DO NOT MERGE - Build for Updated bugfix icd11 generated synonyms #757
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twhetzel
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This was referenced Jan 17, 2025
joeflack4
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Jan 17, 2025
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Looks good!
I spot checked the changes made by the new SPARQL query and the results look good.
Generally all the other files look as expected, with 1 exception. The synonym sync files had a lot of diffs with equal +/-. I investigated, and the reason for this is because of the introduction of new columns in #720. So these big diffs are only temporary, and when these columns stabilize (e.g. after implementing #725, if we do), the diffs will be normal again.
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Resolves #ISSUE(s).
Overview
This PR:
Is a build from
_Updated-bugfix-icd11-generated-synonyms#756 that adds an additional ICD11 processing query to fix a quality control issue with synonym labels in ICD11 Foundation. This build and it's feature branch_Updated-bugfix-icd11-generated-synonymsare an additional branch frombugfix-icd11-generated-synonyms.Examples of changed synonym labels after processing ICD11 with the query:
http://id.who.int/icd/entity/1850911834
Meleda disease (OMIM #248300) --> Meleda disease
http://id.who.int/icd/entity/1907973642
ARCL-1 - [Autosomal recessive cutis laxa, type 1] (MIM 219100) --> ARCL-1 - [Autosomal recessive cutis laxa, type 1]
This changes some synonyms from the "ADDED" category to "CONFIRMED".
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?