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monarch-initiative / mondo

Mondo Disease Ontology
http://obofoundry.org/ontology/mondo
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Create QC to limit rare disease to the human disease branch #6416

Open sabrinatoro opened 1 year ago

sabrinatoro commented 1 year ago

rare diseases should be limited to the human disease branch.

This Sparql query can be used: https://api.triplydb.com/s/CQyBQn-dk

sabrinatoro commented 1 year ago

There are 20 diseases that are 'rare' and are in the susceptibility branch. I will update them. (@matentzn : should I wait and keep these as a test for the QC?)

matentzn commented 1 year ago

You should be able to do this yourself! Just add the query as

src/sparql/qc/mondo/qc-susceptibility-rare.sparql

open a PR like https://github.com/monarch-initiative/mondo/pull/6248/files

and ask me for a review!

sabrinatoro commented 1 year ago

Let me ask the question differently: If I leave these errors (the 20 susceptibility terms that are in the rare subset), will it be caught in the PR adding the QC test? Or will it be caught only after the PR is merged (and therefore through off a failure for everything as soon as the PR is merge)? (I think number 2, but I am hoping for number 1)

Just wondering about order of operations and if I will possibly "break" everyone's PR.

sabrinatoro commented 1 year ago

(and yes :-) I was planning of doing it myself :-) )

matentzn commented 1 year ago

I rcommend to write the failing check first, then fix. Two Different PRs!

So:

  1. Make PR (PR1) that fails.
  2. Fix everything on another PR. Nothing will fail (because the test is still on PR1).
  3. Merge master into PR1
  4. If passes, merge.
sabrinatoro commented 1 year ago

Makes sense. Thank you!

sabrinatoro commented 1 year ago

Issue blocked by #6419