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OMOP
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changes after V4 testing

This commit is contained in:
leeevans 2015-03-20 14:08:48 -04:00
parent 00434c3dde
commit 8b478ae7a0
7 changed files with 436 additions and 4 deletions
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2
Version4/Oracle/VocabImport/concept.ctl
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@ -7,7 +7,7 @@ fields terminated by '\t'
trailing nullcols
(
concept_id,
concept_name,
concept_name CHAR(256),
concept_level,
concept_class,
vocabulary_id,

2
Version4/Oracle/VocabImport/source_to_concept_map.ctl
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@ -8,7 +8,7 @@ trailing nullcols
(
source_code,
source_vocabulary_id,
source_code_description,
source_code_description CHAR(256),
target_concept_id,
target_vocabulary_id,
mapping_type,

131
Version4/PostgreSQL/CDM V4 DDL.sql Normal file
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@ -0,0 +1,131 @@
/*********************************************************************************
# 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
)
;

54
Version4/PostgreSQL/VocabImport/OMOP CDM vocabulary load - PostgreSQL.sql Normal file
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@ -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' ;

117
Version4/SQL Server/CDM V4 DDL.sql Normal file
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@ -0,0 +1,117 @@
/*********************************************************************************
# 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 Sql Server database
last revised: 20 Mar 2015
author: Lee Evans
*************************/
CREATE TABLE CONCEPT(
CONCEPT_ID int NOT NULL,
CONCEPT_NAME varchar(256) NOT NULL,
CONCEPT_LEVEL int NOT NULL,
CONCEPT_CLASS varchar(60) NOT NULL,
VOCABULARY_ID int NOT NULL,
CONCEPT_CODE varchar(40) NOT NULL,
VALID_START_DATE date NOT NULL,
VALID_END_DATE date NOT NULL DEFAULT ('31-Dec-2099'),
INVALID_REASON char(1) NULL
);
CREATE TABLE CONCEPT_ANCESTOR(
ANCESTOR_CONCEPT_ID int NOT NULL,
DESCENDANT_CONCEPT_ID int NOT NULL,
MAX_LEVELS_OF_SEPARATION int NULL,
MIN_LEVELS_OF_SEPARATION int NULL
);
CREATE TABLE CONCEPT_RELATIONSHIP(
CONCEPT_ID_1 int NOT NULL,
CONCEPT_ID_2 int NOT NULL,
RELATIONSHIP_ID int NOT NULL,
VALID_START_DATE date NOT NULL,
VALID_END_DATE date NOT NULL DEFAULT ('31-Dec-2099'),
INVALID_REASON char(1) NULL
);
CREATE TABLE CONCEPT_SYNONYM(
CONCEPT_SYNONYM_ID int NOT NULL,
CONCEPT_ID int NOT NULL,
CONCEPT_SYNONYM_NAME varchar(1000) NOT NULL
);
CREATE TABLE DRUG_STRENGTH(
DRUG_CONCEPT_ID int NOT NULL,
INGREDIENT_CONCEPT_ID int NOT NULL,
AMOUNT_VALUE float NULL,
AMOUNT_UNIT varchar(60) NULL,
CONCENTRATION_VALUE float NULL,
CONCENTRATION_ENUM_UNIT varchar(60) NULL,
CONCENTRATION_DENOM_UNIT varchar(60) NULL,
VALID_START_DATE date NOT NULL,
VALID_END_DATE date NOT NULL,
INVALID_REASON varchar(1) NULL
);
CREATE TABLE RELATIONSHIP(
RELATIONSHIP_ID int NOT NULL,
RELATIONSHIP_NAME varchar(256) NOT NULL,
IS_HIERARCHICAL int NOT NULL,
DEFINES_ANCESTRY int NOT NULL DEFAULT ((1)),
REVERSE_RELATIONSHIP int NULL
);
CREATE TABLE SOURCE_TO_CONCEPT_MAP(
SOURCE_CODE varchar(40) NOT NULL,
SOURCE_VOCABULARY_ID int NOT NULL,
SOURCE_CODE_DESCRIPTION varchar(256) NULL,
TARGET_CONCEPT_ID int NOT NULL,
TARGET_VOCABULARY_ID int NOT NULL,
MAPPING_TYPE varchar(256) NULL,
PRIMARY_MAP char(1) NULL,
VALID_START_DATE date NOT NULL,
VALID_END_DATE date NOT NULL DEFAULT ('31-Dec-2099'),
INVALID_REASON char(1) NULL
);
CREATE TABLE VOCABULARY(
VOCABULARY_ID int NOT NULL,
VOCABULARY_NAME varchar(256) NOT NULL
);

