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Move disease LLM columns to disease categories #2012

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Merged
JacquesVergine merged 23 commits into from
Jan 12, 2026
Merged

Move disease LLM columns to disease categories #2012

JacquesVergine merged 23 commits into from
Jan 12, 2026

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@JacquesVergine JacquesVergine commented Jan 8, 2026 •
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Description of the changes

The columns is_pathogen_caused and is_glucose_dysfunction were previously provided by an LLM as part of Nico's disease list pipeline. Nico moved this logic to the disease_categories pipeline in a previous PR.

This PR updates the disease list pipeline to read these two columns from the disease_categories artefact instead of the disease list one.

Checklist:

  • Added label to PR (e.g. enhancement or bug)
  • Ensured the PR is named descriptively. FYI: This name is used as part of our changelog & release notes.
  • Looked at the diff on github to make sure no unwanted files have been committed.
  • Made corresponding changes to the documentation
  • Added tests that prove my fix is effective or that my feature works
  • Any dependent changes have been merged and published in downstream modules
  • If breaking changes occur or you need everyone to run a command locally after
    pulling in latest main, uncomment the below "Merge Notification" section and
    describe steps necessary for people
  • Ran on sample data using kedro run -e sample -p test_sample (see sample environment guide)

@JacquesVergine JacquesVergine self-assigned this Jan 8, 2026
@JacquesVergine JacquesVergine requested a review from a team as a code owner January 8, 2026 13:54
@JacquesVergine JacquesVergine requested review from leelancashire and removed request for a team and leelancashire January 8, 2026 13:54
@JacquesVergine JacquesVergine changed the title Get is_pathogen_caused and _is_glucose_dysfunction from disease_categories Get is_pathogen_caused and _is_glucose_dysfunction from disease categories Jan 8, 2026
Base automatically changed from jacques/ecdata-824-move-core-entities-code-to-the-matrix-repo to main January 8, 2026 16:49
@JacquesVergine JacquesVergine changed the title Get is_pathogen_caused and _is_glucose_dysfunction from disease categories Get is_pathogen_caused and is_glucose_dysfunction from disease categories Jan 12, 2026
@JacquesVergine JacquesVergine changed the title Get is_pathogen_caused and is_glucose_dysfunction from disease categories Move disease LLM columns to disease categories Jan 12, 2026
@JacquesVergine JacquesVergine merged commit 8a6524a into main Jan 12, 2026
16 checks passed
@JacquesVergine JacquesVergine deleted the jacques/ecdata-916-update-disease-category-logic-to-add-pathogen-and branch January 12, 2026 11:17
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@Dashing-Nelson Dashing-Nelson Dashing-Nelson approved these changes

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