Mapping the outcome

[jaygee-on-github]

Recall that the outcome corresponds to whether the initial classification was "confirmed" or not. In the OMOP CDM this amounts to another CONDITION_OCCURRENCE. This one follows in time the admission CONDITION_OCCURRENCE(s). It has a condition_concept_id corresponding to "COVID_19" in ATHENA (37311061). This concept comes from the SNOMED vocabulary. It subsumes many more specific COVID-19 related conditions, but not "Suspected COVID-19":

The outcome CONDITION_OCCURRENCE also takes a condition_status_concept_id and a condition_type_concept_id. The condition_status_concept_id corresponds to "Confirmed Diagnosis" (32893). "Confirmed Diagnosis" is a concept in the Condition Status vocabulary. This CONDITION_OCCURRENCE takes a condition_type_concept_id in line with its "provenance" (32809). This is the concept for a "Case Report Form" in the Type Concept vocabulary.

[jaygee-on-github]

The ETL produced a 37311061 CONDITION_OCCURRENCE in the synthetic data I am thinking without a "Confirmed Diagnosis" (32893) as the condition_status_concept_id.