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Class: Snv

Description: SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist

Aliases: single nucleotide variant, single nucleotide polymorphism, snp

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

Inheritance

Slots

Name Cardinality and Range Inheritance Examples
has_gene:
Each allele can be associated with any number of genes
*
Gene		 SequenceVariant
hgvs_nomenclature:
HGVS syntax refers to the specific rules and conventions used by the Human Variant Nomenclature Committee to describe the location and change in DNA, RNA, and protein sequence variants. This slot is used to capture all the different forms of HGVS nomenclature that may be used to describe a sequence variant, including genomic, transcript, and protein HGVS expressions/nomenclatures and is thus multivalued. 		*
String		 SequenceVariant
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

LinkML Source

name: snv
description: SNVs are single nucleotide positions in genomic DNA at which different
  sequence alternatives exist
from_schema: https://w3id.org/biolink/biolink-model
aliases:
- single nucleotide variant
- single nucleotide polymorphism
- snp
exact_mappings:
- SO:0001483
is_a: sequence variant