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OHDSI / Eunomia

An R package that facilitates access to a variety of OMOP CDM sample data sets.
https://ohdsi.github.io/Eunomia/
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Eunomia for Lung Cancer Data #27

Open priagopal opened 1 year ago

priagopal commented 1 year ago

Hi Everyone,

I generated lung cancer Synthea data for 1K patients. I was wondering, whether I could create ETL for cancer extension. I was thinking of doing the following. Please let me know, if my understanding is right?

  1. download latest athena
  2. create postgres schema for source and cdm
  3. upload dictionary data into cdm
  4. Create Episode ETL, update measurement,condition and drug_exposure ETLs (this is going to be really challenging. Please provide some tips on what is the best way forward).
  5. load data into cdm schema
fdefalco commented 1 year ago

This sounds interesting. Are you planning on using episode and episode event tables that are part of CDM 5.4?

My suggestion would be to create a branch in the ETL-Synthea (https://github.com/OHDSI/ETL-Synthea) repository. You could follow that approach for the ETL processing and add the necessary steps to populate the new tables using the required vocabularies. You'll find that the package uses the CommonDataModel package and completes step 2 and 3 in your proposal.

Could this work for your purposes?

priagopal commented 1 year ago

Hi Frank,

Thanks for the input. I am planning on using episode and episode event table. I am not entirely sure, how to do it. I will give it a shot. I will create a branch in ETL-Synthea. Can I post questions under ETL-Synthea --> issues?

Thanks, Priya

fdefalco commented 1 year ago

Yes, that would work.