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]
- BiologicalEntity [ ThingWithTaxon]
- NamedThing
Slots
| Name | Cardinality and Range | Inheritance | Examples |
|---|---|---|---|
| has_gene: Each allele can be associated with any number of genes |
0..* 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..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' |
0..* 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. |
0..* 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. |
0..* 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 |
0..* 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 |
0..* 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 |
0..* Attribute |
Entity | |
| deprecated: A boolean flag indicating that an entity is no longer considered current or valid. |
0..1 Boolean |
Entity |
Usages
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
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