CDM Table name: PROCEDURE_OCCURRENCE

Reading from JMDC.Diagnosis

When an ICD10 code in the diagnosis table maps to a concept in the Procedure domain a record should be created in the procedure_occurrence table.

Destination Field Source Field Logic Comment
procedure_occurrence_id      
visit_occurrence_id claim_id Remove ‘C’ prefix  
person_id member_id Remove ‘M’ prefix  
procedure_type_concept_id type_of_claim Outpatient: 32859 (Outpatient claim) InPatient or DPC: 32853 (Inpatient claim)  
procedure_date month_and_year_of_medical_care Use visit_start_date  
procedure_concept_id standard_disease_code   Lookup icd10_level4_code in diagnosis_master table, and use vocab to map to standard concept. Remove ‘-‘ prior to mapping (e.g. ‘I50-‘ should map to ‘I50’), and ignore period (e.g. ‘I500’ should map to ‘I50.0’)
procedure_source_concept_id standard_disease_code   Lookup icd10_level4_code in diagnosis_master table, and use vocab to map to source concept. Remove ‘-‘ prior to mapping (e.g. ‘I50-‘ should map to ‘I50’), and ignore period (e.g. ‘I500’ should map to ‘I50.0’)
procedure_source_value standard_disease_code   Lookup icd10_level4_code in diagnosis_master table
provider_id medical_facility_id   Use dummy provider corresponding to the institute
procedure_datetime      
modifier_concept_id      
quantity      
visit_detail_id      
modifier_source_value      

Reading from JMDC.Procedure

Destination Field Source Field Logic Comment
procedure_occurrence_id      
visit_occurrence_id claim_id Remove ‘C’ prefix  
person_id member_id Remove ‘M’ prefix  
procedure_type_concept_id type_of_claim Outpatient: 32859 (Outpatient claim) Inpatient or DPC: 32853 (Inpatient claim)  
procedure_date month_and_year_of_medical_care date_of_procedure Use date of procedure when populated, otherwise use start of visit  
procedure_concept_id standardized_procedure_code Lookup the standardized_procedure_code in the procedure_master table to obtain the corresponding ICD9Proc code in the icd9cm_level1 field and then map to a standard concept using the Source-to-Standard Query where source_vocabulary_id = ‘ICD9Proc’, ignoring the decimal.

For standardized_procedure_codes that do not have a corresponding icd9cm_level1, map them directly to standard concepts using the Source-to-Standard Query where source_vocabulary_id = ‘JNJ_JMDC_PROCEDURES’
 
procedure_source_concept_id   If the procedure_concept_id is mapped from the icd9cm_level1 code in the procedure_master table, put the concept_id that corresponds with that code here. Otherwise set to 0  
procedure_source_value procedure_master.icd9cm_level1, standardized_procedure_code If the procedure_concept_id is mapped from the icd9cm_level1 code in the procedure_master table, put that value here.Otherwise set to standardized_procedure_code  
provider_id medical_facility_id   Use dummy provider corresponding to the institute
procedure_datetime      
modifier_concept_id      
quantity      
visit_detail_id      
modifier_source_value      

Change Log

April 6, 2022

  • In the native schema the standardized_procedure_id field in the procedure and procedure_master tables has been renamed to ‘standardized_procedure_code’. All CDM fields that reference standardized_procedure_id were changed. Additional mapping instructions for the standardized_procedure_code field were added to describe how to find the corresponding standard concepts.

Please contact Clair Blacketer (https://github.com/clairblacketer) if you have any questions