Data build files following mondo release #782
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twhetzel
added
the
build
| @@ -200,7 +200,6 @@ http://purl.obolibrary.org/obo/MONDO_0007672 http://identifiers.org/hgnc/14373 O | |||
| http://purl.obolibrary.org/obo/MONDO_0007681 http://identifiers.org/hgnc/17098 OMIM:138800 https://omim.org/entry/606241 | |||
| http://purl.obolibrary.org/obo/MONDO_0007686 http://identifiers.org/hgnc/31928 OMIM:139090 https://omim.org/entry/614169 | |||
| http://purl.obolibrary.org/obo/MONDO_0007688 http://identifiers.org/hgnc/6770 OMIM:139210 https://omim.org/entry/600993 | |||
| http://purl.obolibrary.org/obo/MONDO_0007690 http://identifiers.org/hgnc/2594 OMIM:139300 https://omim.org/entry/107910 | |||
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I confirmed this OMIM https://omim.org/entry/139300 no longer matches the rules for disease defining.
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Hmm, I'm debugging the OMIM pipeline and it's currently not even processing OMIM:139300 or OMIM:107910 to add associations for them. It's possible that the data has changed since your build was run, but that would be surprising since the OMIM release ran just 4 days ago. Won't be able to look into this until next week.
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The removal of the disease defining association is correct.
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When did you run this? I just downloaded the file from the release and this entry is not there.
If you didn't run this before Sunday, then maybe there is some problem with mondo-ingest fetching old data.
| @@ -2353,7 +2353,6 @@ http://purl.obolibrary.org/obo/MONDO_0013259 http://identifiers.org/hgnc/10013 O | |||
| http://purl.obolibrary.org/obo/MONDO_0013263 http://identifiers.org/hgnc/34383 OMIM:613428 https://omim.org/entry/613425 | |||
| http://purl.obolibrary.org/obo/MONDO_0013264 http://identifiers.org/hgnc/17142 OMIM:613435 https://omim.org/entry/602432 | |||
| http://purl.obolibrary.org/obo/MONDO_0013268 http://identifiers.org/hgnc/450 OMIM:613451 https://omim.org/entry/605420 | |||
| http://purl.obolibrary.org/obo/MONDO_0013270 http://identifiers.org/hgnc/3811 OMIM:613454 https://omim.org/entry/164874 | |||
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MONDO_0013270 is obsolete in Mondo
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Hmm. The OMIM pipeline doesn't have access to see which Mondo terms are deprecated. It will look for anything inside of these files mondo_exactmatch_omim.sssom.owl and mondo_exactmatch_omimps.sssom.owl, which it downloads from the Mondo master branch.
I don't think it would be easy to filter deprecated in the OMIM repo, but mondo-ingeset is set up much more easily to do that.
Can you make a ticket for this?
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@joeflack4 why is a ticket needed? Seeing this line removed is correct.
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Oh sorry it is red not green. I was focusing more on your words -_- / I figured that the comment was an indication of an issue, rather than showing things were working as expected
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Passes my general spot check, though these seem surprisingly high to me:
src/mappings/ordo.sssom.tsv | 91302 ++++++++--------------
src/ontology/unmapped/ncit-unmapped.owl | 3704 +-
ICD11 is higher because I just updated the release for the first time in many months:
.../reports/mirror_signature-icd11foundation.tsv | 822 +-
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Thanks Joe. Remember these results (src/mappings/ordo.sssom.tsv | 91302) include the "fix ordo" query update that was recently added and the numbers and file changes look to match up with that change. |
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this is an enormous change - is this explainable by recent changes?
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yes, i believe it's explainable by the recent update to the "fix ordo query"
Resolves #ISSUE(s).
Overview
This PR:
Is a full data build from
mainfollowing the Mondo release last week to be merged back intomain.Pre-merge checklist
Documentation
Was the documentation added/updated under
docs/?QC
Was the full pipeline run before submitting this PR using
sh run.sh make build-mondo-ingeston this branch (afterdocker pull obolibrary/odkfull:dev), and no errors occurred?New Packages
Were any new Python packages added?
Were any other non-Python packages added?
PR Review and Conversations Resolved
Has the PR been sufficiently reviewed by at least 1 team member of the Mondo Technical team and all threads resolved?