OMOP/Sql Server/VocabImport/OMOP CDM vocabulary load - SQL Server.sql

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Script to load the common data model, version 5.0 vocabulary tables for SQL Server database

Notes

1) There is no data file load for the SOURCE_TO_CONCEPT_MAP table because that table is deprecated in CDM version 5.0
2) This script assumes the CDM version 5 vocabulary zip file has been unzipped into the "C:\CDMV5Vocabulary" directory. 
3) If you unzipped your CDM version 5 vocabulary files into a different directory then replace all file paths below, with your directory path.
4) Run this SQL query script in the database where you created your CDM Version 5 tables

last revised: 26 Nov 2014

author:  Lee Evans


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TRUNCATE TABLE DRUG_STRENGTH;
BULK INSERT DRUG_STRENGTH 
FROM 'C:\CDMV5VOCAB\DRUG_STRENGTH.csv' 
WITH (
FIRSTROW = 2,
FIELDTERMINATOR = '\t',
ROWTERMINATOR = '0x0a',
ERRORFILE = 'C:\CDMV5VOCAB\DRUG_STRENGTH.bad',
TABLOCK
);

TRUNCATE TABLE CONCEPT;
BULK INSERT CONCEPT 
FROM 'C:\CDMV5VOCAB\CONCEPT.csv' 
WITH (
FIRSTROW = 2,
FIELDTERMINATOR = '\t',
ROWTERMINATOR = '0x0a',
ERRORFILE = 'C:\CDMV5VOCAB\CONCEPT.bad',
TABLOCK
);

TRUNCATE TABLE CONCEPT_RELATIONSHIP;
BULK INSERT CONCEPT_RELATIONSHIP 
FROM 'C:\CDMV5VOCAB\CONCEPT_RELATIONSHIP.csv' 
WITH (
FIRSTROW = 2,
FIELDTERMINATOR = '\t',
ROWTERMINATOR = '0x0a',
ERRORFILE = 'C:\CDMV5VOCAB\CONCEPT_RELATIONSHIP.bad',
TABLOCK
);

TRUNCATE TABLE CONCEPT_ANCESTOR;
BULK INSERT CONCEPT_ANCESTOR 
FROM 'C:\CDMV5VOCAB\CONCEPT_ANCESTOR.csv' 
WITH (
FIRSTROW = 2,
FIELDTERMINATOR = '\t',
ROWTERMINATOR = '0x0a',
ERRORFILE = 'C:\CDMV5VOCAB\CONCEPT_ANCESTOR.bad',
TABLOCK
);

TRUNCATE TABLE CONCEPT_SYNONYM;
BULK INSERT CONCEPT_SYNONYM 
FROM 'C:\CDMV5VOCAB\CONCEPT_SYNONYM.csv' 
WITH (
FIRSTROW = 2,
FIELDTERMINATOR = '\t',
ROWTERMINATOR = '0x0a',
ERRORFILE = 'C:\CDMV5VOCAB\CONCEPT_SYNONYM.bad',
TABLOCK
);

TRUNCATE TABLE VOCABULARY;
BULK INSERT VOCABULARY 
FROM 'C:\CDMV5VOCAB\VOCABULARY.csv' 
WITH (
FIRSTROW = 2,
FIELDTERMINATOR = '\t',
ROWTERMINATOR = '0x0a',
ERRORFILE = 'C:\CDMV5VOCAB\VOCABULARY.bad',
TABLOCK
);

TRUNCATE TABLE RELATIONSHIP;
BULK INSERT RELATIONSHIP 
FROM 'C:\CDMV5VOCAB\RELATIONSHIP.csv' 
WITH (
FIRSTROW = 2,
FIELDTERMINATOR = '\t',
ROWTERMINATOR = '0x0a',
ERRORFILE = 'C:\CDMV5VOCAB\RELATIONSHIP.bad',
TABLOCK
);

TRUNCATE TABLE CONCEPT_CLASS;
BULK INSERT CONCEPT_CLASS 
FROM 'C:\CDMV5VOCAB\CONCEPT_CLASS.csv' 
WITH (
FIRSTROW = 2,
FIELDTERMINATOR = '\t',
ROWTERMINATOR = '0x0a',
ERRORFILE = 'C:\CDMV5VOCAB\CONCEPT_CLASS.bad',
TABLOCK
);

TRUNCATE TABLE DOMAIN;
BULK INSERT DOMAIN 
FROM 'C:\CDMV5VOCAB\DOMAIN.csv' 
WITH (
FIRSTROW = 2,
FIELDTERMINATOR = '\t',
ROWTERMINATOR = '0x0a',
ERRORFILE = 'C:\CDMV5VOCAB\DOMAIN.bad',
TABLOCK
);