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chemkg / chemrof

Schema for chemistry ontology classes
https://chemkg.github.io/chemrof
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metaclasses as species #2

Open wdduncan opened 4 years ago

wdduncan commented 4 years ago

Using metaclasses for species is interesting. Some questions that come to mind are:

  1. What advantages do you get using metaclasses instead subclasses? For example, in your sides, you have nickel atom as a instance of the atom metaclass. What not have nickel as a subclass of atom?
  2. In the OWL representation, the metaclass instances would be punned classes/individuals. I didn't think that reasoners worked on punned entities. Is that an acceptable loss? Or would not have an OWL version, and only have an RDF version?
cmungall commented 4 months ago
  1. I think this is all now answered by the documentation? The entire purpose of chemrof is to put specific entities like nickel or nickel ions in the domain of discourse. The linkml classes are for structuring
  2. reasoners work on punned classes/individuals, this is valid DL. And in any case there is no reliance on punning. You would run reasoners on the generated TBox. See https://chemkg.github.io/chemrof/ontology/
wdduncan commented 4 months ago

Ok. The linkml is generating the OWL.
I'm not sure how some of the OWL classes are generated from the linkml schema. For example, berkelium (symbol Bk) is one of the OWL classes. But I can't find either berkelium or Bk in chemrof.yaml.