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EHDEN / ETL-UK-Biobank

ETL UK-Biobank
https://ehden.github.io/ETL-UK-Biobank/
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GP Covid: semantic mapping of local clinical codes #225

Closed MaximMoinat closed 3 years ago

MaximMoinat commented 3 years ago

Comment Spiros on previous issue (#216)

I've had a closer look at this and my opinion is to ignore EMIS/TPP local codes entirely with some exceptions (see below). These codes are almost exclusively administrative codes for example, requesting a test or referring to a particular clinical in hospital or giving smoking advice. For example, in EMIS, there are a handful of codes which could have some data attached to them but they are so rarely (i.e. 44K times out of 270M records -> ~0.01%) used that it's not definitely not worth the effort of mapping them. The only codes I think we should map are the ones related to COVID-19 (where possible) - see list below:

Local code Number of records Local code definition
EMISNQTE31 700 Tested for 2019-nCoV (novel coronavirus) infection
EMISNQSU106 321 Suspected 2019-nCoV (novel coronavirus) infection
EMISNQEX59 230 Excluded 2019-nCoV (novel coronavirus) infection
EMISNQEM35 146 EMIS COVID-19 care pathway template entry
EMISNQCO303 74 Confirmed 2019-nCoV (novel coronavirus) infection
EMISNQEX58 3 Exposure to 2019-nCoV (novel coronavirus) infection
Y228a 12583 High risk category for developing complication from coronavirus disease 19 caused by severe acute respiratory syndrome coronavirus 2 infection (finding)
Y22b6 10163 Provision of advice, assessment or treatment limited due to coronavirus disease 19 caused by severe acute respiratory syndrome coronavirus 2 pandemic (situation)
Y228b 4913 Moderate risk category for developing complication from coronavirus disease 19 caused by severe acute respiratory syndrome coronavirus 2 infection (finding)
Y212d 2120 Advice given about severe acute respiratory syndrome coronavirus 2 infection (situation)
Y212c 1655 Advice given about severe acute respiratory syndrome coronavirus 2 by telephone (situation)
Y211b 1533 Telephone consultation for suspected severe acute respiratory syndrome coronavirus 2 (procedure)
Y212e 1065 Educated about severe acute respiratory syndrome coronavirus 2 infection (situation)
Y20cf 930 Suspected coronavirus disease 19 caused by severe acute respiratory syndrome coronavirus 2 (situation)
Y228c 774 Low risk category for developing complication from coronavirus disease 19 caused by severe acute respiratory syndrome coronavirus 2 infection (finding)
Y20d2 160 Severe acute respiratory syndrome coronavirus 2 not detected (finding)
Y20fa 113 Coronavirus disease 19 caused by severe acute respiratory syndrome coronavirus 2 (disorder)
Y20ce 71 Exposure to severe acute respiratory syndrome coronavirus 2 infection (event)
Y20d1 63 Severe acute respiratory syndrome coronavirus 2 detected (finding)
Y228d 61 Coronavirus disease 19 caused by severe acute respiratory syndrome coronavirus 2 confirmed by laboratory test (situation)
Y22a2 37 Coronavirus disease 19 caused by severe acute respiratory syndrome coronavirus 2 excluded by laboratory test (situation)
Y210a 21 Pneumonia caused by severe acute respiratory syndrome coronavirus 2 (disorder)
Y228e 20 Coronavirus disease 19 caused by severe acute respiratory syndrome coronavirus 2 confirmed using clinical diagnostic criteria (situation)
Y229d 19 Swab for severe acute respiratory syndrome coronavirus 2 taken by healthcare professional (situation)
Y22aa 19 Signposting to CHMS (COVID-19 Home Management Service) (procedure)
Y229e 17 Close exposure to severe acute respiratory syndrome coronavirus 2 infection (event)
Y22a1 13 Coronavirus disease 19 caused by severe acute respiratory syndrome coronavirus 2 excluded (situation)
Y23f4 12 SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) detection result negative
Y210e 12 Detection of severe acute respiratory syndrome coronavirus 2 using polymerase chain reaction technique (procedure)
Y22a4 9 Assessment using coronavirus disease 19 severity scale (procedure)
Y210b 8 Infection of upper respiratory tract caused by severe acute respiratory syndrome coronavirus 2 (disorder)
Y22a3 7 Coronavirus disease 19 caused by severe acute respiratory syndrome coronavirus 2 excluded using clinical diagnostic criteria (situation)
Y22a0 6 Taking of swab for severe acute respiratory syndrome coronavirus 2 (procedure)
Y0fc2 5 Client provided with any other recovery support elements
Y23f7 3 SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) detection result positive
Y20fd 3 High priority for severe acute respiratory syndrome coronavirus 2 vaccination (finding)
Y229a 3 Self-taking of swab for severe acute respiratory syndrome coronavirus 2 offered (situation)
Y229b 2 Swab for severe acute respiratory syndrome coronavirus 2 taken by subject (situation)
Y0ad9 2 Currently Residing: Specialist rehabilitation/recovery
Y22a5 1 Coronavirus disease 19 severity scale (assessment scale)
Y212a 1 Severe acute respiratory syndrome coronavirus 2 vaccination not indicated (situation)
Y213a 1 Antigen of 2019-nCoV (novel coronavirus)
Y211a 1 Measurement of severe acute respiratory syndrome coronavirus 2 antigen (procedure)
Y210c 1 Severe acute respiratory syndrome coronavirus 2 serology (observable entity)
Y229c 1 Coronavirus disease 19 severity score (observable entity)
MaximMoinat commented 3 years ago

Step 1: Take full list of codes and add frequency form the above table: https://biobank.ndph.ox.ac.uk/showcase/coding.cgi?id=7689&nl=1

Step 2: import all the codes in Usagi

Step 3: Manually curate/approve the codes listed above (with a frequency)