YeastPathways models have imaginary DB ref

[suzialeksander]

Less technical description: Currently the DB ref for a model is something like SGD:SERSYN-PWY, which isn't actually a SGD ID & doesn't appear to be mapped to anything.

More technical description: Referencing https://github.com/geneontology/pathways2GO/issues/37 as it contains some history on how the source field was populated. I'm now realizing this becomes the DB:Reference (aka PMID of evidenced literature) column in GPAD and so should follow the GPAD spec. To conform to the spec, this source needs to be a CURIE.

Note that source currently "works" for Reactome with an example CURIE Reactome:R-HSA-112303 correctly expanding and forwarding to its Reactome pathway page. However, does this "work" for the GPAD reference column? While syntactically correct, is this value meaningful as a literature reference?

For YeastPathways, conveniently, identifiers.org already has sgd.pathways registered so we can just use this. But do we need to add this to a context JSONLD such as go_context.jsonld? Like:

        "sgd.pathways": "https://identifiers.org/sgd.pathways/", 

Originally posted by @dustine32 in https://github.com/geneontology/pathways2GO/issues/126#issuecomment-1190839092

[suzialeksander]

Two proposed options from call with @kltm and @dustine32 :

1. Have SGD add these 220 pathways (names like LIPASYN-PWY-1 PWY-5703) to work in the yeastgenome.org search disambiguation (which is oddly in the dbxrefs.yaml under SGD_LOCUS):

  url_syntax: https://www.yeastgenome.org/search?q=[example_id]&is_quick=true
  example_id: SGD_PWY:LIPASYN-PWY-1
  example_url: https://www.yeastgenome.org/search?q=SGD_PWY:LIPASYN-PWY-1&is_quick=true

2. Add a new namespace in the dbxrefs.yaml likeSGD_PWY: . This would go to https://pathway.yeastgenome.org/ and end up at https://pathway.yeastgenome.org/YEAST/NEW-IMAGE?type=PATHWAY&object=YEAST-SALV-PYRMID-DNTP

[suzialeksander]

SGD is opting for door no.2, changing dbxrefs.yaml. I'll put in a PR.

[suzialeksander]

@dustine32 the SGD_PWY: should now be a real thing, let me know if you need anything else on my end

[dustine32]

@suzialeksander Awesome, thank you! I'll update the code and get some new models into noctua-dev.