mz-health/OMOP
mz-health
/
OMOP
mirror of https://github.com/OHDSI/CommonDataModel.git
1
0
Fork 0
Code Issues Packages Projects Releases Wiki Activity

Query for mapping to standard vocabularies 

Adding a sql query that will aid in mapping source codes to standard concepts
This commit is contained in:
clairblacketer 2017-12-08 12:16:27 -05:00 committed by GitHub
parent df2d439ac0
commit 4a925a87da
No known key found for this signature in database
GPG Key ID: 4AEE18F83AFDEB23
1 changed files with 31 additions and 0 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

31
CodeExcerpts/Vocab_Mapping.sql Normal file
View File

@ -0,0 +1,31 @@
WITH CTE_VOCAB_MAP AS (
SELECT c.concept_code AS SOURCE_CODE, c.concept_id AS SOURCE_CONCEPT_ID, c.concept_name AS SOURCE_CODE_DESCRIPTION, c.vocabulary_id AS SOURCE_VOCABULARY_ID,
c.domain_id AS SOURCE_DOMAIN_ID, c.CONCEPT_CLASS_ID AS SOURCE_CONCEPT_CLASS_ID,
c.VALID_START_DATE AS SOURCE_VALID_START_DATE, c.VALID_END_DATE AS SOURCE_VALID_END_DATE, c.INVALID_REASON AS SOURCE_INVALID_REASON,
c1.concept_id AS TARGET_CONCEPT_ID, c1.concept_name AS TARGET_CONCEPT_NAME, c1.VOCABULARY_ID AS TARGET_VOCABUALRY_ID, c1.domain_id AS TARGET_DOMAIN_ID, c1.concept_class_id AS TARGET_CONCEPT_CLASS_ID,
c1.INVALID_REASON AS TARGET_INVALID_REASON, c1.standard_concept AS TARGET_STANDARD_CONCEPT
FROM CONCEPT C
JOIN CONCEPT_RELATIONSHIP CR
ON C.CONCEPT_ID = CR.CONCEPT_ID_1
AND CR.invalid_reason IS NULL
AND cr.relationship_id = 'Maps To'
JOIN CONCEPT C1
ON CR.CONCEPT_ID_2 = C1.CONCEPT_ID
AND C1.INVALID_REASON IS NULL
UNION
SELECT source_code, SOURCE_CONCEPT_ID, SOURCE_CODE_DESCRIPTION, source_vocabulary_id, c1.domain_id AS SOURCE_DOMAIN_ID, c2.CONCEPT_CLASS_ID AS SOURCE_CONCEPT_CLASS_ID,
c1.VALID_START_DATE AS SOURCE_VALID_START_DATE, c1.VALID_END_DATE AS SOURCE_VALID_END_DATE,
stcm.INVALID_REASON AS SOURCE_INVALID_REASON,target_concept_id, c2.CONCEPT_NAME AS TARGET_CONCEPT_NAME, target_vocabulary_id, c2.domain_id AS TARGET_DOMAIN_ID, c2.concept_class_id AS TARGET_CONCEPT_CLASS_ID,
c2.INVALID_REASON AS TARGET_INVALID_REASON, c2.standard_concept AS TARGET_STANDARD_CONCEPT
FROM source_to_concept_map stcm
LEFT OUTER JOIN CONCEPT c1
ON c1.concept_id = stcm.source_concept_id
LEFT OUTER JOIN CONCEPT c2
ON c2.CONCEPT_ID = stcm.target_concept_id
WHERE stcm.INVALID_REASON IS NULL
)
SELECT *
FROM CTE_VOCAB_MAP
/*EXAMPLE FILTERS*/
WHERE SOURCE_VOCABULARY_ID IN ('NDC')
AND TARGET_VOCABUALRY_ID IN ('RxNORM')