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monarch-initiative / mondo-ingest

Coordinating the mondo-ingest with external sources
https://monarch-initiative.github.io/mondo-ingest/
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OMIM x-ref in DO but not in Mondo #336

Open sabrinatoro opened 1 year ago

sabrinatoro commented 1 year ago

The following DO terms have mapping to OMIM x-ref which are not in Mondo, and not in the omim slurp file Here are some examples:

DO id label OMIM x-ref
DOID:0070372 leukoencephalopathy with vanishing white matter 3 OMIM:620314
DOID:0070376 developmental and epileptic encephalopathy 31B OMIM:620352
DOID:0070364 bradyopsia 2 OMIM:620344
sabrinatoro commented 1 year ago

note: the omim x-refs are not on the exclusion list.

matentzn commented 1 year ago

These are all super new - you don't need to deal with them at all.

Remaining action item:

joeflack4 commented 1 year ago

@sabrinatoro @matentzn Just fixed this via: https://github.com/monarch-initiative/omim/pull/94

Sorry about this! There was a missing -B flag in the github action, so it hasn't actually been re-running, and has been using an old, committed version of omim.ttl.

We previously have been committing it but perhaps it's also time to remove it from commits, since it's in the release.

Anyway, I checked and the new release does have these new MIMs.

sabrinatoro commented 1 year ago

What is the status of this issue?

OMIM:620459 is not in the slurp file. Is this the same issue that still needs to be resolved, or is it a new bug? Thanks!

joeflack4 commented 1 year ago

Just took a look. It's a different bug. Same problem, but different cause. The new cause is https://github.com/monarch-initiative/omim/issues/105. Something appears to have changed in the Python Package Index, I think, which is causing installation failure of Python packages within the GitHub action.

I say this is a GitHub action issue, because I looked at the last successful run on July 16th, and OMIM:620459 doesn't appear there. But I just did a fresh run and it does appear.

I suppose I should bump up the priority of fixing this issue.

For today, I just reran locally and uploaded a new release dated today, so the next time that the mondo-ingest pipeline is run, this term should appear in the slurp now.