Property talk:P594

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Ensembl gene ID
identifier for a gene as per the Ensembl (European Bioinformatics Institute and the Wellcome Trust Sanger Institute) database

Represents	gene (Q7187)
Associated item	Ensembl genome database project (Q1344256)
Applicable "stated in" value	Ensembl genome database project (Q1344256)
Data type	External identifier
Template parameter	en:Template:GNF_Protein_box = Hs_Ensembl (humans) Mm_Ensembl (mouse)
Domain	According to this template: gene According to statements in the property: gene (Q7187) When possible, data should only be stored as statements
Allowed values	(ENS(|MUS|RNO)G\d{11})|(Y[A-P][LR]\d{3}[CW](-[A-G])?) (string of species-specific uppercase prefix, followed by 11 digits or a ORF name)
Example	MB (Q14819296) → ENSG00000198125 (RDF) Mb (Q14819298) → ENSMUSG00000018893 (RDF) FN1 (Q14819473) → ENSG00000115414 (RDF) Fn1 (Q14819475) → ENSMUSG00000026193 (RDF) Fn1 (Q24394377) → ENSRNOG00000014288 (RDF)
Source	https://www.ensembl.org
Formatter URL	https://identifiers.org/ensembl/$1
Tracking: usage	Category:Pages using Wikidata property P594 (Q26250016)
See also	Ensembl protein ID (P705), Ensembl transcript ID (P704)
Lists	Items with the most statements of this property Count of items by number of statements (chart) Items with the most statements Items with the fewest statements Count of items by number of sitelinks (chart) Items with the most sitelinks Items with the most sitelinks, but no link to one Wikipedia (sample: Welsh Wikipedia, cywiki) Items with the fewest sitelinks Most linked wikis Items with the most identifier properties Items with no other external identifier Items with no other statements Most recently created items Items with novalue claims Items with unknown value claims Usage history (total) Usage history (main statement) Chart by item creation date Database reports/Constraint violations/P594 Map Random list
Proposal discussion	Proposal discussion
Current uses	Total 363,320 Main statement 156,411 43.1% of uses Qualifier 5 <0.1% of uses Reference 206,904 56.9% of uses
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Single value: this property generally contains a single value. (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/P594#Single value, SPARQL

Format “(ENS(|MUS|RNO|DAR)G\d{11})|(Y[A-P][LR]\d{3}[CW](-[A-G])?)|(WBGene\d{8})|(FBgn\d{7})|(Q\d{4})”: 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).
List of violations of this constraint: Database reports/Constraint violations/P594#Format, SPARQL

Type “gene (Q7187)”: item must contain property “instance of (P31), subclass of (P279)” with classes “gene (Q7187)” or their subclasses (defined using subclass of (P279)). (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/P594#Type Q7187, SPARQL

Item “found in taxon (P703): Homo sapiens (Q15978631), house mouse (Q83310), brown rat (Q184224), PPT2 (Q27545397), Saccharomyces cerevisiae S288c (Q27510868), Danio rerio (Q169444), Caenorhabditis elegans (Q91703), Drosophila melanogaster (Q130888)”: Items with this property should also have “found in taxon (P703): Homo sapiens (Q15978631), house mouse (Q83310), brown rat (Q184224), PPT2 (Q27545397), Saccharomyces cerevisiae S288c (Q27510868), Danio rerio (Q169444), Caenorhabditis elegans (Q91703), Drosophila melanogaster (Q130888)”. (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/P594#Item P703, search

Distinct values: this property likely contains a value that is different from all other items. (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/P594#Unique value, SPARQL (every item), SPARQL (by value)

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/P594#Scope, hourly updated report, 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/P594#Entity types

This property is being used by: eu:Txantiloi:Gene infotaula automatikoa Please notify projects that use this property before big changes (renaming, deletion, merge with another property, etc.)

Maybe need to be removed:

Not quite unique but close

It happens that in some instances the same Ensembl id can point to what may be in reality and what other databases such as Entrez consider the same thing. See for example Q18048211 and Q18033903 which both might/can/should link to ENSG00000003096 but do appear to be different entities. This can result in cases where there are multiple records with the same ensembl id. In the vast majority of cases these ids are in fact unique. For more information on this please see the thread: https://www.biostars.org/p/16505/#16604

Added format ENSRNOG

There are about 19000 format violations due to Ids starting with "ENSRNOG". Assuming these are correct, I am adding the RNO case to the format constraint. -- LaddΩ chat ;) 13:57, 13 June 2016 (UTC)

How to deal with "legitimate" constraint violations

There are currently a relatively high number of constraint violations reported. Most, if not all are due to the ProteinBoxBot which maintains genes on Wikidata.

The issue is that the ProteinBoxBot, which maintains gene annotations on Wikidata, uses NCBI gene as key. The bot's working is strait forward. On every bot run all NCBI gene annotations are extracted and updates in Wikidata, together with all known external mappings. The Ensembl Gene ID (P594) is part of this set of mappings. Although efforts are in place to harmonize between Ensembl and the NCBI, there stil are cases where one ensembl ID maps to multiple NCBI Gene IDs. I did checks on the constraint violations being reported and they appeared to be "legitimate". There are even cases where 1 Ensembl ID, maps to 14 and 19 NCBI gene IDs. Counts: (2: 486, 3: 48, 4: 12, 5: 3, 6: 3, 7: 1, 8: 1, 10: 1, 14: 1, 19: 1} This is a known issue. The question is how to proceed here. Could we remove the constraint violation on this property? Or do we allow the number of constraint violations reach close to 1000. When more species will get coverage in Wikidata the number of this type of constraint violations will likely increase. --Andrawaag (talk) 22:20, 4 July 2016 (UTC)