[Mapping issue] PCR results are not mapped

[catalamarti]

Describe the problem PCR tests source codes in gold are:

37310282 | 1240581000000104 | Severe acute respiratory syndrome coronavirus 2 detected | Clinical Finding | Non-standard | Valid | Measurement | SNOMED -- | -- | -- | -- | -- | -- | -- | -- 37310281 | 1240591000000102 | Severe acute respiratory syndrome coronavirus 2 not detected | Clinical Finding | Non-standard | Valid | Measurement | SNOMED

Both are mapped to:

756055 | OMOP4873969 | Measurement of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) | Lab Test | Standard | Valid | Measurement | OMOP Extension -- | -- | -- | -- | -- | -- | -- | --

Which is fine and allows us to see the PCR records. But then the result is not mapped so we would expect that for 37310282 the value_as_concept_id is 9191 (Positive) and for 37310281 the value_as_concept_id is 9189 (Negative). But both have a value_as_concept_id = 0 (No matching concept) Currently we have to identify the result from the source codes, it would be nice if we can map the result with standard codes.

Affected databases As far as I know: cdm_gold_202207, cdm_gold_202201, cdm_aurum_p21_000557

Tag for awareness @teenwyman @adelmestri @edward-burn @Xintong-Li-ZnCu

[teenwyman]

@catalamarti In GOLD, you have to select Measurement table with measurement_concept_id in (756065, 706179) And you can find the test results from the value_source_value

For details, please refer to this.