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Removing files that do not pertain to the OMOP CDM v4-to-v5 conversion

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clairblacketer 2017-06-09 09:31:00 -04:00
parent 46ba5fddc2
commit 728a3f4e4f
46 changed files with 0 additions and 6848 deletions
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15
Impala/DataImport/OMOP_CDM_synpuf_load_Impala.sql
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LOAD DATA INPATH '${VAR:OMOP_SYNPUF_PATH}/CDM_CARE_SITE.csv' OVERWRITE INTO TABLE care_site;
LOAD DATA INPATH '${VAR:OMOP_SYNPUF_PATH}/CDM_CONDITION_OCCURRENCE.csv' OVERWRITE INTO TABLE condition_occurrence;
LOAD DATA INPATH '${VAR:OMOP_SYNPUF_PATH}/CDM_DEATH.csv' OVERWRITE INTO TABLE death;
LOAD DATA INPATH '${VAR:OMOP_SYNPUF_PATH}/CDM_DRUG_EXPOSURE.csv' OVERWRITE INTO TABLE drug_exposure;
LOAD DATA INPATH '${VAR:OMOP_SYNPUF_PATH}/CDM_DEVICE_EXPOSURE.csv' OVERWRITE INTO TABLE device_exposure;
LOAD DATA INPATH '${VAR:OMOP_SYNPUF_PATH}/CDM_LOCATION.csv' OVERWRITE INTO TABLE `location`;
LOAD DATA INPATH '${VAR:OMOP_SYNPUF_PATH}/CDM_MEASUREMENT.csv' OVERWRITE INTO TABLE measurement;
LOAD DATA INPATH '${VAR:OMOP_SYNPUF_PATH}/CDM_OBSERVATION.csv' OVERWRITE INTO TABLE observation;
LOAD DATA INPATH '${VAR:OMOP_SYNPUF_PATH}/CDM_OBSERVATION_PERIOD.csv' OVERWRITE INTO TABLE observation_period;
LOAD DATA INPATH '${VAR:OMOP_SYNPUF_PATH}/CDM_PERSON.csv' OVERWRITE INTO TABLE person;
LOAD DATA INPATH '${VAR:OMOP_SYNPUF_PATH}/CDM_PROCEDURE_OCCURRENCE.csv' OVERWRITE INTO TABLE procedure_occurrence;
LOAD DATA INPATH '${VAR:OMOP_SYNPUF_PATH}/CDM_PROVIDER.csv' OVERWRITE INTO TABLE provider;
LOAD DATA INPATH '${VAR:OMOP_SYNPUF_PATH}/CDM_VISIT_OCCURRENCE.csv' OVERWRITE INTO TABLE visit_occurrence;
LOAD DATA INPATH '${VAR:OMOP_SYNPUF_PATH}/CDM_DRUG_ERA.csv' OVERWRITE INTO TABLE drug_era;
LOAD DATA INPATH '${VAR:OMOP_SYNPUF_PATH}/CDM_CONDITION_ERA.csv' OVERWRITE INTO TABLE condition_era;

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Impala/OMOP_CDM_ddl_Impala.sql
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/*********************************************************************************
# Copyright 2014-6 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 create OMOP common data model, version 5.0 for Hadoop (Hive/Impala) database
Based on the PostgreSQL version, with the following changes:
* NULL/NOT NULL is not used.
* Dates are stored as VARCHAR(8). See http://stackoverflow.com/questions/33024309/convert-yyyymmdd-string-to-date-in-impala for how to treat date columns as dates.
* PostgreSQL NUMERIC is stored as DOUBLE for amounts, and DECIMAL(19,4) for prices.
* PostgreSQL TEXT is stored as STRING.
*************************/
/************************
Standardized vocabulary
************************/
CREATE TABLE concept (
concept_id INTEGER,
concept_name VARCHAR(255),
domain_id VARCHAR(20),
vocabulary_id VARCHAR(20),
concept_class_id VARCHAR(20),
standard_concept VARCHAR(1),
concept_code VARCHAR(50),
valid_start_date VARCHAR(8), -- DATE
valid_end_date VARCHAR(8), -- DATE
invalid_reason VARCHAR(1)
)
ROW FORMAT DELIMITED FIELDS TERMINATED BY '\t'
TBLPROPERTIES ("skip.header.line.count"="1")
;
CREATE TABLE vocabulary (
vocabulary_id VARCHAR(20),
vocabulary_name VARCHAR(255),
vocabulary_reference VARCHAR(255),
vocabulary_version VARCHAR(255),
vocabulary_concept_id INTEGER
)
ROW FORMAT DELIMITED FIELDS TERMINATED BY '\t'
TBLPROPERTIES ("skip.header.line.count"="1")
;
CREATE TABLE domain (
domain_id VARCHAR(20),
domain_name VARCHAR(255),
domain_concept_id INTEGER
)
ROW FORMAT DELIMITED FIELDS TERMINATED BY '\t'
TBLPROPERTIES ("skip.header.line.count"="1")
;
CREATE TABLE concept_class (
concept_class_id VARCHAR(20),
concept_class_name VARCHAR(255),
concept_class_concept_id INTEGER
)
ROW FORMAT DELIMITED FIELDS TERMINATED BY '\t'
TBLPROPERTIES ("skip.header.line.count"="1")
;
CREATE TABLE concept_relationship (
concept_id_1 INTEGER,
concept_id_2 INTEGER,
relationship_id VARCHAR(20),
valid_start_date VARCHAR(8), -- DATE
valid_end_date VARCHAR(8), -- DATE
invalid_reason VARCHAR(1)
)
ROW FORMAT DELIMITED FIELDS TERMINATED BY '\t'
TBLPROPERTIES ("skip.header.line.count"="1")
;
CREATE TABLE relationship (
relationship_id VARCHAR(20),
relationship_name VARCHAR(255),
is_hierarchical VARCHAR(1),
defines_ancestry VARCHAR(1),
reverse_relationship_id VARCHAR(20),
relationship_concept_id INTEGER
)
ROW FORMAT DELIMITED FIELDS TERMINATED BY '\t'
TBLPROPERTIES ("skip.header.line.count"="1")
;
CREATE TABLE concept_synonym (
concept_id INTEGER,
concept_synonym_name VARCHAR(1000),
language_concept_id INTEGER
)
ROW FORMAT DELIMITED FIELDS TERMINATED BY '\t'
TBLPROPERTIES ("skip.header.line.count"="1")
;
CREATE TABLE concept_ancestor (
ancestor_concept_id INTEGER,
descendant_concept_id INTEGER,
min_levels_of_separation INTEGER,
max_levels_of_separation INTEGER
)
ROW FORMAT DELIMITED FIELDS TERMINATED BY '\t'
TBLPROPERTIES ("skip.header.line.count"="1")
;
CREATE TABLE source_to_concept_map (
source_code VARCHAR(50),
source_concept_id INTEGER,
source_vocabulary_id VARCHAR(20),
source_code_description VARCHAR(255),
target_concept_id INTEGER,
target_vocabulary_id VARCHAR(20),
valid_start_date VARCHAR(8), -- DATE
valid_end_date VARCHAR(8), -- DATE
invalid_reason VARCHAR(1)
)
ROW FORMAT DELIMITED FIELDS TERMINATED BY '\t'
TBLPROPERTIES ("skip.header.line.count"="1")
;
CREATE TABLE drug_strength (
drug_concept_id INTEGER,
ingredient_concept_id INTEGER,
amount_value DOUBLE, -- NUMERIC
amount_unit_concept_id INTEGER,
numerator_value DOUBLE, -- NUMERIC
numerator_unit_concept_id INTEGER,
denominator_value DOUBLE, -- NUMERIC
denominator_unit_concept_id INTEGER,
box_size INTEGER,
valid_start_date VARCHAR(8), -- DATE
valid_end_date VARCHAR(8), -- DATE
invalid_reason VARCHAR(1)
)
ROW FORMAT DELIMITED FIELDS TERMINATED BY '\t'
TBLPROPERTIES ("skip.header.line.count"="1")
;
CREATE TABLE cohort_definition (
cohort_definition_id INTEGER,
cohort_definition_name VARCHAR(255),
cohort_definition_description STRING, -- TEXT
definition_type_concept_id INTEGER,
cohort_definition_syntax STRING, -- TEXT
subject_concept_id INTEGER,
cohort_initiation_date VARCHAR(8) -- DATE
)
;
CREATE TABLE attribute_definition (
attribute_definition_id INTEGER,
attribute_name VARCHAR(255),
