Mapping the synthetic specimen and lab results source data to OMOP

[jaygee-on-github]

The source specimen table was mapped to the OMOP CDM SPECIMEN and OBSERVATION tables. The source lab results table was mostly mapped to to the OMOP CDM MEASUREMENT table.

With MEASUREMENTs the best practice in the OMOP CDM is to use concepts from LOINC for the measurement_concept_id. The measurement_concept_id for first the PCR test and then the antigen test are as follows:

The selection of these measurement_concept_ids was based on the following considerations:

• As a rule the at home rapid antigen test was not available early on in the pandemic. Instead there were sites (clinic, hospitals, commercial labs) that conducted PCR tests.
• On occasion these sites might conduct an antibody test.
• As a rule the PCR test was considered "the gold standard".
• As a rule nasal swabs were the source of both the PCR tests at first and then the rapid antigen test later. The occasional antibody test used blood.

Here is the measurement_concept_id for the occasional antibody test: