Add concept mapping for baseline fields (e.g. BMI measurement)

EHDEN / ETL-UK-Biobank

ETL UK-Biobank

https://ehden.github.io/ETL-UK-Biobank/

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Add concept mapping for baseline fields (e.g. BMI measurement) #328

Closed MaximMoinat closed 2 years ago

MaximMoinat commented 2 years ago

We have not included BMI (field 21001) in the baseline field mappings. Therefore it is ignored. We should add this AND not ignore baseline fields for which a mapping is missing.

Same for 22420 - LV ejection fraction #325.

[x] Review unprioritised fields for other important fields to include (1)
[x] Look into using the new OMOP UKB vocabulary, to reuse the 'Maps to' (1)
[x] Add mapping for the identified important fields (2)
[x] Test (1)

MaximMoinat commented 2 years ago

An overview from UCL of missing mappings available here: https://docs.google.com/spreadsheets/d/1VAoA4DVb19eYY4kik8Nw5eJzo_Dn8m9fgCVcMNXARPE/edit#gid=1677770576

Marked in blue are missing UKB fields with priority. We should at least make sure a mapping for these is included.

MaximMoinat commented 2 years ago

Made a start in linked PR. To do:

[x] Go through the new discrete_fields.csv mapping in Usagi, specifically the Recent medication, tobacco/smoking status, alcohol consumpiton and mental health fields
[x] Create mappings for all numeric fields from UKB vocabulary (prioritised and not prioritised). With both maps to and maps to unit.