From 4a925a87dac0c258450329e322cbf82d777107f4 Mon Sep 17 00:00:00 2001
From: clairblacketer <clairblacketer@users.noreply.github.com>
Date: Fri, 8 Dec 2017 12:16:27 -0500
Subject: [PATCH] Query for mapping to standard vocabularies

Adding a sql query that will aid in mapping source codes to standard concepts
---
 CodeExcerpts/Vocab_Mapping.sql | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)
 create mode 100644 CodeExcerpts/Vocab_Mapping.sql

diff --git a/CodeExcerpts/Vocab_Mapping.sql b/CodeExcerpts/Vocab_Mapping.sql
new file mode 100644
index 0000000..da6e116
--- /dev/null
+++ b/CodeExcerpts/Vocab_Mapping.sql
@@ -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')