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geneontology / noctua

Graph-based modeling environment for biology, including prototype editor and services
http://noctua.geneontology.org/
BSD 3-Clause "New" or "Revised" License
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Add additional relations to hardcoded relation hierarchy selector #414

Closed cmungall closed 7 years ago

cmungall commented 7 years ago

cc @vanaukenk

kltm commented 7 years ago

Ticket needs an actionable body.

vanaukenk commented 7 years ago

@kltm @cmungall

As discussed on the annotation call this morning, the two additional Noctua relations to be added to the hardcoded GO relation hierarchy are:

id: RO:0002304 name: causally upstream of, positive effect comment: holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y property_value: http://purl.org/dc/elements/1.1/creator "cjm" xsd:string is_a: RO:0002411 ! causally upstream of

id: RO:0002305 name: causally upstream of, negative effect comment: holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y property_value: http://purl.org/dc/elements/1.1/creator "cjm" xsd:string is_a: RO:0002411 ! causally upstream of

Thank you.

kltm commented 7 years ago

How about https://github.com/geneontology/noctua/issues/392

kltm commented 7 years ago

Ideally, we can close these both into one ticket. Is #392 still valid?

cmungall commented 7 years ago

OK, let's move over there

vanaukenk commented 7 years ago

IIRC, there was additional work that needed to be done wrt #392, as discussed in https://github.com/geneontology/go-ontology/issues/12811

balhoff commented 7 years ago

That's right, the Minerva stuff I did for https://github.com/geneontology/go-ontology/issues/12811 is all done except for coordinating with @kltm to actually make the database edits, which hasn't actually happened yet.

kltm commented 7 years ago

@balhoff Which database are you referencing here?

balhoff commented 7 years ago

The embedded Blazegraph store in the production Minerva instance.

balhoff commented 7 years ago

We need to run some SPARQL updates on the content, for which I made a minerva-cli option.

kltm commented 7 years ago

It's slowly coming back to me. You've tested that on the current contents of noctua-models/minerva?

balhoff commented 7 years ago

Not recently, this just jogged my memory. I'll retest sometime soon and let you know. But what we will do is:

  1. Take Minerva offline.
  2. Make a backup copy of the journal.
  3. Run a series of SPARQL updates against the journal using minerva-cli.
  4. Relaunch Minerva.
  5. Trigger the normal dump to ttl procedure and inspect the git diff as a sanity check.
kltm commented 7 years ago

Ah, that explains a bit why this stalled out.

cmungall commented 7 years ago

This ticket seems to be mixing two things:

  1. adding 2 additional relations to the hardcoded selector
  2. rewiring some of the existing models

Can we not just proceed on 1?

cmungall commented 7 years ago

OK, I see we have another ticket with the same title. I marked this as a dupe and then closed this. But I think this ticket has morphed into the ticket about rewiring the models? If so we should retitle it.