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cmungall avatar cmungall commented on June 29, 2024

The challenge here is that client code may need to be generic; for example:

  • using is-a and part-of (BFO:0000050) as defaults
  • using a certain set of mapping predicates (e.g. exactMatch, closeMatch) as defaults

Not every ontology instantiates every one of these, so if we use lookups to determine validity, this will yield false positive errors.

We could do some hardcoding (e.g hardcode a set of RO IDs as never being mapping predicates, hardcode skos to never be a relationship predicate), but this would only catch a subset of errors, and would not be very generic.

What is the algorithm for determining if something is a valid predicate? Unfortunately there are a large number of different ontologies out there that represent things in different ways.

We could simply look up the predicate in the existing ontology.

from ontology-access-kit.

joeflack4 avatar joeflack4 commented on June 29, 2024

Oh, I didn't realize that this could be a difficult thing. I actually thought that (though I see how that is naive) the same predicate would be used in the same way for any ontology. And I also thought that OAK was already doing hard-coding of such 'invalid' predicates.

from ontology-access-kit.

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