V4 control files and DDL

Version4/Oracle/VocabImport/OMOP CDM vocabulary load - Oracle.bat

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+/*********************************************************************************
+# Copyright 2015 Observational Health Data Sciences and Informatics
+#
+# 
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+# 
+#     http://www.apache.org/licenses/LICENSE-2.0
+# 
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.4
+********************************************************************************/
+
+/************************
+
+ ####### #     # ####### ######      #####  ######  #     #              ##   ####### 
+ #     # ##   ## #     # #     #    #     # #     # ##   ##    #    #   # #   #       
+ #     # # # # # #     # #     #    #       #     # # # # #    #    #  #  #   #       
+ #     # #  #  # #     # ######     #       #     # #  #  #    #    # ####### #######  
+ #     # #     # #     # #          #       #     # #     #    #    #     #         # 
+ #     # #     # #     # #          #     # #     # #     #     #  #      #   #     # 
+ ####### #     # ####### #           #####  ######  #     #      ##       # #  #####  
+
+
+script to load the Vocabulary related tables in the OMOP common data model, version 4.5 for Oracle database
+
+last revised: 19 Mar 2015
+
+author:  Lee Evans
+
+Notes
+
+1) This script assumes the CDM version 4.5 vocabulary zip file has been unzipped into the "C:\CDM" directory. 
+2) If you unzipped your CDM version 4.5 vocabulary files into a different directory then replace all file paths below, with your directory path.
+3) If you have existing data in your CDM vocabulary tables then backup that data (if needed) and truncate those tables before loading
+
+
+*************************/
+
+sqlldr CDM/<password> CONTROL=CONCEPT.ctl LOG=C:\CDM\CONCEPT.log BAD=C:\CDM\CONCEPT.bad  
+sqlldr CDM/<password> CONTROL=CONCEPT_ANCESTOR.ctl LOG=C:\CDM\CONCEPT_ANCESTOR.log BAD=C:\CDM\CONCEPT_ANCESTOR.bad  
+sqlldr CDM/<password> CONTROL=CONCEPT_RELATIONSHIP.ctl LOG=C:\CDM\CONCEPT_RELATIONSHIP.log BAD=C:\CDM\CONCEPT_RELATIONSHIP.bad
+sqlldr CDM/<password> CONTROL=CONCEPT_SYNONYM.ctl LOG=C:\CDM\CONCEPT_SYNONYM.log BAD=C:\CDM\CONCEPT_SYNONYM.bad
+sqlldr CDM/<password> CONTROL=DRUG_STRENGTH.ctl LOG=C:\CDM\DRUG_STRENGTH.log BAD=C:\CDM\DRUG_STRENGTH.bad
+sqlldr CDM/<password> CONTROL=RELATIONSHIP.ctl LOG=C:\CDM\RELATIONSHIP.log BAD=C:\CDM\RELATIONSHIP.bad
+sqlldr CDM/<password> CONTROL=VOCABULARY.ctl LOG=C:\CDM\VOCABULARY.log BAD=C:\CDM\VOCABULARY.bad 
+sqlldr CDM/<password> CONTROL=SOURCE_TO_CONCEPT_MAP.ctl LOG=C:\CDM\SOURCE_TO_CONCEPT_MAP.log BAD=C:\CDM\SOURCE_TO_CONCEPT_MAP.bad 

Version4/Oracle/VocabImport/concept.ctl

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+options (skip=1)
+load data
+infile concept.csv 
+into table concept
+replace
+fields terminated by '\t'
+trailing nullcols
+(
+  concept_id,
+  concept_name CHAR(256),
+  concept_level,
+  concept_class,
+  vocabulary_id,
+  concept_code,
+  valid_start_date DATE 'YYYYMMDD',
+  valid_end_date DATE 'YYYYMMDD',
+  invalid_reason
+)

Version4/Oracle/VocabImport/concept_ancestor.ctl

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+options (skip=1)
+load data
+infile concept_ancestor.csv 
+into table concept_ancestor
+replace
+fields terminated by '\t'
+trailing nullcols
+(
+  ancestor_concept_id,
+  descendant_concept_id,
+  min_levels_of_separation,
+  max_levels_of_separation	
+)

Version4/Oracle/VocabImport/concept_relationship.ctl

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+options (skip=1)
+load data
+infile concept_relationship.csv 
+into table concept_relationship
+replace
+fields terminated by '\t'
+trailing nullcols
+(
+  concept_id_1,
+  concept_id_2,
+  relationship_id,
+  valid_start_date DATE 'YYYYMMDD',
+  valid_end_date DATE 'YYYYMMDD',
+  invalid_reason
+)

