IMGT Scientific chart

IMGT prototypes table

Definition

An IMGT prototype is the graphical representation of an entity with IMGT® standardized labels (capital letters, no plural) [1, 2]. IMGT prototypes are defined for molecular entities in IMGT® databases and tools.

Relation with IMGT-ONTOLOGY

An IMGT prototype for a molecular entity (in databases and tools) corresponds to a leafconcept of the 'Molecular_EntityPrototype' (in IMGT-ONTOLOGY) [1].
In the table, the 32 'Molecule_EntityType' leafconcepts are shown with the leafconcepts of 'GeneType', 'ConfigurationType', and 'MoleculeType' that define them.
The three leafconcepts of 'MoleculeUnit' are based on 'MoleculeType' only [1].

(*) An asterisk indicates the 8 leafconcepts that are the most classical representatives of IG and TR identification.
Each "Molecule_EntityType" leafconcept is linked to a "Molecule_EntityPrototype" leafconcept.

Clicking on the links in the table gives access to the IMGT prototypes.

'Molecule_EntityPrototype' leafconcepts and related concepts

IDENTIFICATION					DESCRIPTION
MoleculeUnit leafconcepts	Molecule_EntityType leafconcepts	GeneType leafconcepts	ConfigurationType leafconcepts	MoleculeType leafconcepts	Molecule_EntityPrototype leafconcepts
gene
	V-gene*	V	germline	gDNA	V-GENE
	D-gene*	D			D-GENE
	J-gene*	J			J-GENE
	J-C-gene	J, C			J-C-GENE
	C-gene*	C	undefined		C-GENE
	L-conventional-gene	conventional			L-CONVENTIONAL-GENE
	conventional-gene	conventional			CONVENTIONAL-GENE
	V-D-gene	V, D	partially_rearranged		V-D-GENE
	D-J-gene	D, J	partially_rearranged		D-J-GENE
	V-J-gene*	V, J	rearranged		V-J-GENE
	V-D-J-gene*	V, D, J	rearranged		V-D-J-GENE
transcript
	L-V-transcript	V	germline	mRNA	L-V-TRANSCRIPT
	D-transcript	D			D-TRANSCRIPT
	J-transcript	J			J-TRANSCRIPT
	J-C-transcript	J, C			J-C-TRANSCRIPT
	C-transcript	C	undefined		C-TRANSCRIPT
	L-nt-transcript	conventional			L-NT-TRANSCRIPT
	nt-transcript	conventional			NT-TRANSCRIPT
	L-V-D-transcript	V, D	partially_rearranged		L-V-D-TRANSCRIPT
	D-J-C-transcript	D, J, C	partially_rearranged		D-J-C-TRANSCRIPT
	L-V-J-C-transcript	V, J, C	rearranged		L-V-J-C-TRANSCRIPT
	L-V-D-J-C-transcript	V, D, J, C	rearranged		L-V-D-J-C-TRANSCRIPT
sequence
	L-V-sequence	V	germline	cDNA	L-V-SEQUENCE
	D-sequence	D			D-SEQUENCE
	J-sequence	J			J-SEQUENCE
	J-C-sequence	J, C			J-C-SEQUENCE
	C-sequence	C	undefined		C-SEQUENCE
	L-nt-sequence	conventional			L-nt-SEQUENCE
	nt-sequence	conventional			NT-SEQUENCE
	L-V-D-sequence	V, D	partially_rearranged		L-V-D-SEQUENCE
	D-J-C-sequence	D, J, C	partially_rearranged		D-J-C-SEQUENCE
	L-V-J-C-sequence*	V, J, C	rearranged		L-V-J-C-SEQUENCE
	L-V-D-J-C-sequence*	V, D, J, C	rearranged		L-V-D-J-C-SEQUENCE

References:
[1] Giudicelli, V. and Lefranc, M.-P., "IMGT-ONTOLOGY 2012" Frontiers in Bioinformatics and Computational Biology Online access. Front. Genet. 2012; 3:79. Epub 2012 May 23. PMID: 22654892 LIGM: 401
[2] 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. 2011 Jun 1;2011(6). pii: pdb.ip83. doi: 10.1101/pdb.ip83. PMID: 21632791 LIGM: 384
IMGT booklet (high resolution) (low resolution) (with generous provision from Cold Spring Harbor (CSH) Protocols).
[3] 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. 2011 Jun 1;2011(6). pii: pdb.ip82. doi: 10.1101/pdb.ip82. PMID: 21632792 LIGM: 383
IMGT booklet (high resolution) (low resolution) (with generous provision from Cold Spring Harbor (CSH) Protocols).
[4] Lefranc, M.-P., Immunoglobulin (IG) and T cell receptor genes (TR): IMGT® and the birth and rise of immunoinformatics. Front Immunol. 2014 Feb 05;5:22. doi: 10.3389/fimmu.2014.00022 Open access PMID: 24600447