attribute_description STRING, -- TEXT
attribute_type_concept_id INTEGER,
attribute_syntax STRING -- TEXT
)
;
/**************************
Standardized meta-data
***************************/
CREATE TABLE cdm_source
(
cdm_source_name VARCHAR(255),
cdm_source_abbreviation VARCHAR(25),
cdm_holder VARCHAR(255),
source_description STRING, -- TEXT
source_documentation_reference VARCHAR(255),
cdm_etl_reference VARCHAR(255),
source_release_date VARCHAR(8), -- DATE
cdm_release_date VARCHAR(8), -- DATE
cdm_version VARCHAR(10),
vocabulary_version VARCHAR(20)
)
;
/************************
Standardized clinical data
************************/
CREATE TABLE person (
person_id INTEGER,
gender_concept_id INTEGER,
year_of_birth INTEGER,
month_of_birth INTEGER,
day_of_birth INTEGER,
time_of_birth VARCHAR(10),
race_concept_id INTEGER,
ethnicity_concept_id INTEGER,
location_id INTEGER,
provider_id INTEGER,
care_site_id INTEGER,
person_source_value VARCHAR(50),
gender_source_value VARCHAR(50),
gender_source_concept_id INTEGER,
race_source_value VARCHAR(50),
race_source_concept_id INTEGER,
ethnicity_source_value VARCHAR(50),
ethnicity_source_concept_id INTEGER
)
ROW FORMAT DELIMITED FIELDS TERMINATED BY ','
TBLPROPERTIES ("skip.header.line.count"="1")
;
CREATE TABLE observation_period (
observation_period_id INTEGER,
person_id INTEGER,
observation_period_start_date VARCHAR(8), -- DATE
observation_period_end_date VARCHAR(8), -- DATE
period_type_concept_id INTEGER
)
ROW FORMAT DELIMITED FIELDS TERMINATED BY ','
TBLPROPERTIES ("skip.header.line.count"="1")
;
CREATE TABLE specimen (
specimen_id INTEGER,
person_id INTEGER,
specimen_concept_id INTEGER,
specimen_type_concept_id INTEGER,
specimen_date VARCHAR(8), -- DATE
specimen_time VARCHAR(10),
quantity DOUBLE, -- NUMERIC
unit_concept_id INTEGER,
anatomic_site_concept_id INTEGER,
disease_status_concept_id INTEGER,
specimen_source_id VARCHAR(50),
specimen_source_value VARCHAR(50),
unit_source_value VARCHAR(50),
anatomic_site_source_value VARCHAR(50),
disease_status_source_value VARCHAR(50)
)
;
CREATE TABLE death (
person_id INTEGER,
death_date VARCHAR(8), -- DATE
death_type_concept_id INTEGER,
cause_concept_id INTEGER,
cause_source_value VARCHAR(50),
cause_source_concept_id INTEGER
)
ROW FORMAT DELIMITED FIELDS TERMINATED BY ','
TBLPROPERTIES ("skip.header.line.count"="1")
;
CREATE TABLE visit_occurrence (
visit_occurrence_id INTEGER,
person_id INTEGER,
visit_concept_id INTEGER,
visit_start_date VARCHAR(8), -- DATE
visit_start_time VARCHAR(10),
visit_end_date VARCHAR(8), -- DATE
visit_end_time VARCHAR(10),
visit_type_concept_id INTEGER,
provider_id INTEGER,
care_site_id INTEGER,
visit_source_value VARCHAR(50),
visit_source_concept_id INTEGER
)
ROW FORMAT DELIMITED FIELDS TERMINATED BY ','
TBLPROPERTIES ("skip.header.line.count"="1")
;
CREATE TABLE procedure_occurrence (
procedure_occurrence_id INTEGER,
person_id INTEGER,
procedure_concept_id INTEGER,
procedure_date VARCHAR(8), -- DATE
procedure_type_concept_id INTEGER,
modifier_concept_id INTEGER,
quantity INTEGER,
provider_id INTEGER,
visit_occurrence_id INTEGER,
procedure_source_value VARCHAR(50),
procedure_source_concept_id INTEGER,
qualifier_source_value VARCHAR(50)
)
ROW FORMAT DELIMITED FIELDS TERMINATED BY ','
TBLPROPERTIES ("skip.header.line.count"="1")
;
CREATE TABLE drug_exposure (
drug_exposure_id INTEGER,
person_id INTEGER,
drug_concept_id INTEGER,
drug_exposure_start_date VARCHAR(8), -- DATE
drug_exposure_end_date VARCHAR(8), -- DATE
drug_type_concept_id INTEGER,
stop_reason VARCHAR(20),
refills INTEGER,
quantity DOUBLE, -- NUMERIC
days_supply INTEGER,
sig STRING, -- TEXT
route_concept_id INTEGER,
effective_drug_dose DOUBLE, -- NUMERIC
dose_unit_concept_id INTEGER,
lot_number VARCHAR(50),
provider_id INTEGER,
visit_occurrence_id INTEGER,
drug_source_value VARCHAR(50),
drug_source_concept_id INTEGER,
route_source_value VARCHAR(50),
dose_unit_source_value VARCHAR(50)
)
ROW FORMAT DELIMITED FIELDS TERMINATED BY ','
TBLPROPERTIES ("skip.header.line.count"="1")
;
CREATE TABLE device_exposure (
device_exposure_id INTEGER,
person_id INTEGER,
device_concept_id INTEGER,
device_exposure_start_date VARCHAR(8), -- DATE
device_exposure_end_date VARCHAR(8), -- DATE
device_type_concept_id INTEGER,
unique_device_id VARCHAR(50),
quantity INTEGER,
provider_id INTEGER,
visit_occurrence_id INTEGER,
device_source_value VARCHAR(100),
device_source_concept_id INTEGER
)
ROW FORMAT DELIMITED FIELDS TERMINATED BY ','
TBLPROPERTIES ("skip.header.line.count"="1")
;
CREATE TABLE condition_occurrence (
condition_occurrence_id INTEGER,
person_id INTEGER,
condition_concept_id INTEGER,
condition_start_date VARCHAR(8), -- DATE
condition_end_date VARCHAR(8), -- DATE
condition_type_concept_id INTEGER,
stop_reason VARCHAR(20),
provider_id INTEGER,
visit_occurrence_id INTEGER,
condition_source_value VARCHAR(50),
condition_source_concept_id INTEGER
)
ROW FORMAT DELIMITED FIELDS TERMINATED BY ','
TBLPROPERTIES ("skip.header.line.count"="1")
;
CREATE TABLE measurement (
measurement_id INTEGER,
person_id INTEGER,
measurement_concept_id INTEGER,
measurement_date VARCHAR(8), -- DATE
measurement_time VARCHAR(10),
measurement_type_concept_id INTEGER,
operator_concept_id INTEGER,
value_as_number DOUBLE, -- NUMERIC
value_as_concept_id INTEGER,
unit_concept_id INTEGER,
range_low DOUBLE, -- NUMERIC
range_high DOUBLE, -- NUMERIC
provider_id INTEGER,
visit_occurrence_id INTEGER,
measurement_source_value VARCHAR(50),
measurement_source_concept_id INTEGER,
unit_source_value VARCHAR(50),
value_source_value VARCHAR(50)
)
ROW FORMAT DELIMITED FIELDS TERMINATED BY ','
TBLPROPERTIES ("skip.header.line.count"="1")
;
CREATE TABLE note (
note_id INTEGER,
person_id INTEGER,
note_date VARCHAR(8), -- DATE
note_time VARCHAR(10),
note_type_concept_id INTEGER,
note_text STRING, -- TEXT
provider_id INTEGER,
visit_occurrence_id INTEGER,
note_source_value VARCHAR(50)
)
;
CREATE TABLE observation (
observation_id INTEGER,
person_id INTEGER,
observation_concept_id INTEGER,
observation_date VARCHAR(8), -- DATE
observation_time VARCHAR(10),
observation_type_concept_id INTEGER,
value_as_number DOUBLE, -- NUMERIC
value_as_string VARCHAR(60),
value_as_concept_id INTEGER,
qualifier_concept_id INTEGER,
unit_concept_id INTEGER,
provider_id INTEGER,
visit_occurrence_id INTEGER,
observation_source_value VARCHAR(50),
