24] Lefranc, M-P. Immunoglobulin (IG) and T cell receptor genes (TR): IMGT®, and the birth and rise of immunoinformatics. Front Immunol. Feb 05;5:22 (2014). doi: 10.3389/fimmu.2014.00022. Open access. PMID: 24600447 LIGM: 429
[25] Lefranc M-P et al. IMGT®,, the international ImMunoGeneTics information system®, 25 years on.Nucleic Acids Res. Jan;43(Database issue):D413-22 (2015). doi: 10.1093/nar/gku1056. Epub 2014 Nov 5 Free Article. PMID: 25378316 LIGM: 441