Jim Balhoff

@vanaukenk any thoughts on these UniProt IDs? ``` "UniProtKB-SubCell:SL-0191"^^ "UniProtKB-KW:KW-1003"^^ ```

> Hi [@balhoff](https://github.com/balhoff) - those entries are actually correct. > > I think you could double-check any dodgy-looking entries with the db-xrefs.yaml: > > https://github.com/geneontology/go-site/blob/master/metadata/db-xrefs.yaml Oh, thanks, good to know!

Now that we have [Soufflé](https://souffle-lang.github.io) in ODK, it seems like it would be a good fit for this task: - Convert the basic.owl to N-triples, run a quick [`sed`](https://github.com/INCATools/ubergraph/blob/b26f703d7b51764455d4708ee40f64cdab4d6da7/Makefile#L43) to...

Run this as a report first. Another check: if A and B are both xrefs the terms should be subclass/superclass.

Only do CI checks for when both a parent and child xref are in the ontology. In that case the child either needs to be on a subclass or as...

@pgaudet this is on purpose: https://github.com/geneontology/go-ontology/issues/20770#issuecomment-770626191 Should we change the policy? In the past all trailing qualifiers were removed from the main release, so we filtered narrowMatch xrefs before that...

Removal of trailing qualifiers is supposed to happen due to this line: https://github.com/geneontology/go-ontology/blob/617fba53cbb0022cc5767dd29653a1834c35b823/src/ontology/Makefile#L265

> It seems we didn't do what was requested: > > > probably NARROW and EXACT synonyms are OK; but we may not want to include BROAD synonyms for mappings....

We have been leaving them in the mapping file, but removing them from the ontology, since the stripping of trailing qualifiers was confusing users (looking like there were several equivalent...

One thing I want to add to @pgaudet's comment above is that we can include the skos relationships in the OBO files. There are some technical dependencies preventing me from...