observation_source_concept_id INTEGER,
unit_source_value VARCHAR(50),
qualifier_source_value VARCHAR(50)
)
ROW FORMAT DELIMITED FIELDS TERMINATED BY ','
TBLPROPERTIES ("skip.header.line.count"="1")
;
CREATE TABLE fact_relationship (
domain_concept_id_1 INTEGER,
fact_id_1 INTEGER,
domain_concept_id_2 INTEGER,
fact_id_2 INTEGER,
relationship_concept_id INTEGER
)
;
/************************
Standardized health system data
************************/
CREATE TABLE `location` (
location_id INTEGER,
address_1 VARCHAR(50),
address_2 VARCHAR(50),
city VARCHAR(50),
state VARCHAR(2),
zip VARCHAR(9),
county VARCHAR(20),
location_source_value VARCHAR(50)
)
ROW FORMAT DELIMITED FIELDS TERMINATED BY ','
TBLPROPERTIES ("skip.header.line.count"="1")
;
CREATE TABLE care_site (
care_site_id INTEGER,
care_site_name VARCHAR(255),
place_of_service_concept_id INTEGER,
location_id INTEGER,
care_site_source_value VARCHAR(50),
place_of_service_source_value VARCHAR(50)
)
ROW FORMAT DELIMITED FIELDS TERMINATED BY ','
TBLPROPERTIES ("skip.header.line.count"="1")
;
CREATE TABLE provider (
provider_id INTEGER,
provider_name VARCHAR(255),
NPI VARCHAR(20),
DEA VARCHAR(20),
specialty_concept_id INTEGER,
care_site_id INTEGER,
year_of_birth INTEGER,
gender_concept_id INTEGER,
provider_source_value VARCHAR(50),
specialty_source_value VARCHAR(50),
specialty_source_concept_id INTEGER,
gender_source_value VARCHAR(50),
gender_source_concept_id INTEGER
)
ROW FORMAT DELIMITED FIELDS TERMINATED BY ','
TBLPROPERTIES ("skip.header.line.count"="1")
;
/************************
Standardized health economics
************************/
CREATE TABLE payer_plan_period (
payer_plan_period_id INTEGER,
person_id INTEGER,
payer_plan_period_start_date VARCHAR(8), -- DATE
payer_plan_period_end_date VARCHAR(8), -- DATE
payer_source_value VARCHAR (50),
plan_source_value VARCHAR (50),
family_source_value VARCHAR (50)
)
;
/* The individual cost tables are being phased out and will disappear soon
CREATE TABLE visit_cost (
visit_cost_id INTEGER,
visit_occurrence_id INTEGER,
currency_concept_id INTEGER,
paid_copay DECIMAL(19,4), -- NUMERIC
paid_coinsurance DECIMAL(19,4), -- NUMERIC
paid_toward_deductible DECIMAL(19,4), -- NUMERIC
paid_by_payer DECIMAL(19,4), -- NUMERIC
paid_by_coordination_benefits DECIMAL(19,4), -- NUMERIC
total_out_of_pocket DECIMAL(19,4), -- NUMERIC
total_paid DECIMAL(19,4), -- NUMERIC
payer_plan_period_id INTEGER
)
;
CREATE TABLE procedure_cost (
procedure_cost_id INTEGER,
procedure_occurrence_id INTEGER,
currency_concept_id INTEGER,
paid_copay DECIMAL(19,4), -- NUMERIC
paid_coinsurance DECIMAL(19,4), -- NUMERIC
paid_toward_deductible DECIMAL(19,4), -- NUMERIC
paid_by_payer DECIMAL(19,4), -- NUMERIC
paid_by_coordination_benefits DECIMAL(19,4), -- NUMERIC
total_out_of_pocket DECIMAL(19,4), -- NUMERIC
total_paid DECIMAL(19,4), -- NUMERIC
revenue_code_concept_id INTEGER,
payer_plan_period_id INTEGER,
revenue_code_source_value VARCHAR(50)
)
;
CREATE TABLE drug_cost (
drug_cost_id INTEGER,
drug_exposure_id INTEGER,
currency_concept_id INTEGER,
paid_copay DECIMAL(19,4), -- NUMERIC
paid_coinsurance DECIMAL(19,4), -- NUMERIC
paid_toward_deductible DECIMAL(19,4), -- NUMERIC
paid_by_payer DECIMAL(19,4), -- NUMERIC
paid_by_coordination_benefits DECIMAL(19,4), -- NUMERIC
total_out_of_pocket DECIMAL(19,4), -- NUMERIC
total_paid DECIMAL(19,4), -- NUMERIC
ingredient_cost DECIMAL(19,4), -- NUMERIC
dispensing_fee DECIMAL(19,4), -- NUMERIC
average_wholesale_price DECIMAL(19,4), -- NUMERIC
payer_plan_period_id INTEGER
)
;
CREATE TABLE device_cost (
device_cost_id INTEGER,
device_exposure_id INTEGER,
currency_concept_id INTEGER,
paid_copay DECIMAL(19,4), -- NUMERIC
paid_coinsurance DECIMAL(19,4), -- NUMERIC
paid_toward_deductible DECIMAL(19,4), -- NUMERIC
paid_by_payer DECIMAL(19,4), -- NUMERIC
paid_by_coordination_benefits DECIMAL(19,4), -- NUMERIC
total_out_of_pocket DECIMAL(19,4), -- NUMERIC
total_paid DECIMAL(19,4), -- NUMERIC
payer_plan_period_id INTEGER
)
;
*/
CREATE TABLE cost (
cost_id INTEGER,
cost_event_id INTEGER,
cost_domain_id VARCHAR(20),
cost_type_concept_id INTEGER,
currency_concept_id INTEGER,
total_charge DECIMAL(19,4), -- NUMERIC
total_cost DECIMAL(19,4), -- NUMERIC
total_paid DECIMAL(19,4), -- NUMERIC
paid_by_payer DECIMAL(19,4), -- NUMERIC
paid_by_patient DECIMAL(19,4), -- NUMERIC
paid_patient_copay DECIMAL(19,4), -- NUMERIC
paid_patient_coinsurance DECIMAL(19,4), -- NUMERIC
paid_patient_deductible DECIMAL(19,4), -- NUMERIC
paid_by_primary DECIMAL(19,4), -- NUMERIC
paid_ingredient_cost DECIMAL(19,4), -- NUMERIC
paid_dispensing_fee DECIMAL(19,4), -- NUMERIC
payer_plan_period_id INTEGER,
amount_allowed DECIMAL(19,4), -- NUMERIC
revenue_code_concept_id INTEGER,
reveue_code_source_value VARCHAR(50)
)
;
/************************
Standardized derived elements
************************/
CREATE TABLE cohort (
cohort_definition_id INTEGER,
subject_id INTEGER,
cohort_start_date VARCHAR(8), -- DATE
cohort_end_date VARCHAR(8) -- DATE
)
;
CREATE TABLE cohort_attribute (
cohort_definition_id INTEGER,
cohort_start_date VARCHAR(8), -- DATE
cohort_end_date VARCHAR(8), -- DATE
subject_id INTEGER,
attribute_definition_id INTEGER,
value_as_number DOUBLE, -- NUMERIC
value_as_concept_id INTEGER
)
;
CREATE TABLE drug_era (
drug_era_id INTEGER,
person_id INTEGER,
drug_concept_id INTEGER,
drug_era_start_date VARCHAR(8), -- DATE
drug_era_end_date VARCHAR(8), -- DATE
drug_exposure_count INTEGER,
gap_days INTEGER
)
ROW FORMAT DELIMITED FIELDS TERMINATED BY ','
TBLPROPERTIES ("skip.header.line.count"="1")
;
CREATE TABLE dose_era (
dose_era_id INTEGER,
person_id INTEGER,
drug_concept_id INTEGER,
unit_concept_id INTEGER,
dose_value DOUBLE, -- NUMERIC
dose_era_start_date VARCHAR(8), -- DATE
dose_era_end_date VARCHAR(8) -- DATE
)
;
CREATE TABLE condition_era (
condition_era_id INTEGER,
person_id INTEGER,
condition_concept_id INTEGER,
condition_era_start_date VARCHAR(8), -- DATE
condition_era_end_date VARCHAR(8), -- DATE
condition_occurrence_count INTEGER
)
ROW FORMAT DELIMITED FIELDS TERMINATED BY ','
TBLPROPERTIES ("skip.header.line.count"="1")
;

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Impala/README.md
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Common-Data-Model / Impala
=================
This folder contains the SQL scripts for Impala.
