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geneontology / minerva

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Do PomBase identifiers have root type values in minerva? #408

Closed vanaukenk closed 2 years ago

vanaukenk commented 3 years ago

It's possible to enter various PomBase names or identifiers into Noctua but then they don't display on the Noctua form table. because minerva doesn't have the information about the root type of PomBase entities. The values/ids are there.

This is related to https://github.com/geneontology/noctua-form/issues/122

Perhaps the neo journal loaded into minerva is not up-to-date?

@kltm @balhoff - can you take a look/advice?

Discussed with @tmushayahama on a workbenches call

balhoff commented 3 years ago

I need to defer to @kltm to start off; I think he needs to check what is being deployed with minerva.

kltm commented 3 years ago

@balhoff minerva production is running as: --arachne -g http://skyhook.berkeleybop.org/go-lego-reacto.owl --set-important-relation-parent http://purl.obolibrary.org/obo/LEGOREL_0000000

The operative thing being: http://skyhook.berkeleybop.org/go-lego-reacto.owl. This is the same as noctua-dev.

kltm commented 3 years ago

Also see possibly relevant PomBase GPI issue: https://github.com/geneontology/noctua/issues/727#issuecomment-908775024

balhoff commented 3 years ago

@kltm isn't there more to the command line? Like --ontojournal, etc.?

kltm commented 3 years ago

Of course--and a lot of other stuff--but I trimmed out anything local or not related. (Trimmed as cluttered and I didn't really want to start putting out internal ports and URLs.)

balhoff commented 3 years ago

Okay. http://skyhook.berkeleybop.org/go-lego-reacto.owl doesn't have genes; we need NEO for that. But anyway maybe the GPI change will fix the issue.

kltm commented 3 years ago

Pausing temporarily while we sort: https://github.com/geneontology/noctua/issues/727#issuecomment-909694414 . When done, I'd like to bounce noctua-dev to see if the issue gets cleared on a complete rebuild of the datastores on the server.

kltm commented 3 years ago

Okay looking at the resolution to https://github.com/geneontology/minerva/issues/339, since PomBase should now be available in NEO searching for ("Spom" gets ~5483 results), I believe the next steps would be to wait for a rebuild and check to see if we've cleared this. We could also check this locally so we could iterate before the next outage.

vanaukenk commented 2 years ago

This looks to be fixed on production. See: http://noctua.geneontology.org/workbench/noctua-form/?model_id=gomodel%3A60ff660000001748