OHDSI Home | Forums | Wiki | Github

Bulk load of concept sets, cohort definitions from one Atlas to another Atlas installation


(Lisa Schilling) #1

Hello all,
For the R2D2-C3PO (COVID-19 research collaboration with pSCANNER), we setting up a shared project Atlas for internal project work, and we like to download from the atlas-ohdsi.org and upload into our project Atlas. We know we can do this one by one but is there a way can we do this in bulk? @krfeeney has been teaching some Atlas tricks, I’m including her to. Thanks! Lisa


(Chris Knoll) #2

Yes, it should be fairly simple since you can talk to both systems over HTTP. Assuming you have a list of concept IDs or cohort IDs, you would:

Fetch the expression from the atlas-ohdsi.org WebAPI instance via HTTP.
POST/PUT the content bak to your own instance.

You need to keep track of the IDs between them. atlas-ohdsi.org cohortID of 1717 will not be your imported cohort ID.

This website provides the complete HTTP API to access webapi: http://webapidoc.ohdsi.org/index.html#home. You can navigate to the end points by navigation on the right. Each endpoint will tell you what the path is, and what datastructure it expects.

I suggest starting out writing a simple R script that pulls a given cohort definition from WebAPI. Then try to forward that expression into a POST (create) request on the other WebAPI. After you get those maneuvers down, it’s a simple matter to just feed it a big list and loop through them.


(Lisa Schilling) #3

@Chris_Knoll Thanks so much for the speedy reply! We’ll try this out and let you know. f(yi @krfeeney) Lisa


(Vojtech Huser) #4
  1. I think a concept of CohortGroup should be included in our informatics universe. (and supported by all core tools).

related issue https://github.com/OHDSI/CohortDiagnostics/issues/14

  1. did you mean url without - ? like https://atlas.ohdsi.org/

(Kai Post) #5

Thank you so much for that information. Since the API at https://atlas.ohdsi.org/WebAPI is secured with Google authentication would anyone have any sample code to generate and use the tokens for this purpose?


(Chris Knoll) #6

It’s an open question, and there is discussion on accessing a security-enabled WebAPI here. Since this is directly related to the topic raised (communicating with WebAPI in order to perform batch operations) I have no problem discussing it here, but specific conversations related to secured access should probably go there.


(Kai Post) #7

Thank you very much for your quick reply, this is helpful. I did pose the question regarding sample code for Google authentication on the other thread you mentioned.


t