In order to create your instantiation of the Common Data Model, we recommend following these steps:
1. Create an empty schema.
```bash
impala-shell -q 'CREATE DATABASE omop_cdm'
```
2. Execute the script `OMOP_CDM_ddl_Impala.sql` to create the tables and fields.
```bash
impala-shell -d omop_cdm -f OMOP_CDM_ddl_Impala.sql
```
3. Load your data into the schema.
a. Load the vocabulary tables.
First, download the data from
[http://www.ohdsi.org/web/athena/](http://www.ohdsi.org/web/athena/)
and unzip into a _cdmv5vocab_ directory, then run
```bash
hadoop fs -put cdmv5vocab cdmv5vocab
hadoop fs -chmod +w cdmv5vocab
impala-shell -d omop_cdm -f VocabImport/OMOP_CDM_vocabulary_load_Impala.sql --var=OMOP_VOCAB_PATH=/user/$USER/cdmv5vocab
```
b. Load the patient data.
For example, download the 1000 person sample of simulated CMS SynPUF patient data from
[http://www.ltscomputingllc.com/downloads/](http://www.ltscomputingllc.com/downloads/)
and unzip into a _synpuf_ directory, then run
```bash
hadoop fs -put synpuf synpuf
hadoop fs -chmod +w synpuf
impala-shell -d omop_cdm -f DataImport/OMOP_CDM_synpuf_load_Impala.sql --var=OMOP_SYNPUF_PATH=/user/$USER/synpuf
```
4. Run simple queries to sanity check.
```bash
impala-shell -d omop_cdm -q 'SELECT COUNT(1) FROM concept'
impala-shell -d omop_cdm -q 'SELECT COUNT(1) FROM person'
```

9
Impala/VocabImport/OMOP_CDM_vocabulary_load_Impala.sql
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LOAD DATA INPATH '${VAR:OMOP_VOCAB_PATH}/CONCEPT.csv' OVERWRITE INTO TABLE concept;
LOAD DATA INPATH '${VAR:OMOP_VOCAB_PATH}/VOCABULARY.csv' OVERWRITE INTO TABLE vocabulary;
LOAD DATA INPATH '${VAR:OMOP_VOCAB_PATH}/DOMAIN.csv' OVERWRITE INTO TABLE domain;
LOAD DATA INPATH '${VAR:OMOP_VOCAB_PATH}/CONCEPT_CLASS.csv' OVERWRITE INTO TABLE concept_class;
LOAD DATA INPATH '${VAR:OMOP_VOCAB_PATH}/CONCEPT_RELATIONSHIP.csv' OVERWRITE INTO TABLE concept_relationship;
LOAD DATA INPATH '${VAR:OMOP_VOCAB_PATH}/RELATIONSHIP.csv' OVERWRITE INTO TABLE relationship;
LOAD DATA INPATH '${VAR:OMOP_VOCAB_PATH}/CONCEPT_SYNONYM.csv' OVERWRITE INTO TABLE concept_synonym;
LOAD DATA INPATH '${VAR:OMOP_VOCAB_PATH}/CONCEPT_ANCESTOR.csv' OVERWRITE INTO TABLE concept_ancestor;
LOAD DATA INPATH '${VAR:OMOP_VOCAB_PATH}/DRUG_STRENGTH.csv' OVERWRITE INTO TABLE drug_strength;

544
Oracle/OMOP CDM constraints - Oracle.sql
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/*********************************************************************************
# Copyright 2014 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.
********************************************************************************/
/************************
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# # ## ## # # # # # # # # ## ## # # # # # #### # # #### ##### ##### ## # # # ##### ####
# # # # # # # # # # # # # # # # # # # # # # # ## # # # # # # # # ## # # #
# # # # # # # ###### # # # # # # # # ###### # # # # # # #### # # # # # # # # # # ####
# # # # # # # # # # # # # # # # # # # # # # # ##### ###### # # # # # #
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script to create constraints within OMOP common data model, version 5.0 for Oracle database
last revised: 12 Oct 2014
author: Patrick Ryan
*************************/
/************************
*************************
*************************
*************************
Primary key constraints
*************************
*************************
*************************
************************/
/************************
Standardized vocabulary
************************/
ALTER TABLE concept ADD CONSTRAINT xpk_concept PRIMARY KEY (concept_id);
ALTER TABLE vocabulary ADD CONSTRAINT xpk_vocabulary PRIMARY KEY (vocabulary_id);
ALTER TABLE domain ADD CONSTRAINT xpk_domain PRIMARY KEY (domain_id);
ALTER TABLE concept_class ADD CONSTRAINT xpk_concept_class PRIMARY KEY (concept_class_id);
ALTER TABLE concept_relationship ADD CONSTRAINT xpk_concept_relationship PRIMARY KEY (concept_id_1,concept_id_2,relationship_id);
ALTER TABLE relationship ADD CONSTRAINT xpk_relationship PRIMARY KEY (relationship_id);
ALTER TABLE concept_ancestor ADD CONSTRAINT xpk_concept_ancestor PRIMARY KEY (ancestor_concept_id,descendant_concept_id);
ALTER TABLE source_to_concept_map ADD CONSTRAINT xpk_source_to_concept_map PRIMARY KEY (source_vocabulary_id,target_concept_id,source_code,valid_end_date);
ALTER TABLE drug_strength ADD CONSTRAINT xpk_drug_strength PRIMARY KEY (drug_concept_id, ingredient_concept_id);
ALTER TABLE cohort_definition ADD CONSTRAINT xpk_cohort_definition PRIMARY KEY (cohort_definition_id);
ALTER TABLE attribute_definition ADD CONSTRAINT xpk_attribute_definition PRIMARY KEY (attribute_definition_id);
/**************************
Standardized meta-data
***************************/
/************************
Standardized clinical data
************************/
/**PRIMARY KEY NONCLUSTERED constraints**/
ALTER TABLE person ADD CONSTRAINT xpk_person PRIMARY KEY ( person_id ) ;
ALTER TABLE observation_period ADD CONSTRAINT xpk_observation_period PRIMARY KEY ( observation_period_id ) ;
ALTER TABLE specimen ADD CONSTRAINT xpk_specimen PRIMARY KEY ( specimen_id ) ;
ALTER TABLE death ADD CONSTRAINT xpk_death PRIMARY KEY ( person_id ) ;
ALTER TABLE visit_occurrence ADD CONSTRAINT xpk_visit_occurrence PRIMARY KEY ( visit_occurrence_id ) ;
ALTER TABLE procedure_occurrence ADD CONSTRAINT xpk_procedure_occurrence PRIMARY KEY ( procedure_occurrence_id ) ;
ALTER TABLE drug_exposure ADD CONSTRAINT xpk_drug_exposure PRIMARY KEY ( drug_exposure_id ) ;
ALTER TABLE device_exposure ADD CONSTRAINT xpk_device_exposure PRIMARY KEY ( device_exposure_id ) ;
ALTER TABLE condition_occurrence ADD CONSTRAINT xpk_condition_occurrence PRIMARY KEY ( condition_occurrence_id ) ;
ALTER TABLE measurement ADD CONSTRAINT xpk_measurement PRIMARY KEY ( measurement_id ) ;
ALTER TABLE note ADD CONSTRAINT xpk_note PRIMARY KEY ( note_id ) ;
ALTER TABLE observation ADD CONSTRAINT xpk_observation PRIMARY KEY ( observation_id ) ;
/************************
Standardized health system data
************************/
ALTER TABLE location ADD CONSTRAINT xpk_location PRIMARY KEY ( location_id ) ;
ALTER TABLE care_site ADD CONSTRAINT xpk_care_site PRIMARY KEY ( care_site_id ) ;
ALTER TABLE provider ADD CONSTRAINT xpk_provider PRIMARY KEY ( provider_id ) ;
/************************
Standardized health economics
