Talk:Q8054

Instanciation of this item is usually not precise.

I see that some classes of proteins (such as tumor protein p53 (Q283350)) are reported as instances of protein (Q8054). This seems to me not precise, as these are not material entities, but classes of proteins. It would be more precise to represent them as subclasses of protein (Q8054). TiagoLubiana (talk) 18:52, 18 March 2020 (UTC)

@TiagoLubiana: Your mistake is to take the label as defining the item, which comes from Wikipedia usage, where the title usually defines the topic. In Wikidata the statements are defining, especially if they have references. With tumor protein p53 (Q283350) you can see that every statement points to it being the specific human protein, in particular the external identifiers. By the way we have the p53 family as well: p53 tumour suppressor family (Q24738786) and tumor protein p53 (Q283350) is linked with it via part of (P361).

However, there may be reasons to change tumor protein p53 (Q283350) to a subclass of protein (Q8054). In the real world an instance of a protein is a specific molecule that may have a unique distribution of element isotopes different from any other molecule of the same protein. In other words, what is an instance of (P31) of protein (Q8054) like tumor protein p53 (Q283350) is already a set of possibilities, including combinations of isotopes, mutational variants, post-translational modifications, splice variants, and, last but not least, structural conformations and homooligomers. --SCIdude (talk) 07:02, 4 May 2021 (UTC)

@SCIdude: Nice reply, That last part is the point I was trying to make: a P53 protein is just a type of protein, all real-word moleclules instances of "P53 protein" are instances of protein. Using part of (P361) seems suboptimal, as protein families are really superclasses that englobe the species-specific "protein type". Maybe splitting protein in two items: "class of proteins" and "protein molecule". So P53 would be a subclass of (P279) "protein molecule" and a instance of (P31) "class of proteins". The PRO ontology uses a subclassing system of that sort. TiagoLubiana (talk) 13:53, 4 May 2021 (UTC)

I also think that the IUPAC, which has proteins still as polypeptides, should go ahead and sort out the mess. --SCIdude (talk) 09:31, 28 June 2021 (UTC)

instance vs subclass

Here are recent stats of instances and subclasses of this class

P31			1003460
P279			 768979
P279+			 798642
P279+ but not P279	  29663
both P31 and P279+  	 760986
P279+ but not P31	  37655
P279 but not P31	  17581
P31 but not P279+	 242406
P31 but not P279	 251995

What distinguishes a subclass from an instance? It seems to me that it would be better to make some sort of determination that specific proteins are either instances or subclasses of this class, not both. Peter F. Patel-Schneider (talk) 17:00, 12 January 2024 (UTC)

I can imagine that "subclass" usually used for families while "instance" for specific proteins. How would you distinguish them using only P279? --Infovarius (talk) 21:31, 13 January 2024 (UTC)

One could use instance of (P31) for specific proteins and subclass of (P279)+ for families, but that doesn't seem to be what is happening because so many are both. So what is the distinction between instance of (P31) only, subclass of (P279)+ only, and both? Peter F. Patel-Schneider (talk) 22:19, 13 January 2024 (UTC)

All proteins should use P279. The distinction between specific proteins and classes of proteins can be easily achieved using metaclasses like protein family (Q417841) with P31. Wostr (talk) 22:31, 13 January 2024 (UTC)

That makes sense, but then the 760986 items that are both instances and subclasses should only be one or the other. How can this be fixed? Peter F. Patel-Schneider (talk) 14:26, 14 January 2024 (UTC)