OHDSI Home | Forums | Wiki | Github

COVID, test reason and specimen

Implementers
#1

Hi all,

What are the best ways to store specimen and reason for testing associated with COVID test and to link it back to the original COVID test?

Source:
Test: COVID-19 Qualitative RNA test
Result: Detected
Testing reason: surveillance, symptomatic (one of the 2 values)
Specimen: Nasopharynx

OMOP:
1st record. Measurement.
Measurement_concept_id = COVID-19 Qualitative RNA test
Value_as_concept_id = Detected
2nd record: Observation
Observation_concept_id: 40769732 (Reason for test or procedure) Observation LOINC
Value_as_conсept_id: 1177348 (Surveillance report) Meas Value LOINC
3rd record option A: Specimen
Specimen_concept_id = Nasopharynx
OR 3rd record option B. Measurement:
Measurement_concept_id: 3015746 (Specimen source identified) Measurement Loinc
Value_as_concept_id: Nasopharynx

If to create 1, 2, 3 option B, then we could use observation.observation_of_event_id and measurement.modifier_of_event_id fields to link the associated specimen and test reasons to main COVID record. But I don’t know if it is a good idea to use Measurement instead of Specimen table.

Or we could create 1, 2, 3 option A and to use Fact_relationship table.

Where would you store test reason and speicmen and how would you link it to the main COVID test?

Mapping Microbiology Susceptibility into OMOP CDM4 Observations
#2

The OMOP oncology extension proposal includes MEASUREMENT table change by adding modifiers.
Thus, a measurement (cancer grade, for example) is a modifier of a Condition (cancer diagnosis).

In the case above Specimen and Observation are modifiers of Measurement.
So, should Specimen and Observation tables have modifiers to be added?

Or we just use fact_relationship for this purpose?

#3

Is there a good reason to keep it separately (sampling date, anatomic site, amount)? Otherwise, it might be a part of the Measurement concept’s semantics.

t