************************/
ALTER TABLE payer_plan_period ADD CONSTRAINT xpk_payer_plan_period PRIMARY KEY ( payer_plan_period_id ) ;
ALTER TABLE visit_cost ADD CONSTRAINT xpk_visit_cost PRIMARY KEY ( visit_cost_id ) ;
ALTER TABLE procedure_cost ADD CONSTRAINT xpk_procedure_cost PRIMARY KEY ( procedure_cost_id ) ;
ALTER TABLE drug_cost ADD CONSTRAINT xpk_drug_cost PRIMARY KEY ( drug_cost_id ) ;
ALTER TABLE device_cost ADD CONSTRAINT xpk_device_cost PRIMARY KEY ( device_cost_id ) ;
/************************
Standardized derived elements
************************/
ALTER TABLE cohort ADD CONSTRAINT xpk_cohort PRIMARY KEY ( cohort_definition_id, subject_id, cohort_start_date, cohort_end_date ) ;
ALTER TABLE cohort_attribute ADD CONSTRAINT xpk_cohort_attribute PRIMARY KEY ( cohort_definition_id, subject_id, cohort_start_date, cohort_end_date, attribute_definition_id ) ;
ALTER TABLE drug_era ADD CONSTRAINT xpk_drug_era PRIMARY KEY ( drug_era_id ) ;
ALTER TABLE dose_era ADD CONSTRAINT xpk_dose_era PRIMARY KEY ( dose_era_id ) ;
ALTER TABLE condition_era ADD CONSTRAINT xpk_condition_era PRIMARY KEY ( condition_era_id ) ;
/************************
*************************
*************************
*************************
Foreign key constraints
*************************
*************************
*************************
************************/
/************************
Standardized vocabulary
************************/
ALTER TABLE concept ADD CONSTRAINT fpk_concept_domain FOREIGN KEY (domain_id) REFERENCES domain (domain_id);
ALTER TABLE concept ADD CONSTRAINT fpk_concept_class FOREIGN KEY (concept_class_id) REFERENCES concept_class (concept_class_id);
ALTER TABLE concept ADD CONSTRAINT fpk_concept_vocabulary FOREIGN KEY (vocabulary_id) REFERENCES vocabulary (vocabulary_id);
ALTER TABLE vocabulary ADD CONSTRAINT fpk_vocabulary_concept FOREIGN KEY (vocabulary_concept_id) REFERENCES concept (concept_id);
ALTER TABLE domain ADD CONSTRAINT fpk_domain_concept FOREIGN KEY (domain_concept_id) REFERENCES concept (concept_id);
ALTER TABLE concept_class ADD CONSTRAINT fpk_concept_class_concept FOREIGN KEY (concept_class_concept_id) REFERENCES concept (concept_id);
ALTER TABLE concept_relationship ADD CONSTRAINT fpk_concept_relationship_c_1 FOREIGN KEY (concept_id_1) REFERENCES concept (concept_id);
ALTER TABLE concept_relationship ADD CONSTRAINT fpk_concept_relationship_c_2 FOREIGN KEY (concept_id_2) REFERENCES concept (concept_id);
ALTER TABLE concept_relationship ADD CONSTRAINT fpk_concept_relationship_id FOREIGN KEY (relationship_id) REFERENCES relationship (relationship_id);
ALTER TABLE relationship ADD CONSTRAINT fpk_relationship_concept FOREIGN KEY (relationship_concept_id) REFERENCES concept (concept_id);
ALTER TABLE relationship ADD CONSTRAINT fpk_relationship_reverse FOREIGN KEY (reverse_relationship_id) REFERENCES relationship (relationship_id);
ALTER TABLE concept_synonym ADD CONSTRAINT fpk_concept_synonym_concept FOREIGN KEY (concept_id) REFERENCES concept (concept_id);
ALTER TABLE concept_ancestor ADD CONSTRAINT fpk_concept_ancestor_concept_1 FOREIGN KEY (ancestor_concept_id) REFERENCES concept (concept_id);
ALTER TABLE concept_ancestor ADD CONSTRAINT fpk_concept_ancestor_concept_2 FOREIGN KEY (descendant_concept_id) REFERENCES concept (concept_id);
ALTER TABLE source_to_concept_map ADD CONSTRAINT fpk_source_to_concept_map_v_1 FOREIGN KEY (source_vocabulary_id) REFERENCES vocabulary (vocabulary_id);
ALTER TABLE source_to_concept_map ADD CONSTRAINT fpk_source_to_concept_map_v_2 FOREIGN KEY (target_vocabulary_id) REFERENCES vocabulary (vocabulary_id);
ALTER TABLE source_to_concept_map ADD CONSTRAINT fpk_source_to_concept_map_c_1 FOREIGN KEY (target_concept_id) REFERENCES concept (concept_id);
ALTER TABLE drug_strength ADD CONSTRAINT fpk_drug_strength_concept_1 FOREIGN KEY (drug_concept_id) REFERENCES concept (concept_id);
ALTER TABLE drug_strength ADD CONSTRAINT fpk_drug_strength_concept_2 FOREIGN KEY (ingredient_concept_id) REFERENCES concept (concept_id);
ALTER TABLE drug_strength ADD CONSTRAINT fpk_drug_strength_unit_1 FOREIGN KEY (amount_unit_concept_id) REFERENCES concept (concept_id);
ALTER TABLE drug_strength ADD CONSTRAINT fpk_drug_strength_unit_2 FOREIGN KEY (numerator_unit_concept_id) REFERENCES concept (concept_id);
ALTER TABLE drug_strength ADD CONSTRAINT fpk_drug_strength_unit_3 FOREIGN KEY (denominator_unit_concept_id) REFERENCES concept (concept_id);
ALTER TABLE cohort_definition ADD CONSTRAINT fpk_cohort_definition_concept FOREIGN KEY (definition_type_concept_id) REFERENCES concept (concept_id);
/**************************
Standardized meta-data
***************************/
/************************
Standardized clinical data
************************/
ALTER TABLE person ADD CONSTRAINT fpk_person_gender_concept FOREIGN KEY (gender_concept_id) REFERENCES concept (concept_id);
ALTER TABLE person ADD CONSTRAINT fpk_person_race_concept FOREIGN KEY (race_concept_id) REFERENCES concept (concept_id);
ALTER TABLE person ADD CONSTRAINT fpk_person_ethnicity_concept FOREIGN KEY (ethnicity_concept_id) REFERENCES concept (concept_id);
ALTER TABLE person ADD CONSTRAINT fpk_person_gender_concept_s FOREIGN KEY (gender_source_concept_id) REFERENCES concept (concept_id);
ALTER TABLE person ADD CONSTRAINT fpk_person_race_concept_s FOREIGN KEY (race_source_concept_id) REFERENCES concept (concept_id);
ALTER TABLE person ADD CONSTRAINT fpk_person_ethnicity_concept_s FOREIGN KEY (ethnicity_source_concept_id) REFERENCES concept (concept_id);
ALTER TABLE person ADD CONSTRAINT fpk_person_location FOREIGN KEY (location_id) REFERENCES location (location_id);
ALTER TABLE person ADD CONSTRAINT fpk_person_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
ALTER TABLE person ADD CONSTRAINT fpk_person_care_site FOREIGN KEY (care_site_id) REFERENCES care_site (care_site_id);
ALTER TABLE observation_period ADD CONSTRAINT fpk_observation_period_person FOREIGN KEY (person_id) REFERENCES person (person_id);
ALTER TABLE observation_period ADD CONSTRAINT fpk_observation_period_concept FOREIGN KEY (period_type_concept_id) REFERENCES concept (concept_id);
ALTER TABLE specimen ADD CONSTRAINT fpk_specimen_person FOREIGN KEY (person_id) REFERENCES person (person_id);
ALTER TABLE specimen ADD CONSTRAINT fpk_specimen_concept FOREIGN KEY (specimen_concept_id) REFERENCES concept (concept_id);
ALTER TABLE specimen ADD CONSTRAINT fpk_specimen_type_concept FOREIGN KEY (specimen_type_concept_id) REFERENCES concept (concept_id);
