IMGT-KG

IMGT-KG Description

The IMGT-KG data model can be divided into five levels of description, from nucleotide to protein sequence. The initial level comprises the depiction of genes and alleles. The subsequent level provides details about the genomic loci of these genes. The following level describes the sequence characteristics of the genes. The fourth level transitions to the protein level, presenting a description pertaining to the sequence of the protein chain and its domains. Finally, the last model describes the chain that belongs to the structure. In the data model, every class has an annotation label (rdfs:label) , a definition (skos:definition) and a comment (rdfs:comment) when it is possible. A dinamyc visualisation of the data model made with Vis-Network is provided. However a table with additional annotation properties is provided, when they exist.


                                    PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> 

                                    PREFIX faldo: <http://biohackathon.org/resource/faldo#> 

                                    PREFIX skos: <http://www.w3.org/2004/02/skos/core#> 

                                    PREFIX obo: <http://purl.obolibrary.org/obo/> 

                                    PREFIX : <http://www.imgt.org/imgt-ontology#>

At the gene level, we have a Gene which can be member of (obo:RO_0002350) Group, that could be a member of a SubGroup and/or Clan. A Clan or a SubGroup can also be member of a Group. A Gene concept is defined by a gene type (variable, diversity ...) and a structure type. An allele is a gene variant that is associated with it. An Allele has a functionality type that indicates its functionality (functional,pseudogene...) and it is associated to a sequence region (faldo:Region), which can be a reference or literature sequence. Every Gene is ordered in a Locus and belongs to a taxon (obo:NCBITaxon_1).

	AnnotationProperty	Description
Gene
Gene	imgt_link	a link that points to imgt website
Allele
	has_fcode	a code for functionality type
	has_number	number of Allele

A Locus belongs to a taxon with a location type that indicates its location (major locus, orphon ...). It is part of (obo:BFO_0000050) chromosome (obo:SO_0000340). Each chromosome is member of a given assembly (obo:SO_0001248) which has a version number (obo:SWO_0004000), data origin (obo:NCIT_C103167) and belongs also to a taxon.

The sequence level characterizes the features of the sequence. A feature is a sequence region which is associated with a location, and a label. Therefore, each region has a label and a location (faldo:ExactPosition) with a start and end positions. A region at the nucleotide sequence level is part of (obo:BFO_0000050) a DNA or RNA sequence (obo:GENO_0000960) with an accession number (obo:NCIT_C25402). A region can be a prototype entity or a cluster (A DNA fragment covering several genomic entities). The Cluster and the prototype entity are part of a biological sequence (obo:GENO_0000702)thanks to isPrototypeInSeq and isClusterInSeq relation, respectively. The biological sequence contains other regions which are related to each other. Every region in the same biological sequence has an Allen interval relationship , for example, a region A can be next to (adjacent) to other regions.


	AnnotationProperty	Description
Region
	has_nucleotide_sequence	composition in nucleotides of the region when it's a coding region
	has_imgt_qualifier	a qualifier imgt to describe the region
obo:GENO_0000960
	has_nucleotide_sequence	composition in nucleotides of the sequence

This level is the transition from nucleotide sequences to protein sequences. A chain obo:NCIT_C41207 can have protein domains obo:NCIT_C13303 with a domain type. It also has regions and residues obo:NCIT_C48795 with the associated amino acids obo:CHEBI_33709 and an IMGT numbering. Each chain and domain have a label and a location. The associated region of a Chain is the reference sequence of an Allele with a similarity score. The Chains belong to a taxon and a structure obo:NCIT_C13303 .


	AnnotationProperty	Description
Chain
	code4A	code of the chain
	has_imgt_chain_description	a description of the chain in its different domains
	imgt_link	a link that points to imgt website
Domain
	has_imgt_collier_perles	imgt collier de perles link
	has_sheet	different sheets of domain
Residue
	abreviation	short name or abreviation of the residue
	has_phi_angle	phi angle
	has_psi_angle	psi angle

A Structure obo:NCIT_C13303 can belong to a crystal structure sio:SIO_001100, has a label and a molecular component. A Structure is attached to a entry of amino acid sequence obo:GENO_0000720. This sequence has a accession number, a related bibliographic reference and the acquisition experiment.


	AnnotationProperty	Description
Structure
	common_name	common name
	commercial_name	commercial name
	inn_name	INN name
	immune_epitope	an external link that points to the predict epitope of a structure in IEDB
Amino acide sequence
	contact_analysis	a link that points to pair contacts analyses
	has_amino_sequence	amino acide sequence
	imgt_link	a link that points to imgt website
	interaction_paratope_epitope	a link that points to interaction paratope epitope
	is_entry_from	amino sequence's database
	jmol_visualisation	a link to explore the structure in Jmol
	pdb_link	a external link to pdb database
Article
	dc:title	article's title
	dc:contributor	article's contributors
	dc:date	publication date
	has_journal	journal of publication

IMGT-KG Statistics

IMGT-KG provides access to 79 670 110 triplets without inferences, 95 508 660 triplets with inferences applied, 10 430 268 entities, 15 848 105 distinct subjects, 21 861 727 distinct objects, 673 distinct concepts or classes and 171 distinct properties or relations. We provide below Figures demonstrating the main features of IMGT-KG.