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How to link cohort definitions from github repository to ATLAS front-end

Developers
#1

My understanding is that cohort definitions are stored and versioned in github repositories, along with related artifacts. I was looking to validate this assumption by trying out sample definitions.

Starting with a cohort definition that is saved in a github repository (e.g. github.com/ohdsi-studies/Covid19CharacterizationCharybdis/blob/master/inst/cohorts/125.json), how can I view the definition in an ATLAS front-end?

I tried searching for URL atlas-demo.ohdsi.org/#/cohortdefinition/125, but that was not a valid URL.

  1. Is the ID ‘125’ represent a cohort in a different instance of ATLAS (other than atlas-demo.ohdsi.org)?
  2. Is the ID that links back to the ATLAS front-end found in a different part of the same github repository?
#2

Hi @Raj_Manickam

Great question! We aim to make OHDSI studies fully transparent and reproducible, so knowing what the cohort definitions were is important.

The number 125 probably corresponds to an ATLAS instance somewhere (I think in this case it was an ATLAS specifically instantiated for the COVID study-a-thon). Fortunately, you don’t need access to that ATLAS instance. You can view the cohort definition in any ATLAS instance, by following these steps:

  1. Go to the inst/cohorts folder of that study package, and locate the corresponding JSON file. For cohort 125, you can find it here.
  2. Click on ‘raw’, and copy all the JSON in your clipboard.
  3. Open an ATLAS instance, click on ‘Cohort Definitions’, then ‘New Cohort’, then ‘Export’ (I know, clicking Export to import is dumb), then JSON, and replace the JSON there with the JSON on your clipboard. Click ‘Reload’, and you have your cohort definition.
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#3

Thank you @schuemie :smiley:

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