FINNGEN / ETL

second version for the ETL of the detailed longitudinal data to the OMOP-CDM
https://finngen.github.io/ETL/
MIT License
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Update birth mother registry ETL for DF12 #162

Closed shanmukhasampath closed 1 month ago

shanmukhasampath commented 1 year ago

In DF11 release, birth mother registry data had different delivery dates for twins, triplets and more which was captured in the column APPROX_BIRTH_DATE. This is mainly due to the fact that register team was adding offset to APPROX_BIRTH_DATE to mask the original date randomly. To bypass this, we used finngenid birthday + mother's birth event age.

In DF12, this problem is fixed by introducing APPROX_DELIVERY_DATE which now shows same day or a difference in a day for twins, triplets and more other birth types. Given this, the birth mother stem medical events SQL should be updated to capture this information.

javier-gracia-tabuenca-tuni commented 9 months ago

is this completed ?

shanmukhasampath commented 9 months ago

Hi @javier-gracia-tabuenca-tuni, no it is finished.

  1. APPROX_DELIVERY_DATE is done but needs testing.
  2. Twin births might be scrapped because there are only two instances where twins is not properly addressed the rest of them have correct codes for twin births which we already took care of. I checked this before I went for holidays.