Clean up xref handling in ontology outputs

[balhoff]

We have been annotating xrefs using qualifiers like skos:narrowMatch and skos:exactMatch (#20620). Right now the degree to which these annotations are carried through the pipeline varies, and likewise the handling of these qualifiers in outputs varies. We will make handling of these more sensible in a few ways:

• Only allow exact and narrow mappings into x2go files
• Only allow exact and narrow mappings into production OBO files (This is a change; currently narrow are filtered out. @cmungall suggests go.obo stays consistent with x2go files. We will discuss in an ontology call)
  • Discussed with @pgaudet; eventually we want only exact and narrow xrefs in all products (including go-plus). Broad and related would only get released as direct SKOS relations.
• Ensure trailing qualifiers are NOT included in OBO files. These should continue to be filtered out (handling xref type annotations in go.obo and go.owl #20770 (comment))
• Generate direct skos triples from the qualified xrefs, as a more straightforward representation of mappings in the ontology generate SKOS triples from xrefs #27247
  • We should make sure that the OBO representation of these triples uses CURIEs, by specifying the needed IDSPACEs (related: Save go-edit.obo using Protege 5.6.4 #28012)
    • This should be aligned with db-xrefs.yaml; update rdf_uri_prefix as needed.
  • This should fix the issue that the qualifiers are not represented in the JSON ontology format: broad/narrow xref qualifiers are not exported in OBO JSON format #28558
• Generate SSSOM versions of mappings files, which is able to represent the qualifiers Migrate xrefs to a new system that allows to specify meanings of xrefs #20147
• Ensure xref qualifiers are correctly structured add check for source annotation property on xref axioms #28417
• remove enzyme xrefs from obsolete terms #28557
• Add check for database definition cross references to also be a general cross reference #28523
• Discussion point: would it be easier for editors to directly enter SKOS relations rather than xrefs with axiom annotations?
• Ensure that x2go mappings that are not coming out of the ontology are also converted to SSSOM and have a defined mapping type

[pgaudet]

I am assigning myself to add documentation once this is done.

[ValWood]

tagging myself so that I can remove my filter when it's fixed.

[balhoff]

We should discuss URI expansions for SKOS predicate values in the OBO prefixes Slack channel.

[balhoff]

Consider merging external x2go mappings into the built ontology for release:

go-ontology/src/ontology/Makefile

Lines 612 to 622 in 111d6fb

	wget https://ftp.ebi.ac.uk/pub/databases/GO/goa/external2go/interpro2go -O external2go/interpro2go
	wget https://ftp.ebi.ac.uk/pub/databases/GO/goa/external2go/pfam2go -O external2go/pfam2go
	wget https://ftp.ebi.ac.uk/pub/databases/GO/goa/external2go/pirsf2go -O external2go/pirsf2go
	wget https://ftp.ebi.ac.uk/pub/databases/GO/goa/external2go/prints2go -O external2go/prints2go
	wget https://ftp.ebi.ac.uk/pub/databases/GO/goa/external2go/prosite2go -O external2go/prosite2go
	wget https://ftp.ebi.ac.uk/pub/databases/GO/goa/external2go/smart2go -O external2go/smart2go
	wget https://ftp.ebi.ac.uk/pub/databases/GO/goa/external2go/uniprotkb_kw2go -O external2go/uniprotkb_kw2go
	wget https://ftp.ebi.ac.uk/pub/databases/GO/goa/external2go/uniprotkb_sl2go -O external2go/uniprotkb_sl2go
	wget https://ftp.ebi.ac.uk/pub/databases/GO/goa/external2go/unirule2go -O external2go/unirule2go
	wget https://ftp.ebi.ac.uk/pub/databases/GO/goa/external2go/hamap2go -O external2go/hamap2go
	wget https://ftp.ebi.ac.uk/pub/databases/Rfam/CURRENT/rfam2go -O external2go/rfam2go

Also, consider retrieving external x2go mappings directly as SSSOM.