Class: SequenceVariant

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

URI: biolink:SequenceVariant

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Identifier prefixes

• CAID
• CLINVAR
• WIKIDATA
• DBSNP
• MGI
• ZFIN
• FB
• RGD
• AGRKB
• SPDI
• WB
• WormBase
• PHARMGKB.VARIANT

Parents

• is_a: BiologicalEntity

Uses Mixins

• mixin: GenomicEntity
• mixin: PhysicalEssence - Semantic mixin concept. Pertains to entities that have physical properties such as mass, volume, or charge.
• mixin: OntologyClass - a concept or class in an ontology, vocabulary or thesaurus. Note that nodes in a biolink compatible KG can be considered both instances of biolink classes, and OWL classes in their own right. In general you should not need to use this class directly. Instead, use the appropriate biolink class. For example, for the GO concept of endocytosis (GO:0006897), use bl:BiologicalProcess as the type.

Children

• Snv - SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist

Referenced by class

• GenotypeToVariantAssociation object _1..1 SequenceVariant
• GenomicEntity has frameshift variant _0..* SequenceVariant
• GenomicEntity has missense variant _0..* SequenceVariant
• GenomicEntity has nearby variant _0..* SequenceVariant
• GenomicEntity has non coding variant _0..* SequenceVariant
• GenomicEntity has nonsense variant _0..* SequenceVariant
• GenomicEntity has sequence variant _0..* SequenceVariant
• GenomicEntity has splice site variant _0..* SequenceVariant
• GenomicEntity has synonymous variant _0..* SequenceVariant
• SequenceVariantModulatesTreatmentAssociation subject _1..1 SequenceVariant
• Association sequence variant qualifier _0..1 SequenceVariant
• VariantAsAModelOfDiseaseAssociation subject _1..1 SequenceVariant
• VariantToEntityAssociationMixin subject _1..1 SequenceVariant
• VariantToPhenotypicFeatureAssociation subject _1..1 SequenceVariant
• VariantToPopulationAssociation subject _1..1 SequenceVariant

Attributes

Own

• has biological sequence _0..1
  • Description: connects a genomic feature to its sequence
  • Range: BiologicalSequence
• has gene _0..*
  • Description: connects an entity associated with one or more genes
  • Range: Gene
• id _1..1
  • Description: A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI
  • Range: String
  • in subsets: (translator_minimal)

Inherited from entity:

• id _1..1
  • Description: A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI
  • Range: String
  • in subsets: (translator_minimal)
• iri _0..1
  • Description: An IRI for an entity. This is determined by the id using expansion rules.
  • Range: IriType
  • in subsets: (translator_minimal,samples)
• category _0..*
  • Description: 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}
  • Range: CategoryType
  • in subsets: (translator_minimal)
• type _0..*
  • Range: String
• description _0..1
  • Description: a human-readable description of an entity
  • Range: NarrativeText
  • in subsets: (translator_minimal)
• has attribute _0..*
  • Description: connects any entity to an attribute
  • Range: Attribute
  • in subsets: (samples)

Inherited from gene product mixin:

• xref _0..*
  • Description: 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.
  • Range: Uriorcurie
  • in subsets: (translator_minimal)

Inherited from macromolecular machine mixin:

• name _0..1
  • Description: A human-readable name for an attribute or entity.
  • Range: LabelType
  • in subsets: (translator_minimal,samples)

Inherited from named thing:

• provided by _0..*
  • Description: 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.
  • Range: String
• category _0..*
  • Description: 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}
  • Range: CategoryType
  • in subsets: (translator_minimal)

Inherited from thing with taxon:

• in taxon _0..*
  • Description: connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see ‘thing with taxon’
  • Range: OrganismTaxon
  • in subsets: (translator_minimal)
• in taxon label _0..1
  • Description: The human readable scientific name for the taxon of the entity.
  • Range: LabelType
  • in subsets: (translator_minimal)

Domain for slot:

• has biological sequence _0..1
  • Description: connects a genomic feature to its sequence
  • Range: BiologicalSequence
• has gene _0..*
  • Description: connects an entity associated with one or more genes
  • Range: Gene
• id _1..1
  • Description: A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI
  • Range: String
  • in subsets: (translator_minimal)

Other properties