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

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MaximMoinat opened this issue Dec 13, 2021 · 2 comments · Fixed by #334
Closed
4 tasks done

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

MaximMoinat opened this issue Dec 13, 2021 · 2 comments · Fixed by #334
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@MaximMoinat
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MaximMoinat commented Dec 13, 2021

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.

  • Review unprioritised fields for other important fields to include (1)
  • Look into using the new OMOP UKB vocabulary, to reuse the 'Maps to' (1)
  • Add mapping for the identified important fields (2)
  • Test (1)
@MaximMoinat MaximMoinat changed the title Baseline BMI measurement missing Add concept mapping for baseline fields (e.g. BMI measurement) Feb 13, 2022
@MaximMoinat
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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
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MaximMoinat commented Mar 4, 2022

Made a start in linked PR.
To do:

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

@MaximMoinat MaximMoinat self-assigned this Mar 7, 2022
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