ALTER TABLE specimen ADD CONSTRAINT fpk_specimen_unit_concept FOREIGN KEY (unit_concept_id) REFERENCES concept (concept_id);
ALTER TABLE specimen ADD CONSTRAINT fpk_specimen_site_concept FOREIGN KEY (anatomic_site_concept_id) REFERENCES concept (concept_id);
ALTER TABLE specimen ADD CONSTRAINT fpk_specimen_status_concept FOREIGN KEY (disease_status_concept_id) REFERENCES concept (concept_id);
ALTER TABLE death ADD CONSTRAINT fpk_death_person FOREIGN KEY (person_id) REFERENCES person (person_id);
ALTER TABLE death ADD CONSTRAINT fpk_death_type_concept FOREIGN KEY (death_type_concept_id) REFERENCES concept (concept_id);
ALTER TABLE death ADD CONSTRAINT fpk_death_cause_concept FOREIGN KEY (cause_concept_id) REFERENCES concept (concept_id);
ALTER TABLE death ADD CONSTRAINT fpk_death_cause_concept_s FOREIGN KEY (cause_source_concept_id) REFERENCES concept (concept_id);
ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_person FOREIGN KEY (person_id) REFERENCES person (person_id);
ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_concept FOREIGN KEY (visit_concept_id) REFERENCES concept (concept_id);
ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_type_concept FOREIGN KEY (visit_type_concept_id) REFERENCES concept (concept_id);
ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_care_site FOREIGN KEY (care_site_id) REFERENCES care_site (care_site_id);
ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_concept_s FOREIGN KEY (visit_source_concept_id) REFERENCES concept (concept_id);
ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_person FOREIGN KEY (person_id) REFERENCES person (person_id);
ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_concept FOREIGN KEY (procedure_concept_id) REFERENCES concept (concept_id);
ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_type_concept FOREIGN KEY (procedure_type_concept_id) REFERENCES concept (concept_id);
ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_modifier FOREIGN KEY (modifier_concept_id) REFERENCES concept (concept_id);
ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id);
ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_concept_s FOREIGN KEY (procedure_source_concept_id) REFERENCES concept (concept_id);
ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_person FOREIGN KEY (person_id) REFERENCES person (person_id);
ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_concept FOREIGN KEY (drug_concept_id) REFERENCES concept (concept_id);
ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_type_concept FOREIGN KEY (drug_type_concept_id) REFERENCES concept (concept_id);
ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_route_concept FOREIGN KEY (route_concept_id) REFERENCES concept (concept_id);
ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_dose_unit_concept FOREIGN KEY (dose_unit_concept_id) REFERENCES concept (concept_id);
ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id);
ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_concept_s FOREIGN KEY (drug_source_concept_id) REFERENCES concept (concept_id);
ALTER TABLE device_exposure ADD CONSTRAINT fpk_device_person FOREIGN KEY (person_id) REFERENCES person (person_id);
ALTER TABLE device_exposure ADD CONSTRAINT fpk_device_concept FOREIGN KEY (device_concept_id) REFERENCES concept (concept_id);
ALTER TABLE device_exposure ADD CONSTRAINT fpk_device_type_concept FOREIGN KEY (device_type_concept_id) REFERENCES concept (concept_id);
ALTER TABLE device_exposure ADD CONSTRAINT fpk_device_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
ALTER TABLE device_exposure ADD CONSTRAINT fpk_device_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id);
ALTER TABLE device_exposure ADD CONSTRAINT fpk_device_concept_s FOREIGN KEY (device_source_concept_id) REFERENCES concept (concept_id);
ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_person FOREIGN KEY (person_id) REFERENCES person (person_id);
ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_concept FOREIGN KEY (condition_concept_id) REFERENCES concept (concept_id);
ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_type_concept FOREIGN KEY (condition_type_concept_id) REFERENCES concept (concept_id);
ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id);
ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_concept_s FOREIGN KEY (condition_source_concept_id) REFERENCES concept (concept_id);
ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_person FOREIGN KEY (person_id) REFERENCES person (person_id);
ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_concept FOREIGN KEY (measurement_concept_id) REFERENCES concept (concept_id);
ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_type_concept FOREIGN KEY (measurement_type_concept_id) REFERENCES concept (concept_id);
ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_operator FOREIGN KEY (operator_concept_id) REFERENCES concept (concept_id);
ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_value FOREIGN KEY (value_as_concept_id) REFERENCES concept (concept_id);
ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_unit FOREIGN KEY (unit_concept_id) REFERENCES concept (concept_id);
ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id);
ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_concept_s FOREIGN KEY (measurement_source_concept_id) REFERENCES concept (concept_id);
ALTER TABLE note ADD CONSTRAINT fpk_note_person FOREIGN KEY (person_id) REFERENCES person (person_id);
ALTER TABLE note ADD CONSTRAINT fpk_note_type_concept FOREIGN KEY (note_type_concept_id) REFERENCES concept (concept_id);
ALTER TABLE note ADD CONSTRAINT fpk_note_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
ALTER TABLE note ADD CONSTRAINT fpk_note_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id);
ALTER TABLE observation ADD CONSTRAINT fpk_observation_person FOREIGN KEY (person_id) REFERENCES person (person_id);
ALTER TABLE observation ADD CONSTRAINT fpk_observation_concept FOREIGN KEY (observation_concept_id) REFERENCES concept (concept_id);
ALTER TABLE observation ADD CONSTRAINT fpk_observation_type_concept FOREIGN KEY (observation_type_concept_id) REFERENCES concept (concept_id);
ALTER TABLE observation ADD CONSTRAINT fpk_observation_value FOREIGN KEY (value_as_concept_id) REFERENCES concept (concept_id);
ALTER TABLE observation ADD CONSTRAINT fpk_observation_qualifier FOREIGN KEY (qualifier_concept_id) REFERENCES concept (concept_id);
