Variation Descriptor

Computational Definition

This descriptor class is used for describing VRS Variation value objects.

Information Model

Some VariationDescriptor attributes are inherited from Value Object Descriptor.

Field	Type	Limits	Description
id	CURIE	1..1	Descriptor ID; MUST be unique within document.
type	string	1..1	MUST be “VariationDescriptor”.
label	string	0..1	A primary label for the value object.
description	string	0..1	A free-text description of the value object.
xrefs	CURIE	0..m	List of CURIEs representing associated concepts.
alternate_labels	string	0..m	List of strings representing alternate labels for the value object.
extensions	Extension	0..m	List of resource-specific Extensions needed to describe the value object.
variation_id	CURIE	0..1	This SHOULD be provided if variation is omitted.
variation	Variation	0..1	This SHOULD be provided if variation_id is omitted.
molecule_context	string	0..1	The molecular context of this variant. Must be one of “genomic”, “transcript”, or “protein”.
structural_type	CURIE	0..1	The structural variant type associated with this variant. We RECOMMEND a descendent term of SO:0001537.
expressions	Expression	0..1	Typically HGVS or ISCN nomenclature expressions. Other systems relevant to the description of variation MAY be used.
vcf_record	VCF Record	0..1	A VCF Record of the variant. This SHOULD be a single allele, the VCF genotype (GT) field should be represented in the allelic_state attribute.
gene_context	CURIE | Gene Descriptor	0..1	A specific gene context that applies to this variant.
vrs_ref_allele_seq	Sequence	0..1	A VRS Sequence corresponding to a “ref allele”, describing the sequence expected at a VRS SequenceLocation reference.
allelic_state	CURIE	0..1	We RECOMMEND that the allelic_state of a variation be described by terms from the Genotype Ontology (GENO). These SHOULD descend from concept GENO:0000875 <http://purl.obolibrary.org/obo/GENO_0000875>.

Location Descriptor

This descriptor is intended to reference VRS Location value objects. In addition to the attributes inherited from its Value Object Descriptor parent class, the Sequence Location Descriptor has the following attributes:

Field	Type	Limits	Description
type	string	1..1	MUST be “LocationDescriptor”
location_id	CURIE	0..1	This MUST be provided if location is omitted
location	VRS Location	0..1	This MUST be provided if location_id is omitted

Sequence Descriptor

This descriptor is intended to reference VRS Sequence value objects. In addition to the attributes inherited from its Value Object Descriptor parent class, the Sequence Descriptor has the following attributes:

Field	Type	Limits	Description
type	string	1..1	MUST be “SequenceDescriptor”
sequence_id	CURIE	0..1	This MUST be provided if sequence is omitted
sequence	VRS Sequence	0..1	This MUST be provided if sequence_id is omitted
residue_type	CURIE	0..1	CURIE MUST be SO:0000348 (nucleic acid), SO:0001407 (peptidyl), or a descendent of one of these concepts.

Gene Descriptor

This descriptor is intended to reference VRS Gene value objects. In addition to the attributes inherited from its Value Object Descriptor parent class, the Gene Descriptor has the following attributes:

Field	Type	Limits	Description
type	string	1..1	MUST be “GeneDescriptor”
gene_id	CURIE	0..1	This MUST be provided if gene is omitted
gene	VRS Gene	0..1	This MUST be provided if gene_id is omitted

Categorical Variation Descriptor

Computational Definition

This descriptor class is used for describing Categorical Variation value objects.

Information Model

Some CategoricalVariationDescriptor attributes are inherited from Value Object Descriptor.

Field	Type	Limits	Description
id	CURIE	1..1	Descriptor ID; MUST be unique within document.
type	string	1..1	MUST be “VariationDescriptor”.
label	string	0..1	A primary label for the value object.
description	string	0..1	A free-text description of the value object.
xrefs	CURIE	0..m	List of CURIEs representing associated concepts.
alternate_labels	string	0..m	List of strings representing alternate labels for the value object.
extensions	Extension	0..m	List of resource-specific Extensions needed to describe the value object.
version	string	0..1	The version of the Categorical Variation Descriptor.
categorical_variation_id	CURIE	0..1	This SHOULD be provided if categorical_variation is omitted.
categorical_variation	CategoricalVariation	0..1	This SHOULD be provided if variation_id is omitted.
members	VariationMember	0..m	VariationMember instances that fall within the functional domain of the Categorical Variation.