Version4/Oracle/VocabImport/concept_synonym.ctl

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+options (skip=1)
+load data
+infile concept_synonym.csv 
+into table concept_synonym
+replace
+fields terminated by '\t'
+trailing nullcols
+(
+  concept_synonym_id,
+  concept_id,
+  concept_synonym_name CHAR(1000)
+)

Version4/Oracle/VocabImport/drug_strength.ctl

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+options (skip=1)
+load data
+infile drug_strength.csv 
+into table drug_strength
+replace
+fields terminated by '\t'
+trailing nullcols
+(
+  drug_concept_id,
+  ingredient_concept_id,
+  amount_value,
+  amount_unit,
+  concentration_value,
+  concentration_enum_unit,
+  concentration_denom_unit,
+  valid_start_date DATE 'YYYYMMDD',
+  valid_end_date DATE 'YYYYMMDD',
+  invalid_reason
+)

Version4/Oracle/VocabImport/relationship.ctl

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+options (skip=1)
+load data
+infile relationship.csv 
+into table relationship
+replace
+fields terminated by '\t'
+trailing nullcols
+(
+  relationship_id,
+  relationship_name,
+  is_hierarchical,
+  defines_ancestry,
+  reverse_relationship
+)

Version4/Oracle/VocabImport/source_to_concept_map.ctl

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+options (skip=1)
+load data
+infile source_to_concept_map.csv 
+into table source_to_concept_map
+replace
+fields terminated by '\t'
+trailing nullcols
+(
+  source_code,
+  source_vocabulary_id,
+  source_code_description CHAR(256),
+  target_concept_id,
+  target_vocabulary_id,
+  mapping_type,
+  primary_map,
+  valid_start_date DATE 'YYYYMMDD',
+  valid_end_date DATE 'YYYYMMDD',
+  invalid_reason
+)

Version4/Oracle/VocabImport/vocabulary.ctl

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+options (skip=1)
+load data
+infile vocabulary.csv 
+into table vocabulary
+replace
+fields terminated by '\t'
+trailing nullcols
+(
+  vocabulary_id,
+  vocabulary_name
+)

Version4/PostgreSQL/CDM V4 DDL.sql

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+
+/*********************************************************************************
+# Copyright 2015 Observational Health Data Sciences and Informatics
+#
+# 
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+# 
+#     http://www.apache.org/licenses/LICENSE-2.0
+# 
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.4
+********************************************************************************/
+
+/************************
+
+ ####### #     # ####### ######      #####  ######  #     #              ##   ####### 
+ #     # ##   ## #     # #     #    #     # #     # ##   ##    #    #   # #   #       
+ #     # # # # # #     # #     #    #       #     # # # # #    #    #  #  #   #       
+ #     # #  #  # #     # ######     #       #     # #  #  #    #    # ####### #######  
+ #     # #     # #     # #          #       #     # #     #    #    #     #         # 
+ #     # #     # #     # #          #     # #     # #     #     #  #      #   #     # 
+ ####### #     # ####### #           #####  ######  #     #      ##       # #  #####  
+
+
+script to create OMOP common data model, version 4.5 for PostgreSQL database
+
+last revised: 20 Mar 2015
+
+author:  Lee Evans
+
+
+*************************/
+
+CREATE TABLE concept (
+  concept_id integer NOT NULL,
+  concept_name varchar(256) NOT NULL,
+  concept_level integer NOT NULL,
+  concept_class varchar(60) NOT NULL,
+  vocabulary_id integer NOT NULL,
+  concept_code varchar(40) NOT NULL,
+  valid_start_date date NOT NULL,
+  valid_end_date date NOT NULL DEFAULT '2099-12-31'::date,
+  invalid_reason varchar(1)
+)
+;
+
+
+CREATE TABLE concept_ancestor (
+  ancestor_concept_id		INTEGER		NOT NULL,
+  descendant_concept_id		INTEGER		NOT NULL,
+  min_levels_of_separation	INTEGER		NOT NULL,
+  max_levels_of_separation	INTEGER		NOT NULL
+)
+;
+
+
+CREATE TABLE concept_relationship (
+  concept_id_1 integer NOT NULL,
+  concept_id_2 integer NOT NULL,
+  relationship_id integer NOT NULL,
+  valid_start_date date NOT NULL,
+  valid_end_date date NOT NULL DEFAULT '2099-12-31'::date,
+  invalid_reason varchar(1)
+)
+;
+
+
+CREATE TABLE concept_synonym (
+  concept_synonym_id integer NOT NULL,
+  concept_id integer NOT NULL,
+  concept_synonym_name varchar(1000) NOT NULL
+)
+;
+
+
+
+CREATE TABLE drug_strength (
+  drug_concept_id integer NOT NULL,
+  ingredient_concept_id integer NOT NULL,
+  amount_value double precision,
+  amount_unit varchar(60),
+  concentration_value double precision,
+  concentration_enum_unit character varying(60),
+  concentration_denom_unit character varying(60),
+  valid_start_date date NOT NULL,
+  valid_end_date date NOT NULL,
+  invalid_reason varchar(1)
+)
+;
+
+
+
+
+CREATE TABLE relationship (
+  relationship_id			VARCHAR(20)	NOT NULL,
+  relationship_name			VARCHAR(256)	NOT NULL,
+  is_hierarchical			integer		NOT NULL,
+  defines_ancestry			integer		DEFAULT 1,
+  reverse_relationship			integer		
+)
+;
+
+
+
+CREATE TABLE source_to_concept_map (
+  source_code				VARCHAR(40)		NOT NULL,
+  source_vocabulary_id		INTEGER		NOT NULL,
+  source_code_description	VARCHAR(256),
+  target_concept_id			INTEGER			NOT NULL,
+  target_vocabulary_id		INTEGER		NOT NULL,
+  mapping_type			VARCHAR(256),
+  primary_map			VARCHAR(1),
+  valid_start_date			DATE			NOT NULL,
+  valid_end_date			DATE			NOT NULL,
+  invalid_reason			VARCHAR(1)		NULL
+)
+;
+
+
+
+
+CREATE TABLE vocabulary (
+  vocabulary_id			integer		NOT NULL,
+  vocabulary_name		VARCHAR(256)	NOT NULL
+)
+;

