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Remove duplicates/keep only standard terms in SNOMED assessment list #236

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3 tasks

alyssadai opened this issue Jan 26, 2025 · 0 comments

Open

3 tasks

Remove duplicates/keep only standard terms in SNOMED assessment list #236

alyssadai opened this issue Jan 26, 2025 · 0 comments

Contributor

alyssadai commented Jan 26, 2025 •

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Related to Standardize static vocabulary JSON files between tools #216

In https://github.com/neurobagel/annotation_tool/blob/9f04d93b18bb7dee49876a43caaa1b142972483c/static/assessmentTerms.json, there is at least one instance of a term duplicate ("Hoehn and Yahr Scale") which has two entries with different IDs.

Examining them in ATHENA reveals that one of these terms is a "non-standard" concept and is classified as "invalid".

To avoid these types of terms ending up in annotations, we should:

update the script that extracts assessments to only include standard & valid concepts
update the annotation tool
update the API

alyssadai added the flag:schedule label

neurobagel-bot bot added this to Neurobagel

rmanaem moved this to Backlog in Neurobagel

rmanaem removed the flag:schedule label

rmanaem moved this from Backlog to Specify - Done in Neurobagel

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