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Property talk:P3331

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Documentation

HGVS nomenclature
Sequence Variant Nomenclature from the Human Genome Variation Society (HGVS)

Description

Sequence Variant Nomenclature from the Human Genome Variation Society (HGVS)

Data type

External identifier

Allowed values

.{10,100}|([NX][A-Z]_\d+|ENST\d+|(CM000674.|chr)\d+:g)\.\d.+|

Example

rs1801133 (Q4048578) → "chr1:g.11856378G>A" (note: this information should be moved to a property statement; use property Wikidata property example (P1855), Wikidata property example for properties (P2271), Wikidata property example for lexemes (P5192), Wikidata property example for forms (P5193) or Wikidata property example for senses (P5977))

Source

https://civic.genome.wustl.edu/#/home

Formatter URL

http://reg.clinicalgenome.org/allele?hgvs=$1

Robot and gadget jobs

yes

Lists

Proposal discussion

Proposal discussion

Current uses

Total	2,885
Main statement	2,884	>99.9% of uses
Reference	1	<0.1% of uses

Search for values

[create Create a translatable help page (preferably in English) for this property to be included here]

Scope is as main value (Q54828448), as reference (Q54828450): the property must be used by specified way only (Help)

List of violations of this constraint: Database reports/Constraint violations/P3331#Scope, hourly updated report, SPARQL

Format “.{10,100}|”: value must be formatted using this pattern (PCRE syntax). (Help)

List of violations of this constraint: Database reports/Constraint violations/P3331#Format, hourly updated report, SPARQL

Format “([NX][A-Z]_\d+|ENST\d+|(CM000674.|chr)\d+:g)\.\d.+|”: value must be formatted using this pattern (PCRE syntax). (Help)

Exceptions are possible as rare values may exist. Exceptions can be specified using exception to constraint (P2303). Known exceptions: VHL *214G (c.640T>G) (Q56615791)
List of violations of this constraint: Database reports/Constraint violations/P3331#Format, SPARQL

Allowed entity types are Wikibase item (Q29934200): the property may only be used on a certain entity type (Help)

Exceptions are possible as rare values may exist. Exceptions can be specified using exception to constraint (P2303).
List of violations of this constraint: Database reports/Constraint violations/P3331#Entity types

Pattern ^N/A$ will be automatically replaced to novalue.
Testing: TODO list

v t e Wikidata properties related to genetics (Q7162)

Basic	subclass of genomic start genomic end molecular function ortholog encodes encoded by found in taxon chromosome strand orientation cytogenetic location chromosome count

Optional	regulates (molecular biology) biological process Gene Atlas image mode of inheritance ploidy increased expression in gene deletion association with gene duplication association with gene insertion association with gene inversion association with gene substitution association with posttranslational modification association with altered regulation leads to genome size genetic association positive therapeutic predictor for negative therapeutic predictor for positive diagnostic predictor for negative diagnostic predictor for positive prognostic predictor for negative prognostic predictor for biological variant of antisense inhibitor of mtDNA haplogroup Y-DNA Haplogroup recognition sequence cutting site of restriction enzyme produces cohesive end isoschizomer neoschizomer isocaudomer expressed in

Databases	Entrez Gene ID UniProt protein ID HGNC gene symbol HGNC ID OMIM ID EC enzyme number HomoloGene ID Ensembl gene ID RefSeq protein ID PDB structure ID RefSeq RNA ID KEGG ID GeneReviews ID Mouse Genome Informatics ID Gene Ontology ID Ensembl transcript ID Ensembl protein ID ClinVar Variation ID RefSeq genome ID NCBI locus tag UCSC Genome Browser assembly ID mirTarBase ID CIViC variant ID HGVS nomenclature FAO 2007 genetic resource ID GeneDB ID Saccharomyces Genome Database ID Pfam ID Human Phenotype Ontology ID REBASE Enzyme Number CIViC gene ID

Qualifiers	RefSeq genomic assembly

See also: Wikidata:WikiProject Molecular biology - Wikidata:WikiProject Medicine - Wikidata:WikiProject Haplogroups

a formatter URL?

http://myvariant.info/v1/variant/$1 close but no cookie right now. --I9606 (talk) 00:11, 8 November 2016 (UTC)[reply]

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