4
Version4/SQL Server/README.md
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@ -1,7 +1,7 @@
Common-Data-Model / Oracle
Common-Data-Model / SQL Server
=================
This folder contains the SQL scripts for Oracle.
This folder contains the SQL scripts for SQL Server.
In order to create your instantiation of the Common Data Model, we recommend following these steps:

130
Version4/SQL Server/VocabImport/OMOP CDM vocabulary load - SQL Server.sql Normal file
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@ -0,0 +1,130 @@
/*********************************************************************************
# 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 SQL Server 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
*************************/
TRUNCATE TABLE CONCEPT;
BULK INSERT CONCEPT
FROM 'C:\CDM\CONCEPT.csv'
WITH (
FIRSTROW = 2,
FIELDTERMINATOR = '\t',
ROWTERMINATOR = '0x0a',
ERRORFILE = 'C:\CDM\CONCEPT.bad',
TABLOCK
);
TRUNCATE TABLE CONCEPT_ANCESTOR;
BULK INSERT CONCEPT_ANCESTOR
FROM 'C:\CDM\CONCEPT_ANCESTOR.csv'
WITH (
FIRSTROW = 2,
FIELDTERMINATOR = '\t',
ROWTERMINATOR = '0x0a',
ERRORFILE = 'C:\CDM\CONCEPT_ANCESTOR.bad',
TABLOCK
);
TRUNCATE TABLE CONCEPT_RELATIONSHIP;
BULK INSERT CONCEPT_RELATIONSHIP
FROM 'C:\CDM\CONCEPT_RELATIONSHIP.csv'
WITH (
FIRSTROW = 2,
FIELDTERMINATOR = '\t',
ROWTERMINATOR = '0x0a',
ERRORFILE = 'C:\CDM\CONCEPT_RELATIONSHIP.bad',
TABLOCK
);
TRUNCATE TABLE CONCEPT_SYNONYM;
BULK INSERT CONCEPT_SYNONYM
FROM 'C:\CDM\CONCEPT_SYNONYM.csv'
WITH (
FIRSTROW = 2,
FIELDTERMINATOR = '\t',
ROWTERMINATOR = '0x0a',
ERRORFILE = 'C:\CDM\CONCEPT_SYNONYM.bad',
TABLOCK
);
TRUNCATE TABLE DRUG_STRENGTH;
BULK INSERT DRUG_STRENGTH
FROM 'C:\CDM\DRUG_STRENGTH.csv'
WITH (
FIRSTROW = 2,
FIELDTERMINATOR = '\t',
ROWTERMINATOR = '0x0a',
ERRORFILE = 'C:\CDM\DRUG_STRENGTH.bad',
TABLOCK
);
TRUNCATE TABLE RELATIONSHIP;
BULK INSERT RELATIONSHIP
FROM 'C:\CDM\RELATIONSHIP.csv'
WITH (
FIRSTROW = 2,
FIELDTERMINATOR = '\t',
ROWTERMINATOR = '0x0a',
ERRORFILE = 'C:\CDM\RELATIONSHIP.bad',
TABLOCK
);
TRUNCATE TABLE SOURCE_TO_CONCEPT_MAP;
BULK INSERT SOURCE_TO_CONCEPT_MAP
FROM 'C:\CDM\SOURCE_TO_CONCEPT_MAP.csv'
WITH (
FIRSTROW = 2,
FIELDTERMINATOR = '\t',
ROWTERMINATOR = '0x0a',
ERRORFILE = 'C:\CDM\SOURCE_TO_CONCEPT_MAP.bad',
TABLOCK
);
TRUNCATE TABLE VOCABULARY;
BULK INSERT VOCABULARY
FROM 'C:\CDM\VOCABULARY.csv'
WITH (
FIRSTROW = 2,
FIELDTERMINATOR = '\t',
ROWTERMINATOR = '0x0a',
ERRORFILE = 'C:\CDM\VOCABULARY.bad',
TABLOCK
);