diff --git a/Version4 To Version5 Conversion/OMOP CDMv4 to CDMv5 - OHDSI-SQL.sql b/Version4 To Version5 Conversion/OMOP CDMv4 to CDMv5 - OHDSI-SQL.sql index c8af412..743316e 100644 --- a/Version4 To Version5 Conversion/OMOP CDMv4 to CDMv5 - OHDSI-SQL.sql +++ b/Version4 To Version5 Conversion/OMOP CDMv4 to CDMv5 - OHDSI-SQL.sql @@ -479,7 +479,7 @@ SELECT person_id ,CAST(NULL AS INT) AS cause_source_concept_id FROM @SOURCE_CDMV4_SCHEMA.DEATH LEFT JOIN #concept_map_distinct cm1 ON DEATH.DEATH_TYPE_CONCEPT_ID = CM1.SOURCE_CONCEPT_ID - AND LOWER(DOMAIN_ID) IN ('death type'); + AND LOWER(DOMAIN_ID) IN ('death type', 'Type Concept'); INSERT INTO @TARGET_CDMV5_SCHEMA.ETL_WARNINGS (WARNING_MESSAGE) SELECT 'DEATH: ' + CAST(NUM_INVALID_RECORDS AS VARCHAR) + ' records in the source CDMv4 database have invalid DEATH_TYPE_CONCEPT_ID' @@ -492,7 +492,7 @@ FROM ( WHERE CONCEPT_ID = 0 OR ( STANDARD_CONCEPT = 'S' - AND LOWER(DOMAIN_ID) IN ('death type') + AND LOWER(DOMAIN_ID) IN ('death type', 'Type Concept') ) ) HAVING COUNT(PERSON_ID) > 0 @@ -589,7 +589,7 @@ INNER JOIN #concept_map_distinct cmdis ON cm1.source_concept_id = cmdis.source_c AND cm1.domain_id = cmdis.domain_id AND cmdis.targetConceptCount = 1 LEFT JOIN #concept_map cm2 ON PROCEDURE_OCCURRENCE.PROCEDURE_TYPE_CONCEPT_ID = cm2.source_concept_id - AND LOWER(cm2.domain_id) IN ('procedure type') + AND LOWER(cm2.domain_id) IN ('procedure type', 'Type Concept') LEFT JOIN #concept_map_distinct cmdis2 ON cm2.source_concept_id = cmdis2.source_concept_id AND cm2.domain_id = cmdis2.domain_id AND cmdis2.targetConceptCount = 1 @@ -632,7 +632,7 @@ SELECT procedure_occurrence_id FROM @SOURCE_CDMV4_SCHEMA.PROCEDURE_OCCURRENCE LEFT JOIN #concept_map cm1 ON procedure_concept_id = cm1.source_concept_id LEFT JOIN #concept_map cm2 ON procedure_concept_id = cm2.source_concept_id - AND LOWER(cm2.domain_id) IN ('procedure type') + AND LOWER(cm2.domain_id) IN ('procedure type', 'Type Concept') WHERE procedure_concept_id <> 0 AND cm1.domain_id IS NULL @@ -680,7 +680,7 @@ FROM ( AND cm1.domain_id = cmdis.domain_id AND cmdis.targetConceptCount > 1 LEFT JOIN #concept_map cm2 ON PROCEDURE_OCCURRENCE.PROCEDURE_TYPE_CONCEPT_ID = cm2.source_concept_id - AND LOWER(cm2.domain_id) IN ('procedure type') + AND LOWER(cm2.domain_id) IN ('procedure type', 'Type Concept') UNION ALL @@ -801,7 +801,7 @@ FROM ( WHERE CONCEPT_ID = 0 OR ( STANDARD_CONCEPT = 'S' - AND LOWER(DOMAIN_ID) IN ('procedure type') + AND LOWER(DOMAIN_ID) IN ('procedure type', 'Type Concept') ) ) HAVING COUNT(PERSON_ID) > 0 @@ -877,7 +877,7 @@ INNER JOIN #concept_map_distinct cmdis ON cm1.source_concept_id = cmdis.source_c AND cm1.domain_id = cmdis.domain_id AND cmdis.targetConceptCount = 1 LEFT JOIN #concept_map cm2 ON drug_exposure.drug_type_concept_id = cm2.source_concept_id - AND