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OHDSI / Atlas

ATLAS is an open source software tool for researchers to conduct scientific analyses on standardized observational data
http://atlas-demo.ohdsi.org/
Apache License 2.0
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Concept set display in cohort editor does not use vocabulary #2626

Open anthonysena opened 3 years ago

anthonysena commented 3 years ago

Expected behavior

Concepts displayed in a concept set expression are resolved against the vocabulary daimon.

Actual behavior

Concepts are displayed based on their definition in the cohort expression JSON which may differ from the concept's name in the vocabulary.

Steps to reproduce behavior

  1. Create a cohort with a concept set with at least 1 concept in the concept set expression
  2. Go to Export tab -> JSON -> edit a concept name, press Reload
  3. Save the cohort definition. Navigate to the concept set expression and observe that the name is not resolved against the vocabulary:

image

Context

Since cohort definitions may be created programmatically outside of ATLAS, we need some mechanism to make sure that the concept set names stored in the JSON are ignored in favor of the concept id's name in the vocabulary.

chrisknoll commented 1 year ago

This is also related to a separate issue, but it sounds like that when we open a concept set expression, we need to perform some sort of data-synchronization with the vocabulary. The problem is, what do we do with mismatches (ie, you move to a vocabulary where the concepts in your concept set expression are gone or renamed)? I think it should be an opt-in operation where the user can refresh their concepts in their concept set expression with the chosen vocabulary.