mz-health/OMOP
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OMOP
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Including the 'Type Concept' domain_id from the latest version of the vocabulary.

This commit is contained in:
Anthony Sena 2015-12-15 10:03:41 -05:00
parent 8badc57395
commit 11188fee37
1 changed files with 14 additions and 14 deletions
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28
Version4 To Version5 Conversion/OMOP CDMv4 to CDMv5 - OHDSI-SQL.sql
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@ -479,7 +479,7 @@ SELECT person_id
,CAST(NULL AS INT) AS cause_source_concept_id ,CAST(NULL AS INT) AS cause_source_concept_id
FROM @SOURCE_CDMV4_SCHEMA.DEATH FROM @SOURCE_CDMV4_SCHEMA.DEATH
LEFT JOIN #concept_map_distinct cm1 ON DEATH.DEATH_TYPE_CONCEPT_ID = CM1.SOURCE_CONCEPT_ID 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) 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' 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 WHERE CONCEPT_ID = 0
OR ( OR (
STANDARD_CONCEPT = 'S' STANDARD_CONCEPT = 'S'
AND LOWER(DOMAIN_ID) IN ('death type') AND LOWER(DOMAIN_ID) IN ('death type', 'Type Concept')
) )
) )
HAVING COUNT(PERSON_ID) > 0 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 cm1.domain_id = cmdis.domain_id
AND cmdis.targetConceptCount = 1 AND cmdis.targetConceptCount = 1
LEFT JOIN #concept_map cm2 ON PROCEDURE_OCCURRENCE.PROCEDURE_TYPE_CONCEPT_ID = cm2.source_concept_id 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 LEFT JOIN #concept_map_distinct cmdis2 ON cm2.source_concept_id = cmdis2.source_concept_id
AND cm2.domain_id = cmdis2.domain_id AND cm2.domain_id = cmdis2.domain_id
AND cmdis2.targetConceptCount = 1 AND cmdis2.targetConceptCount = 1
@ -632,7 +632,7 @@ SELECT procedure_occurrence_id
FROM @SOURCE_CDMV4_SCHEMA.PROCEDURE_OCCURRENCE FROM @SOURCE_CDMV4_SCHEMA.PROCEDURE_OCCURRENCE
LEFT JOIN #concept_map cm1 ON procedure_concept_id = cm1.source_concept_id 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 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 WHERE procedure_concept_id <> 0
AND cm1.domain_id IS NULL AND cm1.domain_id IS NULL
@ -680,7 +680,7 @@ FROM (
AND cm1.domain_id = cmdis.domain_id AND cm1.domain_id = cmdis.domain_id
AND cmdis.targetConceptCount > 1 AND cmdis.targetConceptCount > 1
LEFT JOIN #concept_map cm2 ON PROCEDURE_OCCURRENCE.PROCEDURE_TYPE_CONCEPT_ID = cm2.source_concept_id 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 UNION ALL
@ -801,7 +801,7 @@ FROM (
WHERE CONCEPT_ID = 0 WHERE CONCEPT_ID = 0
OR ( OR (
STANDARD_CONCEPT = 'S' STANDARD_CONCEPT = 'S'
AND LOWER(DOMAIN_ID) IN ('procedure type') AND LOWER(DOMAIN_ID) IN ('procedure type', 'Type Concept')
) )
) )
HAVING COUNT(PERSON_ID) > 0 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 cm1.domain_id = cmdis.domain_id
AND cmdis.targetConceptCount = 1 AND cmdis.targetConceptCount = 1
LEFT JOIN #concept_map cm2 ON drug_exposure.drug_type_concept_id = cm2.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')
INNER JOIN #concept_map_distinct cmdis2 ON cm2.source_concept_id = cmdis2.source_concept_id INNER JOIN #concept_map_distinct cmdis2 ON cm2.source_concept_id = cmdis2.source_concept_id
AND cm2.domain_id = cmdis2.domain_id AND cm2.domain_id = cmdis2.domain_id
AND cmdis2.targetConceptCount = 1 AND cmdis2.targetConceptCount = 1
@ -939,7 +939,7 @@ SELECT drug_exposure_id
FROM @SOURCE_CDMV4_SCHEMA.DRUG_EXPOSURE FROM @SOURCE_CDMV4_SCHEMA.DRUG_EXPOSURE
LEFT JOIN #concept_map cm1 ON drug_concept_id = cm1.source_concept_id 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 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 WHERE drug_concept_id <> 0
AND cm1.domain_id IS NULL AND cm1.domain_id IS NULL
@ -1004,7 +1004,7 @@ FROM (
AND cm1.domain_id = cmdis.domain_id AND cm1.domain_id = cmdis.domain_id
AND cmdis.targetConceptCount > 1 AND cmdis.targetConceptCount > 1
LEFT JOIN #concept_map cm2 ON drug_exposure.drug_type_concept_id = cm2.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')
UNION ALL UNION ALL
@ -1170,7 +1170,7 @@ FROM (
WHERE CONCEPT_ID = 0 WHERE CONCEPT_ID = 0
OR ( OR (
STANDARD_CONCEPT = 'S' STANDARD_CONCEPT = 'S'
AND LOWER(DOMAIN_ID) IN ('drug type') AND LOWER(DOMAIN_ID) IN ('drug type', 'Type Concept')
) )
) )
HAVING COUNT(PERSON_ID) > 0 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 cm1.domain_id = cmdis.domain_id
AND cmdis.targetConceptCount = 1 AND cmdis.targetConceptCount = 1
LEFT JOIN #concept_map cm2 ON condition_occurrence.condition_type_concept_id = cm2.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 -- This condition will map those concepts that were mapped to valid concepts in V4 WHERE condition_concept_id > 0 -- This condition will map those concepts that were mapped to valid concepts in V4
UNION ALL UNION ALL
@ -1238,7 +1238,7 @@ SELECT condition_occurrence_id
FROM @SOURCE_CDMV4_SCHEMA.CONDITION_OCCURRENCE 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 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 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 WHERE condition_concept_id <> 0
AND cm1.domain_id IS NULL AND cm1.domain_id IS NULL
@ -1281,7 +1281,7 @@ FROM (
AND cm1.domain_id = cmdis.domain_id AND cm1.domain_id = cmdis.domain_id
AND cmdis.targetConceptCount > 1 AND cmdis.targetConceptCount > 1
LEFT JOIN #concept_map cm2 ON condition_occurrence.condition_type_concept_id = cm2.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 -- This condition will map those concepts that were mapped to valid concepts in V4 WHERE condition_concept_id > 0 -- This condition will map those concepts that were mapped to valid concepts in V4
UNION ALL UNION ALL
@ -1369,7 +1369,7 @@ FROM (
WHERE CONCEPT_ID = 0 WHERE CONCEPT_ID = 0
OR ( OR (
STANDARD_CONCEPT = 'S' STANDARD_CONCEPT = 'S'
AND LOWER(DOMAIN_ID) IN ('condition type') AND LOWER(DOMAIN_ID) IN ('condition type', 'Type Concept')
) )
) )
HAVING COUNT(PERSON_ID) > 0 HAVING COUNT(PERSON_ID) > 0