Class: SequenceVariant

Description: A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration.

Aliases: allele

classDiagram class SequenceVariant GenomicEntity <|-- SequenceVariant PhysicalEssence <|-- SequenceVariant OntologyClass <|-- SequenceVariant BiologicalEntity <|-- SequenceVariant SequenceVariant <|-- Snv SequenceVariant : category SequenceVariant : deprecated SequenceVariant : description SequenceVariant : full_name SequenceVariant : has_attribute SequenceVariant --|> Attribute : has_attribute SequenceVariant : has_biological_sequence SequenceVariant : has_gene SequenceVariant --|> Gene : has_gene SequenceVariant : id SequenceVariant : in_taxon SequenceVariant --|> OrganismTaxon : in_taxon SequenceVariant : in_taxon_label SequenceVariant : iri SequenceVariant : name SequenceVariant : provided_by SequenceVariant : synonym SequenceVariant : type SequenceVariant : xref

Inheritance

Entity
- NamedThing
  - BiologicalEntity [ ThingWithTaxon]
    - SequenceVariant [ GenomicEntity PhysicalEssence OntologyClass]
      - Snv

Slots

Name	Cardinality and Range	Inheritance	Examples
has_gene: Each allele can be associated with any number of genes	* Gene	direct
has_biological_sequence: The state of the sequence w.r.t a reference sequence	0..1 BiologicalSequence	GenomicEntity
id: A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI	1 String	OntologyClass, Entity	ZFIN:ZDB-ALT-980203-1091, CLINVAR:17681
in_taxon: connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'	* OrganismTaxon	ThingWithTaxon
in_taxon_label: The human readable scientific name for the taxon of the entity.	0..1 LabelType	ThingWithTaxon
provided_by: The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.	* String	NamedThing
xref: A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.	* Uriorcurie	NamedThing
full_name: a long-form human readable name for a thing	0..1 LabelType	NamedThing
synonym: Alternate human-readable names for a thing	* LabelType	NamedThing
iri: An IRI for an entity. This is determined by the id using expansion rules.	0..1 IriType	Entity
category: Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}	1..* Uriorcurie	Entity
type: None	* String	Entity
name: A human-readable name for an attribute or entity.	0..1 LabelType	Entity
description: a human-readable description of an entity	0..1 NarrativeText	Entity
has_attribute: connects any entity to an attribute	* Attribute	Entity
deprecated: A boolean flag indicating that an entity is no longer considered current or valid.	0..1 Boolean	Entity

Usages

used by	used in	type	used
GenotypeToVariantAssociation	object	range	SequenceVariant
VariantToEntityAssociationMixin	subject	range	SequenceVariant
VariantToGeneAssociation	subject	range	SequenceVariant
VariantToGeneExpressionAssociation	subject	range	SequenceVariant
VariantToPopulationAssociation	subject	range	SequenceVariant
VariantToPhenotypicFeatureAssociation	subject	range	SequenceVariant
VariantToDiseaseAssociation	subject	range	SequenceVariant
VariantAsAModelOfDiseaseAssociation	subject	range	SequenceVariant
SequenceVariantModulatesTreatmentAssociation	subject	range	SequenceVariant

Valid ID Prefixes

Instances of this class should have identifiers with one of the following prefixes, ordered with the most preferred first:

ID Prefix	Usage
CAID	SequenceVariant
CLINVAR	SequenceVariant
WIKIDATA	SequenceVariant
DBSNP	SequenceVariant
MGI	Gene SequenceVariant
ZFIN	Gene Genotype SequenceVariant
FB	Pathway Gene Transcript Polypeptide Protein GeneFamily Genotype SequenceVariant
RGD	Gene SequenceVariant
AGRKB	SequenceVariant
SPDI	SequenceVariant
WB	Gene SequenceVariant
WormBase	Gene MicroRNA SiRNA SequenceVariant
PHARMGKB.VARIANT	SequenceVariant

LinkML Source

name: sequence variant
id_prefixes:
- CAID
- CLINVAR
- WIKIDATA
- DBSNP
- MGI
- ZFIN
- FB
- RGD
- AGRKB
- SPDI
- WB
- WormBase
- PHARMGKB.VARIANT
local_names:
  agr:
    local_name_source: agr
    local_name_value: allele
description: A sequence_variant is a non exact copy of a sequence_feature or genome
  exhibiting one or more sequence_alteration.
alt_descriptions:
  AGR:
    source: AGR
    description: An entity that describes a single affected, endogenous allele. These
      can be of any type that matches that definition
  VMC:
    source: VMC
    description: A contiguous change at a Location
comments:
- This class is for modeling the specific state at a locus. A single DBSNP rs ID could
  correspond to more than one sequence variants (e.g CIViC:1252 and CIViC:1253, two
  distinct BRCA2 alleles for rs28897743)
in_subset:
- model_organism_database
from_schema: https://w3id.org/biolink/biolink-model
aliases:
- allele
exact_mappings:
- WIKIDATA:Q15304597
close_mappings:
- dcid:Allele
- SO:0001060
- VMC:Allele
- GENO:0000002
- SIO:010277
- SO:0001060
is_a: biological entity
mixins:
- genomic entity
- physical essence
- ontology class
slots:
- has gene
slot_usage:
  has gene:
    name: has gene
    description: Each allele can be associated with any number of genes
    multivalued: true
  has biological sequence:
    name: has biological sequence
    description: The state of the sequence w.r.t a reference sequence
  id:
    name: id
    examples:
    - value: ZFIN:ZDB-ALT-980203-1091
      description: ti282a allele from ZFIN
    - value: CLINVAR:17681
      description: NM_007294.3(BRCA1):c.2521C>T (p.Arg841Trp)