ALTER TABLE observation ADD CONSTRAINT fpk_observation_unit FOREIGN KEY (unit_concept_id) REFERENCES concept (concept_id);
ALTER TABLE observation ADD CONSTRAINT fpk_observation_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
ALTER TABLE observation ADD CONSTRAINT fpk_observation_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id);
ALTER TABLE observation ADD CONSTRAINT fpk_observation_concept_s FOREIGN KEY (observation_source_concept_id) REFERENCES concept (concept_id);
ALTER TABLE fact_relationship ADD CONSTRAINT fpk_fact_domain_1 FOREIGN KEY (domain_concept_id_1) REFERENCES concept (concept_id);
ALTER TABLE fact_relationship ADD CONSTRAINT fpk_fact_domain_2 FOREIGN KEY (domain_concept_id_2) REFERENCES concept (concept_id);
ALTER TABLE fact_relationship ADD CONSTRAINT fpk_fact_relationship FOREIGN KEY (relationship_concept_id) REFERENCES concept (concept_id);
/************************
Standardized health system data
************************/
ALTER TABLE care_site ADD CONSTRAINT fpk_care_site_location FOREIGN KEY (location_id) REFERENCES location (location_id);
ALTER TABLE care_site ADD CONSTRAINT fpk_care_site_place FOREIGN KEY (place_of_service_concept_id) REFERENCES concept (concept_id);
ALTER TABLE provider ADD CONSTRAINT fpk_provider_specialty FOREIGN KEY (specialty_concept_id) REFERENCES concept (concept_id);
ALTER TABLE provider ADD CONSTRAINT fpk_provider_care_site FOREIGN KEY (care_site_id) REFERENCES care_site (care_site_id);
ALTER TABLE provider ADD CONSTRAINT fpk_provider_gender FOREIGN KEY (gender_concept_id) REFERENCES concept (concept_id);
ALTER TABLE provider ADD CONSTRAINT fpk_provider_specialty_s FOREIGN KEY (specialty_source_concept_id) REFERENCES concept (concept_id);
ALTER TABLE provider ADD CONSTRAINT fpk_provider_gender_s FOREIGN KEY (gender_source_concept_id) REFERENCES concept (concept_id);
/************************
Standardized health economics
************************/
ALTER TABLE payer_plan_period ADD CONSTRAINT fpk_payer_plan_period FOREIGN KEY (person_id) REFERENCES person (person_id);
ALTER TABLE visit_cost ADD CONSTRAINT fpk_visit_cost_id FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id);
ALTER TABLE visit_cost ADD CONSTRAINT fpk_visit_cost_currency FOREIGN KEY (currency_concept_id) REFERENCES concept (concept_id);
ALTER TABLE visit_cost ADD CONSTRAINT fpk_visit_cost_period FOREIGN KEY (payer_plan_period_id) REFERENCES payer_plan_period (payer_plan_period_id);
ALTER TABLE procedure_cost ADD CONSTRAINT fpk_procedure_cost_id FOREIGN KEY (procedure_occurrence_id) REFERENCES procedure_occurrence (procedure_occurrence_id);
ALTER TABLE procedure_cost ADD CONSTRAINT fpk_procedure_cost_currency FOREIGN KEY (currency_concept_id) REFERENCES concept (concept_id);
ALTER TABLE procedure_cost ADD CONSTRAINT fpk_procedure_cost_period FOREIGN KEY (payer_plan_period_id) REFERENCES payer_plan_period (payer_plan_period_id);
ALTER TABLE procedure_cost ADD CONSTRAINT fpk_procedure_cost_revenue FOREIGN KEY (revenue_code_concept_id) REFERENCES concept (concept_id);
ALTER TABLE drug_cost ADD CONSTRAINT fpk_drug_cost_id FOREIGN KEY (drug_exposure_id) REFERENCES drug_exposure (drug_exposure_id);
ALTER TABLE drug_cost ADD CONSTRAINT fpk_drug_cost_currency FOREIGN KEY (currency_concept_id) REFERENCES concept (concept_id);
ALTER TABLE drug_cost ADD CONSTRAINT fpk_drug_cost_period FOREIGN KEY (payer_plan_period_id) REFERENCES payer_plan_period (payer_plan_period_id);
ALTER TABLE device_cost ADD CONSTRAINT fpk_device_cost_id FOREIGN KEY (device_exposure_id) REFERENCES device_exposure (device_exposure_id);
ALTER TABLE device_cost ADD CONSTRAINT fpk_device_cost_currency FOREIGN KEY (currency_concept_id) REFERENCES concept (concept_id);
ALTER TABLE device_cost ADD CONSTRAINT fpk_device_cost_period FOREIGN KEY (payer_plan_period_id) REFERENCES payer_plan_period (payer_plan_period_id);
/************************
Standardized derived elements
************************/
ALTER TABLE cohort ADD CONSTRAINT fpk_cohort_definition FOREIGN KEY (cohort_definition_id) REFERENCES cohort_definition (cohort_definition_id);
ALTER TABLE cohort_attribute ADD CONSTRAINT fpk_ca_cohort_definition FOREIGN KEY (cohort_definition_id) REFERENCES cohort_definition (cohort_definition_id);
ALTER TABLE cohort_attribute ADD CONSTRAINT fpk_ca_attribute_definition FOREIGN KEY (attribute_definition_id) REFERENCES attribute_definition (attribute_definition_id);
ALTER TABLE cohort_attribute ADD CONSTRAINT fpk_ca_value FOREIGN KEY (value_as_concept_id) REFERENCES concept (concept_id);
ALTER TABLE drug_era ADD CONSTRAINT fpk_drug_era_person FOREIGN KEY (person_id) REFERENCES person (person_id);
ALTER TABLE drug_era ADD CONSTRAINT fpk_drug_era_concept FOREIGN KEY (drug_concept_id) REFERENCES concept (concept_id);
ALTER TABLE dose_era ADD CONSTRAINT fpk_dose_era_person FOREIGN KEY (person_id) REFERENCES person (person_id);
ALTER TABLE dose_era ADD CONSTRAINT fpk_dose_era_concept FOREIGN KEY (drug_concept_id) REFERENCES concept (concept_id);
ALTER TABLE dose_era ADD CONSTRAINT fpk_dose_era_unit_concept FOREIGN KEY (unit_concept_id) REFERENCES concept (concept_id);
ALTER TABLE condition_era ADD CONSTRAINT fpk_condition_era_person FOREIGN KEY (person_id) REFERENCES person (person_id);
ALTER TABLE condition_era ADD CONSTRAINT fpk_condition_era_concept FOREIGN KEY (condition_concept_id) REFERENCES concept (concept_id);

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@ -1,740 +0,0 @@
/*********************************************************************************
# Copyright 2014-6 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 create OMOP common data model, version 5.0 for Oracle database
last revised: 1-May-2016
Authors: Patrick Ryan, Christian Reich
*************************/
/************************
Standardized vocabulary
************************/
CREATE TABLE concept (
concept_id INTEGER NOT NULL,
concept_name VARCHAR(255) NOT NULL,
domain_id VARCHAR(20) NOT NULL,
vocabulary_id VARCHAR(20) NOT NULL,
concept_class_id VARCHAR(20) NOT NULL,
standard_concept VARCHAR(1) NULL,
concept_code VARCHAR(50) NOT NULL,
valid_start_date DATE NOT NULL,
valid_end_date DATE NOT NULL,
invalid_reason VARCHAR(1) NULL
)
;
CREATE TABLE vocabulary (
vocabulary_id VARCHAR(20) NOT NULL,
vocabulary_name VARCHAR(255) NOT NULL,
vocabulary_reference VARCHAR(255) NULL,
vocabulary_version VARCHAR(255) NULL,
vocabulary_concept_id INTEGER NOT NULL
)
;
CREATE TABLE domain (
