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 : hgvs_nomenclature
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 |
* Gene |
direct | |
| 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 |
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
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
- hgvs nomenclature
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)