Closed balhoff closed 3 years ago
Same thing with PCO
.
@balhoff Yes, OBO context is being imported but somehow PATO and PCO is not being included in the generated JSON-LD context.
ENVO
is also missing from the JSON-LD context.
I believe there is a bug in linkML where prefixes for CURIEs in certain slots are not imported from the upstream JSON-LD context. i.e. even if PATO
and PCO
exist in OBO context, somehow linkML doesn't see that it should be importing them.
I have a fix for this. The bug is in jsonldcontextgen.py
Out of curiosity -- is this a (bio)LinkML issue or a biolink-model issue?
This was originally reported in Biolink Model. But the bug is originating from linkML.
Specifically, ContextGenerator in jsonldcontextgen.py only looks at CURIEs (and their prefixes) for the mappings
slot of a class. It fails to check related_mappings
, close_mappings
, narrow_mappings
, exact_mappings
, and broad_mappings
.
PR #345 adds a fix for this issue.
is this now fixed?
Yes, this was fixed almost a month ago. Should have closed the ticket when the PR #345 was merged.
Biolink model references PATO several times, but there is no PATO prefix in the context. I thought Biolink was merging in the OBO prefix set; is this not true?