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tompollard / omopetl

Package for creating OMOP ETLs.
MIT License
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Transform MIMIC-IV to OMOP `person` table #8

Open tompollard opened 3 days ago

tompollard commented 3 days ago

We need to work out how to transform MIMIC-IV to the OMOP person table. We could base our initial transform on the approach at: https://github.com/OHDSI/MIMIC/blob/master/etl/etl/cdm_person.sql

There is demo source data (from MIMIC-IV v2.2 demo) at: https://github.com/tompollard/omopetl/tree/main/omopetl/templates/demo/data/source

tompollard commented 3 days ago

Looking at the OHDSI transform, two issues are:

  1. we do not have a transform that supports this function:
FARM_FINGERPRINT(GENERATE_UUID()) AS person_id,
  1. I'm not sure we have a transform for coalesce.