Version4/PostgreSQL/VocabImport/OMOP CDM vocabulary load - PostgreSQL.sql

@@ -0,0 +1,54 @@
+/*********************************************************************************
+# Copyright 2015 Observational Health Data Sciences and Informatics
+#
+# 
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+# 
+#     http://www.apache.org/licenses/LICENSE-2.0
+# 
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+********************************************************************************/
+
+/************************
+
+ ####### #     # ####### ######      #####  ######  #     #           ####### 
+ #     # ##   ## #     # #     #    #     # #     # ##   ##    #    # #       
+ #     # # # # # #     # #     #    #       #     # # # # #    #    # #       
+ #     # #  #  # #     # ######     #       #     # #  #  #    #    # ######  
+ #     # #     # #     # #          #       #     # #     #    #    #       # 
+ #     # #     # #     # #          #     # #     # #     #     #  #  #     # 
+ ####### #     # ####### #           #####  ######  #     #      ##    #####  
+
+
+Script to load the common data model, version 4.5 vocabulary tables for PostgreSQL database
+
+Notes
+
+1) This script assumes the CDM version 4.5 vocabulary zip file has been unzipped into the "C:\CDM" directory. 
+2) If you unzipped your CDM version 4.5 vocabulary files into a different directory then replace all file paths below, with your directory path.
+3) Run this SQL query script in the database where you created your CDM Version 4.5 tables
+
+last revised: 20th March 2015
+
+author:  Lee Evans
+
+
+*************************/
+
+COPY CONCEPT FROM 'C:\CDM\CONCEPT.csv' WITH DELIMITER E'\t' CSV HEADER QUOTE E'\b' ;
+COPY CONCEPT_ANCESTOR FROM 'C:\CDM\CONCEPT_ANCESTOR.csv' WITH DELIMITER E'\t' CSV HEADER QUOTE E'\b' ;
+COPY CONCEPT_RELATIONSHIP FROM 'C:\CDM\CONCEPT_RELATIONSHIP.csv' WITH DELIMITER E'\t' CSV HEADER QUOTE E'\b' ;
+COPY CONCEPT_SYNONYM FROM 'C:\CDM\CONCEPT_SYNONYM.csv' WITH DELIMITER E'\t' CSV HEADER QUOTE E'\b' ;
+COPY DRUG_STRENGTH FROM 'C:\CDM\DRUG_STRENGTH.csv' WITH DELIMITER E'\t' CSV HEADER QUOTE E'\b' ;
+COPY RELATIONSHIP FROM 'C:\CDM\RELATIONSHIP.csv' WITH DELIMITER E'\t' CSV HEADER QUOTE E'\b' ;
+COPY SOURCE_TO_CONCEPT_MAP FROM 'C:\CDM\SOURCE_TO_CONCEPT_MAP.csv' WITH DELIMITER E'\t' CSV HEADER QUOTE E'\b' ;
+COPY VOCABULARY FROM 'C:\CDM\VOCABULARY.csv' WITH DELIMITER E'\t' CSV HEADER QUOTE E'\b' ;
+
+
+