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National-COVID-Cohort-Collaborative / Data-Ingestion-and-Harmonization

Data Ingestion and Harmonization
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SDoH answer codes can be submitted in multiple flavors, i.e. LOINC:LA prefix or LA prefix #84

Closed stephanieshong closed 2 years ago

stephanieshong commented 2 years ago

Support both instances in mapping SDoH answer codes to the correct value_as_concept_id. Extract LA%-% to map to OMOP concept table to find the correct concept_ids.

stephanieshong commented 2 years ago

sdoh_answer_code_xwalk dataset is built to include all of the LOINC coded answer concepts submitted for the SDoH concepts and for the xwalk table to contain the proper LOINC coded answer concept_ids. String text are added to the value_set_mapping tables. Add the code in the observation to left join with the sdo_answer_code_xwalk to find the correct LOINC coded LA%-% concept_ids.

stephanieshong commented 2 years ago

PR submitted in the TrinetX template source code.

stephanieshong commented 2 years ago

code changes are in step 4: observation.sql and sdoh_answer_code_xwalk.sql