broad/narrow xref qualifiers are not exported in OBO JSON format

[balhoff]

These are included in go-plus.owl, but not go-plus.json.

[cmungall]

See also geneontology/obographs#102

[pgaudet]

Hi @balhoff

RHEA folks also noted that in the go.owl and go.obo, only broad and exact RHEAs are exported, but narrow are missing.

Could all xrefs be added to all files?

Thanks, Pascale

[parit]

An example for GO-Rhea narrowMatch would be GO:0004126 -> RHEA:13433 and RHEA:16069

[balhoff]

@pgaudet this is on purpose: #20770 (comment)

Should we change the policy? In the past all trailing qualifiers were removed from the main release, so we filtered narrowMatch xrefs before that happened. But now that I look at go.owl and go-basic.obo, I see trailing qualifiers. To be honest I'm not sure how that changed. So perhaps we should just stop filtering the narrow xrefs.

[balhoff]

Removal of trailing qualifiers is supposed to happen due to this line:

go-ontology/src/ontology/Makefile

Line 265 in 617fba5

ontology-release-runner --catalog-xml catalog-v001.xml --ignoreLock --skip-release-folder --skip-format owx --skip-format metadata --outdir $(BUILD_DIR) --allow-overwrite --asserted --simple --no-reasoner --remove-trailing-qualifiers $< &&\

[pgaudet]

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 dont have NARROWs but we have BROADs .

In the normal files we should have all mappings, making sure to include types, and we can discuss making simpler files if needed.

Does that make sense?

[balhoff]

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 dont have NARROWs but we have BROADs .

The mapping files are generated before the narrows are removed. My understanding is that @cmungall wanted the narrow xrefs to remain in the mappings files. But probably I should have revisited that workflow when we started using 'broad' as well.

[pgaudet]

But NARROW are valid to make GO annotations. Why would we remove those?

[balhoff]

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 xrefs). But now it seems like the trailing qualifiers are not stripped anyway, which I don't understand after checking the makefile (this was not changed).

[pgaudet]

I'll put this on next Monday's call.

[pgaudet]

The other issue is that the mapping file doesn't contain the mapping type, so it is not possible to use that file to make annotations.

[sjm41]

These are included in go-plus.owl, but not go-plus.json.

Looks like the broad/narrow/exact/related xref qualifiers are also omitted from the go-basic.obo file, which is the one that FlyBase consumes. We want/need to be able to filter xrefs based on these qualifiers, so we'd also want them to appear in the go-basic.obo file.

[pgaudet]

Right - we need all the cross-references in all the files, otherwise it creates more confusion.