LOWER(cm2.domain_id) IN ('drug type') + AND LOWER(cm2.domain_id) IN ('drug type', 'Type Concept') INNER JOIN #concept_map_distinct cmdis2 ON cm2.source_concept_id = cmdis2.source_concept_id AND cm2.domain_id = cmdis2.domain_id AND cmdis2.targetConceptCount = 1 @@ -939,7 +939,7 @@ SELECT drug_exposure_id FROM @SOURCE_CDMV4_SCHEMA.DRUG_EXPOSURE LEFT JOIN #concept_map cm1 ON drug_concept_id = cm1.source_concept_id LEFT JOIN #concept_map cm2 ON drug_exposure.drug_type_concept_id = cm2.source_concept_id - AND LOWER(cm2.domain_id) IN ('drug type') + AND LOWER(cm2.domain_id) IN ('drug type', 'Type Concept') WHERE drug_concept_id <> 0 AND cm1.domain_id IS NULL @@ -1004,7 +1004,7 @@ FROM ( AND cm1.domain_id = cmdis.domain_id AND cmdis.targetConceptCount > 1 LEFT JOIN #concept_map cm2 ON drug_exposure.drug_type_concept_id = cm2.source_concept_id - AND LOWER(cm2.domain_id) IN ('drug type') + AND LOWER(cm2.domain_id) IN ('drug type', 'Type Concept') UNION ALL @@ -1170,7 +1170,7 @@ FROM ( WHERE CONCEPT_ID = 0 OR ( STANDARD_CONCEPT = 'S' - AND LOWER(DOMAIN_ID) IN ('drug type') + AND LOWER(DOMAIN_ID) IN ('drug type', 'Type Concept') ) ) HAVING COUNT(PERSON_ID) > 0 @@ -1201,7 +1201,7 @@ INNER JOIN #concept_map_distinct cmdis ON cm1.source_concept_id = cmdis.source_c AND cm1.domain_id = cmdis.domain_id AND cmdis.targetConceptCount = 1 LEFT JOIN #concept_map cm2 ON condition_occurrence.condition_type_concept_id = cm2.source_concept_id - AND LOWER(cm2.domain_id) IN ('condition type') + AND LOWER(cm2.domain_id) IN ('condition type', 'Type Concept') WHERE condition_concept_id > 0 -- This condition will map those concepts that were mapped to valid concepts in V4 UNION ALL @@ -1238,7 +1238,7 @@ SELECT condition_occurrence_id FROM @SOURCE_CDMV4_SCHEMA.CONDITION_OCCURRENCE LEFT JOIN #concept_map cm1 ON condition_occurrence.condition_concept_id = cm1.source_concept_id LEFT JOIN #concept_map cm2 ON condition_occurrence.condition_type_concept_id = cm2.source_concept_id - AND LOWER(cm2.domain_id) IN ('condition type') + AND LOWER(cm2.domain_id) IN ('condition type', 'Type Concept') WHERE condition_concept_id <> 0 AND cm1.domain_id IS NULL @@ -1281,7 +1281,7 @@ FROM ( AND cm1.domain_id = cmdis.domain_id AND cmdis.targetConceptCount > 1 LEFT JOIN #concept_map cm2 ON condition_occurrence.condition_type_concept_id = cm2.source_concept_id - AND LOWER(cm2.domain_id) IN ('condition type') + AND LOWER(cm2.domain_id) IN ('condition type', 'Type Concept') WHERE condition_concept_id > 0 -- This condition will map those concepts that were mapped to valid concepts in V4 UNION ALL @@ -1369,7 +1369,7 @@ FROM ( WHERE CONCEPT_ID = 0 OR ( STANDARD_CONCEPT = 'S' - AND LOWER(DOMAIN_ID) IN ('condition type') + AND LOWER(DOMAIN_ID) IN ('condition type', 'Type Concept') ) ) HAVING COUNT(PERSON_ID) > 0