Specs for xrefs types

[pgaudet]

Hello,

Following the request in #20135 we have implemented xref types. Specifically @balhoff added {source="skos:narrowMatch"}
when a term was merged into another term.

From the W3.org standards (https://www.w3.org/TR/skos-reference/#mapping), we could envision having:

skos:mappingRelation

• skos:closeMatch probably too confusing
• skos:exactMatch: GO term meaning is exactly the same as the xreferenced term; single EXACT or RELATED match allowed per term for any xref type
• skos:broadMatch: GO term meaning is narrower than that of the xreferenced term. More than one BROAD xref is allowed per term, and BROAD xref can be mapped to multiple terms
• skos:narrowMatch: GO term meaning is more general than that of the xreferenced term. More than one NARROW xref is allowed per term, but a given NARROW xref can only be mapped to a single term
• skos:relatedMatch: GO term meaning is not exactly the same as the xreferenced term, but the best match; single EXACT or RELATED match allowed per term for any xref type

We need to define the following

1. Should we add a type to all xrefs ?
2. If so - what are the rules: possibly

• if there is more than 1 xref of the same type, all would be automatically set to NARROW, and we can manually select an EXACT or RELATED as appropriate

3. What should we export ?

• go-basic.obo : only export EXACT or RELATED xref
• others: go.obo, go.owl, go-plus.owl : Export all xref types, plus the skos value

@balhoff @cmungall @hdrabkin

I'll put this for discussion for the first 2021 ontology editors call.

Thanks, Pascale

[balhoff]

The ontology build for go.obo, go.owl, go-basic, etc. specifically uses an option --remove-trailing-qualifiers

go-ontology/src/ontology/Makefile

Line 253 in 3fe0b62

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 $< &&\

This is a problem for outputting all these qualifiers. @cmungall do you know why this was originally used? I can make a diff to see what comes out if this is turned off.

[balhoff]

It looks like besides the skos:narrowMatch qualifiers, the only other ones that are being removed are a few GO_REF like this:

relationship: part_of GO:1902270 {http://purl.org/dc/terms/source="GO_REF:0000090"} ! (R)-carnitine transmembrane transport

[cmungall]

I believe I added these 7 years ago

https://github.com/geneontology/go-site/blob/master/metadata/gorefs/goref-0000090.md

it's fine to remove the axiom annotations on release, and also OK to change them to oio:source

[balhoff]

@cmungall they're already being removed — the change I want to make would stop removing them. Also fine? :-)

[cmungall]

I think it's safest to remove, if they are being remove already

[pgaudet]

Is goref-0000090 obsolete then ?

[pgaudet]

• Also, we need to
• 1. Document that we remove the NARROW xref mappings from go.obo and go.owl handling xref type annotations in go.obo and go.owl #20770
• 2. Decide what we do for other xref types
• 3. Decide which mapping we keep for the external to GO
• 4. Implement for all xref types (EC, MetaCyc, Reactome, wikipedia, etc

[pgaudet]

Need to make a decision:

• which we export
• make SSOM files
• decide what editors do

[pgaudet]

See manuscript submitted in Dec 2021 https://arxiv.org/abs/2112.07051