Comments (2)
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.
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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.
Related Issues (20)
- pronto_implementation returns a pronto Definition object which interacts oddly with KGCL
- simple obo diffs creates duplicate `Classes added` HOT 6
- Problem using llm adapter HOT 2
- runoak diff erroneously names "relationships" --> "mappings" in markdown summary HOT 4
- Add option to `relationships` for walking up subclass hierarchy
- `validate-mappings`: `NotImplementedError: ... NoneType`
- Missing `defusedxml` dependency HOT 3
- Run subset of tests in environment with no extras installed
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- Breaking change in Synonymizer? HOT 3
- Document instructions for running the obographs-compliance suite HOT 4
- Update SemSimianImplementation and CLI to allow using custom IC maps and frequencies
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- Integrate notebooks into sphinx documentation (will break URLs) HOT 2
- Define behavior when conflicting idspaces are specified
- Calculating ICs with an annotation corpus as background is slow
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