Property talk:P7963

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[create Create a translatable help page (preferably in English) for this property to be included here]
Format “CL_[0-9]{7}: value must be formatted using this pattern (PCRE syntax). (Help)
List of this constraint violations: Database reports/Constraint violations/P7963#Format, hourly updated report, SPARQL, SPARQL (new)
Distinct values: this property likely contains a value that is different from all other items. (Help)
Exceptions are possible as rare values may exist.
List of this constraint violations: Database reports/Constraint violations/P7963#Unique value, SPARQL (every item), SPARQL (by value), SPARQL (new)
Single value: this property generally contains a single value. (Help)
Exceptions are possible as rare values may exist.
List of this constraint violations: Database reports/Constraint violations/P7963#Single value, SPARQL, SPARQL (new)
Type “anatomical structure (Q4936952): element must contain property “instance of (P31)” with classes “anatomical structure (Q4936952)” or their subclasses (defined using subclass of (P279)). (Help)
Exceptions are possible as rare values may exist.
List of this constraint violations: Database reports/Constraint violations/P7963#type Q4936952, SPARQL, SPARQL (new)

type constraint[edit]

@TiagoLubiana, ArthurPSmith, Gtsulab: I made the type constraint (Q21503250) here relation (P2309) instance of (Q21503252) AND class (P2308) cell type (Q189118) as per the proposal - but I think the type constraint (Q21503250) should allow either:

If only one constraint can be captured I think relation (P2309) subclass of (Q21514624) AND class (P2308) cell (Q7868) may be better.

I'm unsure how to capture such a constraint though and I am trying to figure it out, but in the mean time if you disagree with the proposed constraint please raise objections here. Iwan.Aucamp (talk) 10:02, 15 March 2020 (UTC)

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Discussion[edit]

  • Hello @Iwan.Aucamp:. As far as I know, there are no instances of cells in the cell ontology, only instances of cell types. An instance of a cell would be something very specific, like the ovule that gave rise do Dolly, the cloned sheep. It is so specific that I believe there is not even an item for that. All cell types that are currently classified as instances of cells are actually misclassified. The concepts are often mixed, even in the academic literature.TiagoLubiana (talk) 16:26, 15 March 2020 (UTC)
@TiagoLubiana: Currently the constraint is ( relation (P2309) instance of (Q21503252) AND class (P2308) cell type (Q189118)) - which is how I understood your proposal. If we look at your examples though:
However, for macrophage (Q184204) there is only:
There is no
Therefore adding Cell Ontology ID (P7963) to macrophage (Q184204) will violate the property constraint (which it does, as I added it from examples).
The alternative property constraint ( relation (P2309) subclass of (Q21514624) AND class (P2308) cell (Q7868)) will not be violated by having Cell Ontology ID (P7963) to macrophage (Q184204). Now I would guess that macrophage (Q184204) instance of (P31) cell type (Q189118) should exist but this still leaves the question which is the better type constraint (Q21503250) of these two:
  1. ( relation (P2309) subclass of (Q21514624) AND class (P2308) cell (Q7868))
  2. ( relation (P2309) instance of (Q21503252) AND class (P2308) cell type (Q189118))
I think the first, but that is what I want to confirm here. If you prefer something completely different please clarify. I don't want to make anything instance of (P31) cell (Q7868). Iwan.Aucamp (talk) 16:41, 15 March 2020 (UTC)
@Eihel: You really should try and consult in property pages before making changes to them as per Help:Properties#Editing_properties and at least get some consensus. Further from Help:Basic_membership_properties "subclass of (P279) is used to state that all the instances of one class are instances of another". Translating that here bronchial epithelial cell (Q30029740) subclass of (P279) cell (Q7868) would imply that all bronchial epithelial cells are also cells - which is the case.
If on the other hand something is bronchial epithelial cell (Q30029740) instance of (P31) cell (Q7868) it means that bronchial epithelial cell (Q30029740) is an individual cell (Q7868) - it is no longer a class of cell, or a type of cell - which would be wrong because bronchial epithelial cell (Q30029740) is in fact a class of cell. Put differently, say I have a particular cell (Q7868) which is noteworthy, maybe it had left-handed DNA, and this particular cell (Q7868) was designated "Sample Cell 9994". This cell seems notable so I want to make a wikidata item for it, and I now want to say "Sample Cell 9994" is a cell (Q7868), which it is - so I put Sample Cell 9994 instance of (P31) bronchial epithelial cell (Q30029740) - which is correct - but now, if bronchial epithelial cell (Q30029740) instance of (P31) cell (Q7868) - I have an instance of an instance ... which does not make any sense and will raise a warning anyway.
This is in line with Help:Basic_membership_properties. I'm fairly sure the amount of times a property is used is not relevant. If there are specific guidelines that is in line with what you suggest please reference them.
Property constraints are there to tell you when you are doing something wrong - in this case if the property constraint is ( relation (P2309) subclass of (Q21514624) AND class (P2308) cell (Q7868)) it will indeed say there is a violation if you put Cell Ontology ID (P7963) on bronchial epithelial cell (Q30029740) - but this is by design - because bronchial epithelial cell (Q30029740) is wrong. Iwan.Aucamp (talk) 13:54, 21 March 2020 (UTC)

