ACT CDM OBSERVATION_FACT domain mapping logic for measurement Target - National-Clinical-Cohort-Collaborative/Data-Ingestion-and-Harmonization GitHub Wiki

Following additional logic applied in mapping transformation.

ACT CDM OBSERVATION_FACT Domain - Measurement Target

measurement columns mapping logic
measurement_type_concept_id 5001
Operator_concept_id only relevant when the value is numeric: If the valtype_cd = N then Use the tval_char values as the operator_concept_id Else 0 As operator_concept_id
Value_as_number(numeric) If valtype_cd is T then NULL else If valtype_cd is N then nval_num As the value as number
value_as_concept_id ( qualitative ) 1. If valtype_cd is T and tval_char is null then use valueflag_cd as value_as_concept_id 2.If valtype_cd is T and tval_char is not null then use tval_char as value_as_concept_id
Unit_concept_id unit concept id is only relevant when the value is numeric use Units_cd as unit_concept_id if valtype_cd = T else set it 0
range low set to 0, not used in ACT
range high set to 0, not used in ACT

NOTE ON LOCAL CODE MAPPINGS

  • If concept_cd = ACT|LOCAL:REMDESIVIR then map to Drug_Exposure with 37499271 as the drug concept id. 37499271 2284718 remdesivir Ingredient Standard Valid Drug RxNorm
  • Insert using:
  • target domain= Drug
  • target concept id = 37499271 **Special thank you to Michele Morris for providing this logic.