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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Vision registry successfully added. Corrections in birth registry. #157

Closed shanmukhasampath closed 4 months ago

shanmukhasampath commented 1 year ago

This is for issue #156

Vision registry is properly mapped except for visual field diameter columns.

Visual field diameter (VFD) columns OHALK and VHALK have only non-standard codes in FGVisitType vocabulary but do not have standard code to map to.

All tests PASS.

javier-gracia-tabuenca-tuni commented 1 year ago

looks good, can we have the documentation also, to see if the code match the specs ?? do i understand correct that, the measurement don't have a standard concept ??

shanmukhasampath commented 1 year ago

Hi Javier, I am not sure I understand this "code match the specs"

Yes, the measurement of visual field diameter is something that is not used any standard vocabulary. There is no standard code to capture the measurement from vision registry. So, I introduced two non-standard measurement codes with the hope that this may change in future.

Yes, I can make a new issue of updating Vision documentation

shanmukhasampath commented 1 year ago

Hi Javier, I have pushed all the changes we talked about regarding mapping codes. Now there is no separate vision to condition occurrence sql but rather will go through the STEM table.

javier-gracia-tabuenca-tuni commented 4 months ago

add to documentation

shanmukhasampath commented 4 months ago

add to documentation

  • vision table description to page Appendix > Source Tables
  • duration of the birth and vision registers in the mermade plot in Appendix > Registers time duration

Hi Javier, I have added the documentation for both.