neurobagel / annotation_tool

https://annotate.neurobagel.org/
MIT License
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Make custom version where the Assessment tool list comes from SNOMED-CT #769

Closed surchs closed 3 weeks ago

surchs commented 1 month ago

We have now heard many times that Cognitive Atlas has insufficient coverage of clinical assessments (makes sense). It seems that SNOMED-CT has better coverage. Long term, we want to add a "clinical assessment" category and rename the current assessments to "cognitive assessment" - or something along those lines.

This issue is about an experimental, short term change that we will not publicly deploy. We want:

The goal is not (necessarily) to make graph files with the data dictionaries, we may only use the data dictionaries to manually harmonize clinical assessments across a number of datasets to find out how many participants have these tools.

@rmanaem: this is the issue I mentioned to you yesterday.

rmanaem commented 1 month ago

@surchs What are your thoughts on creating an env var that switches between the two vocabs for assessment tool options?

surchs commented 1 month ago

up to you, but I'd prefer to not ship something to production that can be user configured to run SNOMED. When we switch we should switch for everyone

rmanaem commented 1 month ago

For reviewer: check the app preview on the open draft PR to view the changes and discard the failing test cases as they're specific to terms from cogatlas.