Wikidata:Property proposal/isotopically modified form of

isotopically modified form ofEdit

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   Under discussion

MotivationEdit

Another property to model relations between molecular entities. Label 'isotopically modified form of' instead of 'isotopically modified compound of' has been chosen because to be able to link other molecular entities (other than compounds, like ions) with each other. This is IMO the only possible method to link molecular entity with natural isotopic composition (assuming that every item about a molecular entity is that by default) with isotopically modified molecular entities. isotopically modified form subclass of (P279) regular item about a molecular entity would be possible if (1) chemical compounds in WD are classes (right now every chemical compound is classified as an instance of a class), (2) items about molecular entities in WD are assumed to with any/undefined isotopic composition, not with natural isotopic composition. This property is designed based on hydrated form of (P4770), i.e. unidirectional + item requires statement constraint (Q21503247) that requires isotopic compound (Q22332141) as a superclass. Wostr (talk) 18:34, 18 October 2020 (UTC)

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DiscussionEdit

  • I think subclass of (P279) is the right approach here, it is what we use for the isotopes themselves. There isn't any one "natural" isotopic composition anyway - there are some standard Earth surface ones, but I think it's a bit silly to say that a compound found, say, on Mars, is not identified by the associated wikidata item for the generic compound, even if the isotopic composition is different. ArthurPSmith (talk) 16:58, 19 October 2020 (UTC)
    • @ArthurPSmith: as I wrote above, this approach is not possible right now and won't be possible in the foreseeable future. The reasons are that chemical compounds are now classified as instances — i.e. it's not possible to add a subclass or an instance to an instance — and there was no agreement to change that. The problem is that chemical compound (Q11173) has dual use now — it is a part of classification of chemical species (most classes of chemical compounds classified as structural class of chemical compounds (Q47154513) and group of chemical compounds (Q56256086) /with subclasses/ have chemical compound (Q11173) as a superclass at some point) and is a metaclass for every item describing stereochemically or isotopically defined compound (just like structural class of chemical compounds (Q47154513) is a metaclass for structural classes o chemical compounds). That led to the existing situation in which most compounds are classified using instance of (P31). I don't see any possibility to change this situation right now, because there is no good data model proposed for chemical species and every discussion in WikiProject Chemistry leads to the same result: no consensus due to too few people participating in the discussion. Wostr (talk) 18:07, 19 October 2020 (UTC)
    • About the rest of your comment: almost every item about chemical species have 'mass' as a property, usually calculated using CIAAW data. So every such chemical species is assumed to have some default (natural) isotopic composition. Wostr (talk) 18:20, 19 October 2020 (UTC)
      • @Wostr: You state "it's not possible to add a subclass or an instance to an instance" - why not? We have that all over the place in Wikidata. Every chemical species is a class in the sense that it represents all the various possible real-world manifestation of that species, which would be instances of the class. As to the existing mass property, they probably should have the determination method (P459) qualifier reflecting the isotopic assumptions. ArthurPSmith (talk) 18:41, 19 October 2020 (UTC)
        • @ArthurPSmith: as to why not — because right now chemical species are not classes in WD. All chemical species instance of (P31) chemical compound (Q11173) and adding isotopically modified compound subclass of (P279) regular chemical compound (or even isotopically modified compound instance of (P31) regular chemical compound) triggers a violation (and rightly so) — as an example, you can't add liothyronine I-131 (Q27269725) subclass of (P279) liothyronine (Q327362) until there is no subclass of (P279) in liothyronine (Q327362) (ideally liothyronine (Q327362) subclass of (P279) DL-triiodothyronine (Q27163652) without redundant liothyronine (Q327362) subclass of (P279) chemical compound (Q11173)). Wostr (talk) 19:30, 19 October 2020 (UTC)
          • Well, this is exactly why I argued that subclass of (P279) should be used much more broadly for such abstract concepts (there is very likely no Wikidata item that refers to, for example, a single specific physical molecule of anything). What if you want to define both stereochemically and isotopically? Subclasses work, the current distinction between instance and class in these cases is just broken. ArthurPSmith (talk) 13:15, 21 October 2020 (UTC)
            • While I agree this is some kind of subclass you still need to indicate the fact that the isotopic content is different, together with the compound you are doing this relation. If you are happy with a long list of P279 statements that each has a qualifier as to the kind of subclass, then we can abandon other properties altogether. --SCIdude (talk) 13:23, 27 October 2020 (UTC)
              • @SCIdude: I assume the isotopic content would be indicated by has part (P527) statements on the isotopic compound item. What other superclasses are you thinking there should be for such items? I guess you could have 2 or 3, but I wouldn't expect a "long list of P279 statements" - can you explain a bit more why you think that would happen? ArthurPSmith (talk) 18:02, 27 October 2020 (UTC)
                • How should I know the future? If any property that can be interpreted as subclass is abandoned in favor of subclass then the number of such statements will rise. "antagonist of" will be subclass of antagonist, "inhibits" will be subclass of inhibitor, "tautomer", "stereoisomer" just to name a few. Be consistent! --SCIdude (talk) 18:13, 27 October 2020 (UTC)
                • I don't think that has part (P527) (and its inverse) should be used for chemical compounds for elemental composition, it is too general, right now it is used for different things which makes it very inconsistent. With classes like compound of carbon (Q2901852) in a classification tree, using has part (P527) could be abandoned. Also, there is a possibility to have classes like 'compound of carbon-14' (being a subclass of 'compound of carbon' and 'isotopically modified compound'). Wostr (talk) 13:45, 28 October 2020 (UTC)