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────────────────────────────────────────────────────────────────────────────────────────────────────I am not a specialist in biology Iwan.Aucamp. Okay, if there are notable cells at bronchial epithelial cell (Q30029740), let's put bronchial epithelial cell (Q30029740) subclass of (P279) cell (Q7868) as you suggested. Attention: I never said that bronchial epithelial cell (Q30029740) was right: for me, even instance of (P31) is wrong in this Item. Regarding Help:Properties#Editing properties, my change to the property you created is not a major change and therefore does not require the opinion of the community. It is precisely your responsibility that it works. Precisely, that leads us to the next paragraph.

It is not cell (Q7868) that I introduced in the constraint, but anatomical structure (Q4936952). One more reason it works, because bronchial epithelial cell (Q30029740) nowhere contains cell or cell type. There are flaws in my choices on the constraint, but they are minimal and thwarted by the other constraints. I repeat again: here, the desired effect is not to "link data", but to prevent someone from taking this property in a bad Item. My choice is not in contradiction with what we write. You get stuck on cell type and cell, but I went further. I write my choice more clearly:

property constraint
Normal rank type constraint Arbcom ru editing.svg edit
class anatomical structure
relation instance or subclass of
▼ 0 reference
+ add reference


+ add value

Eihel (talk) 18:00, 21 March 2020 (UTC)

@Eihel: First off - you are suggesting that we accommodate bronchial epithelial cell (Q30029740) with the property constraint - if you don't think that bronchial epithelial cell (Q30029740) instance of (P31) anatomical structure (Q4936952) is right then it is really hard to understand why you want to accommodate it and I would appreciate if you can explain the reason why we should change this property to accommodate something which me, you and and others agree is wrong. Iwan.Aucamp (talk) 21:15, 21 March 2020 (UTC)
@Eihel: Next, the reason why bronchial epithelial cell (Q30029740) instance of (P31) anatomical structure (Q4936952) is wrong has absolutely nothing to do with whether there are notable cells. If there is never a notable cell ever on wikidata it still won't make bronchial epithelial cell (Q30029740) instance of (P31) anatomical structure (Q4936952) correct. CC @ChristianKl: Iwan.Aucamp (talk) 21:16, 21 March 2020 (UTC)
@Eihel: Now, to get to your proposal. We start with the property constraint (P2302) type constraint (Q21503250) / relation (P2309) instance or subclass of (Q30208840) aspect of it. For this to be justified (as opposed to property constraint (P2302) type constraint (Q21503250) / relation (P2309) subclass of (Q21514624)) we would need one of the following:
If you present either of these things I will agree with property constraint (P2302) type constraint (Q21503250) / relation (P2309) instance or subclass of (Q30208840) aspect of your proposed constraint. Without either of these the constraint is not justified. Iwan.Aucamp (talk) 21:53, 21 March 2020 (UTC)
@Eihel: on to the second part of your proposal property constraint (P2302) type constraint (Q21503250) / class (P2308) anatomical structure (Q4936952). For this aspect of the constraint to be justified we would need one of the following:
As with the other aspect, if you present either of these things I will agree with the property constraint (P2302) type constraint (Q21503250) / class (P2308) anatomical structure (Q4936952) aspect of your proposal. Without either of those I don't see any justification for it. Iwan.Aucamp (talk) 23:47, 21 March 2020 (UTC)