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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

classDiagram class SequenceVariant GenomicEntity <|-- SequenceVariant PhysicalEssence <|-- SequenceVariant OntologyClass <|-- SequenceVariant BiologicalEntity <|-- SequenceVariant SequenceVariant <|-- Snv SequenceVariant : category 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 --|> organism taxon : in_taxon SequenceVariant : in_taxon_label SequenceVariant : iri SequenceVariant : name SequenceVariant : provided_by SequenceVariant : synonym SequenceVariant : type SequenceVariant : xref

Inheritance

Slots

Name Cardinality and Range Description Inheritance
has_gene 0..*
Gene		 Each allele can be associated with any number of genes direct
has_biological_sequence 0..1
BiologicalSequence		 The state of the sequence w GenomicEntity
id 1..1
String		 A unique identifier for an entity Entity, OntologyClass
in_taxon 0..*
OrganismTaxon		 connects an entity to its taxonomic classification ThingWithTaxon
in_taxon_label 0..1
LabelType		 The human readable scientific name for the taxon of the entity ThingWithTaxon
provided_by 0..*
String		 The value in this node property represents the knowledge provider that create... NamedThing
xref 0..*
Uriorcurie		 A database cross reference or alternative identifier for a NamedThing or edge... NamedThing
full_name 0..1
LabelType		 a long-form human readable name for a thing NamedThing
synonym 0..*
LabelType		 Alternate human-readable names for a thing NamedThing
iri 0..1
IriType		 An IRI for an entity Entity
category 1..*
CategoryType		 Name of the high level ontology class in which this entity is categorized Entity
type 0..*
String		 Entity
name 0..1
LabelType		 A human-readable name for an attribute or entity Entity
description 0..1
NarrativeText		 a human-readable description of an entity Entity
has_attribute 0..*
Attribute		 connects any entity to an attribute Entity

Usages

used by used in type used
GenotypeToVariantAssociation object 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

Aliases

  • allele

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)

Identifier and Mapping Information

Valid ID Prefixes

Instances of this class should have identifiers with one of the following prefixes:

  • CAID

  • CLINVAR

  • WIKIDATA

  • DBSNP

  • MGI

  • ZFIN

  • FB

  • RGD

  • AGRKB

  • SPDI

  • WB

  • WormBase

  • PHARMGKB.VARIANT

Schema Source

  • from schema: https://w3id.org/biolink/biolink-model

Mappings

Mapping Type Mapped Value
self biolink:SequenceVariant
native biolink:SequenceVariant
exact WIKIDATA:Q15304597
close dcid:Allele, SO:0001060, VMC:Allele, GENO:0000002, SIO:010277, SO:0001060

LinkML Source

Direct

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
    domain_of:
    - sequence variant
  has biological sequence:
    name: has biological sequence
    description: The state of the sequence w.r.t a reference sequence
    domain_of:
    - genomic entity
    - epigenomic entity
  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)
    domain_of:
    - ontology class
    - entity