Property talk:P1057
Latest comment: 4 years ago by SCIdude in topic remove allowed type non-coding RNA
Documentation
chromosome
chromosome on which an entity is localized
chromosome on which an entity is localized
| Description | the chromosome on which an entity is localized | ||||||||||||
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| Represents | chromosome (Q37748) | ||||||||||||
| Data type | Item | ||||||||||||
| Domain | According to this template:
any item that can be localized to a set of genomic coordinates, e.g. a gene (Q7187), sequence variant (Q15304597), etc
According to statements in the property:
When possible, data should only be stored as statementsgene (Q7187), sequence variant (Q15304597), noncoding DNA (Q1458444) or chromosome abnormality (Q744962) | ||||||||||||
| Allowed values | any type of chromosome (Q37748) (see latest list), e.g. human chromosome 1 (Q430258), mouse chromosome 1 (Q14864323) (note: this should be moved to the property statements) | ||||||||||||
| Example | RELN (Q414043) → human chromosome 7 (Q657319) rs267601217 (Q15304616) → human chromosome 7 (Q657319) Reln (Q14331135) → mouse chromosome 5 (Q15304656) | ||||||||||||
| Robot and gadget jobs | To be populated by the Gene Wiki bot | ||||||||||||
| Tracking: usage | Category:Pages using Wikidata property P1057 (Q29168735) | ||||||||||||
| Lists | |||||||||||||
| Proposal discussion | Proposal discussion | ||||||||||||
| Current uses |
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| Search for values |
[create Create a translatable help page (preferably in English) for this property to be included here]
Value type “chromosome (Q37748)”: This property should use items as value that contain property “instance of (P31)”. On these, the value for instance of (P31) should be an item that uses subclass of (P279) with value chromosome (Q37748) (or a subclass thereof). (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/P1057#Value type Q37748, SPARQL
Type “gene (Q7187), sequence variant (Q15304597), noncoding DNA (Q1458444), chromosome abnormality (Q744962)”: item must contain property “instance of (P31), subclass of (P279)” with classes “gene (Q7187), sequence variant (Q15304597), noncoding DNA (Q1458444), chromosome abnormality (Q744962)” 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/P1057#Type Q7187, Q15304597, Q1458444, Q744962, SPARQL
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This property is being used by: Please notify projects that use this property before big changes (renaming, deletion, merge with another property, etc.) |
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Replaces P643
editUse this property instead of P643 (P643). LaddΩ chat ;) 02:16, 11 February 2014 (UTC)
remove allowed type non-coding RNA
editI'm very sorry but RNA in general has no direct assocation with a chromosome. It may have an association with a gene or pseudogene. Mixing pseudogenes with RNA in one object is simply laziness and will hurt people or AIs in later searches. --SCIdude (talk) 07:29, 20 August 2019 (UTC) Ok, there may be a need for those cases where the DNA is intergenic, so I'll add the class noncoding DNA. So every genic noncoding RNA/intergenic RNA needs an pseudogene/noncoding DNA association for specifying the chromosome. --SCIdude (talk) 07:42, 20 August 2019 (UTC)
- @SCIdude: I agree with you on principle, but this currently creates constraint violations in all microRNA articles such as hsa-mir-6085 (Q27591293), so we should probably remove the P1057 property from these and ensure they all have encoded by (P702) ? --Hannes Röst (talk) 18:01, 8 October 2020 (UTC)
- Exactly, there are 4,558 such items (microRNA and mature microRNA). Note there are multiple issues like strand orientation, genomic start/end (should be both on gene), and the genes having P31+P279-->non-coding RNA. Of course, this is on my list but not at the top. --SCIdude (talk) 06:49, 9 October 2020 (UTC)