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EHDEN / ETL-UK-Biobank

ETL UK-Biobank
https://ehden.github.io/ETL-UK-Biobank/
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Add explicit postive COVID19 test from covid specimen #340

Closed MaximMoinat closed 2 years ago

MaximMoinat commented 2 years ago

Currently, the covid_to_observation only captures what sample was taken and that it was positive or negative.

Observation concept id = Nasal fluid sample specimen concept value = positive data_source = covid

We also have to capture explicitly that a COVID19 test was positive/negative.

MaximMoinat commented 2 years ago

Add an additional mapping of the covid table to measurement. Use this measurement concept, that is also used in the AESI study. "Measurement of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)" https://athena.ohdsi.org/search-terms/terms/756055

With positive/negative as value concept.