domain_id VARCHAR(20) NOT NULL,
domain_name VARCHAR(255) NOT NULL,
domain_concept_id INTEGER NOT NULL
)
;
CREATE TABLE concept_class (
concept_class_id VARCHAR(20) NOT NULL,
concept_class_name VARCHAR(255) NOT NULL,
concept_class_concept_id INTEGER NOT NULL
)
;
CREATE TABLE concept_relationship (
concept_id_1 INTEGER NOT NULL,
concept_id_2 INTEGER NOT NULL,
relationship_id VARCHAR(20) NOT NULL,
valid_start_date DATE NOT NULL,
valid_end_date DATE NOT NULL,
invalid_reason VARCHAR(1) NULL)
;
CREATE TABLE relationship (
relationship_id VARCHAR(20) NOT NULL,
relationship_name VARCHAR(255) NOT NULL,
is_hierarchical VARCHAR(1) NOT NULL,
defines_ancestry VARCHAR(1) NOT NULL,
reverse_relationship_id VARCHAR(20) NOT NULL,
relationship_concept_id INTEGER NOT NULL
)
;
CREATE TABLE concept_synonym (
concept_id INTEGER NOT NULL,
concept_synonym_name VARCHAR(1000) NOT NULL,
language_concept_id INTEGER NOT NULL
)
;
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 source_to_concept_map (
source_code VARCHAR(50) NOT NULL,
source_concept_id INTEGER NOT NULL,
source_vocabulary_id VARCHAR(20) NOT NULL,
source_code_description VARCHAR(255) NULL,
target_concept_id INTEGER NOT NULL,
target_vocabulary_id VARCHAR(20) NOT NULL,
valid_start_date DATE NOT NULL,
valid_end_date DATE NOT NULL,
invalid_reason VARCHAR(1) NULL
)
;
CREATE TABLE drug_strength (
drug_concept_id INTEGER NOT NULL,
ingredient_concept_id INTEGER NOT NULL,
amount_value FLOAT NULL,
amount_unit_concept_id INTEGER NULL,
numerator_value FLOAT NULL,
numerator_unit_concept_id INTEGER NULL,
denominator_value FLOAT NULL,
denominator_unit_concept_id INTEGER NULL,
box_size INTEGER NULL,
valid_start_date DATE NOT NULL,
valid_end_date DATE NOT NULL,
invalid_reason VARCHAR(1) NULL
)
;
CREATE TABLE cohort_definition (
cohort_definition_id INTEGER NOT NULL,
cohort_definition_name VARCHAR(255) NOT NULL,
cohort_definition_description CLOB NULL,
definition_type_concept_id INTEGER NOT NULL,
cohort_definition_syntax CLOB NULL,
subject_concept_id INTEGER NOT NULL,
cohort_initiation_date DATE NULL
)
;
CREATE TABLE attribute_definition (
attribute_definition_id INTEGER NOT NULL,
attribute_name VARCHAR(255) NOT NULL,
attribute_description CLOB NULL,
attribute_type_concept_id INTEGER NOT NULL,
attribute_syntax CLOB NULL
)
;
/**************************
Standardized meta-data
***************************/
CREATE TABLE cdm_source
(
cdm_source_name VARCHAR(255) NOT NULL,
cdm_source_abbreviation VARCHAR(25) NULL,
cdm_holder VARCHAR(255) NULL,
source_description CLOB NULL,
source_documentation_reference VARCHAR(255) NULL,
cdm_etl_reference VARCHAR(255) NULL,
source_release_date DATE NULL,
cdm_release_date DATE NULL,
cdm_version VARCHAR(10) NULL,
vocabulary_version VARCHAR(20) NULL
)
;
/************************
Standardized clinical data
************************/
CREATE TABLE person
(
person_id INTEGER NOT NULL ,
gender_concept_id INTEGER NOT NULL ,
year_of_birth INTEGER NOT NULL ,
month_of_birth INTEGER NULL,
day_of_birth INTEGER NULL,
time_of_birth VARCHAR(10) NULL,
race_concept_id INTEGER NOT NULL,
ethnicity_concept_id INTEGER NOT NULL,
location_id INTEGER NULL,
provider_id INTEGER NULL,
care_site_id INTEGER NULL,
person_source_value VARCHAR(50) NULL,
gender_source_value VARCHAR(50) NULL,
gender_source_concept_id INTEGER NULL,
race_source_value VARCHAR(50) NULL,
race_source_concept_id INTEGER NULL,
ethnicity_source_value VARCHAR(50) NULL,
ethnicity_source_concept_id INTEGER NULL
)
;
CREATE TABLE observation_period
(
observation_period_id INTEGER NOT NULL ,
person_id INTEGER NOT NULL ,
observation_period_start_date DATE NOT NULL ,
observation_period_end_date DATE NOT NULL ,
period_type_concept_id INTEGER NOT NULL
)
;
CREATE TABLE specimen
(
specimen_id INTEGER NOT NULL ,
person_id INTEGER NOT NULL ,
specimen_concept_id INTEGER NOT NULL ,
specimen_type_concept_id INTEGER NOT NULL ,
specimen_date DATE NOT NULL ,
specimen_time VARCHAR(10) NULL ,
quantity FLOAT NULL ,
unit_concept_id INTEGER NULL ,
anatomic_site_concept_id INTEGER NULL ,
disease_status_concept_id INTEGER NULL ,
specimen_source_id VARCHAR(50) NULL ,
specimen_source_value VARCHAR(50) NULL ,
unit_source_value VARCHAR(50) NULL ,
anatomic_site_source_value VARCHAR(50) NULL ,
disease_status_source_value VARCHAR(50) NULL
)
;
CREATE TABLE death
(
person_id INTEGER NOT NULL ,
death_date DATE NOT NULL ,
death_type_concept_id INTEGER NOT NULL ,
cause_concept_id INTEGER NULL ,
cause_source_value VARCHAR(50) NULL,
cause_source_concept_id INTEGER NULL
)
;
CREATE TABLE visit_occurrence
(
visit_occurrence_id INTEGER NOT NULL ,
person_id INTEGER NOT NULL ,
visit_concept_id INTEGER NOT NULL ,
visit_start_date DATE NOT NULL ,
visit_start_time VARCHAR(10) NULL ,
visit_end_date DATE NOT NULL ,
visit_end_time VARCHAR(10) NULL ,
visit_type_concept_id INTEGER NOT NULL ,
provider_id INTEGER NULL,
care_site_id INTEGER NULL,
visit_source_value VARCHAR(50) NULL,
visit_source_concept_id INTEGER NULL
)
;
CREATE TABLE procedure_occurrence
(
procedure_occurrence_id INTEGER NOT NULL ,
person_id INTEGER NOT NULL ,
procedure_concept_id INTEGER NOT NULL ,
procedure_date DATE NOT NULL ,
procedure_type_concept_id INTEGER NOT NULL ,
modifier_concept_id INTEGER NULL ,
quantity INTEGER NULL ,
provider_id INTEGER NULL ,
visit_occurrence_id INTEGER NULL ,
procedure_source_value VARCHAR(50) NULL ,
procedure_source_concept_id INTEGER NULL ,
qualifier_source_value VARCHAR(50) NULL
)
;
CREATE TABLE drug_exposure
(
drug_exposure_id INTEGER NOT NULL ,
person_id INTEGER NOT NULL ,
drug_concept_id INTEGER NOT NULL ,
drug_exposure_start_date DATE NOT NULL ,
drug_exposure_end_date DATE NULL ,
drug_type_concept_id INTEGER NOT NULL ,
stop_reason VARCHAR(20) NULL ,
refills INTEGER NULL ,
quantity FLOAT NULL ,
days_supply INTEGER NULL ,
sig CLOB NULL ,
route_concept_id INTEGER NULL ,
effective_drug_dose FLOAT NULL ,
dose_unit_concept_id INTEGER NULL ,
lot_number VARCHAR(50) NULL ,
provider_id INTEGER NULL ,
visit_occurrence_id INTEGER NULL ,
drug_source_value VARCHAR(50) NULL ,
drug_source_concept_id INTEGER NULL ,
route_source_value VARCHAR(50) NULL ,
dose_unit_source_value VARCHAR(50) NULL
)
;
CREATE TABLE device_exposure
(
device_exposure_id INTEGER NOT NULL ,
person_id INTEGER NOT NULL ,
device_concept_id INTEGER NOT NULL ,
device_exposure_start_date DATE NOT NULL ,
device_exposure_end_date DATE NULL ,
device_type_concept_id INTEGER NOT NULL ,
unique_device_id VARCHAR(50) NULL ,
quantity INTEGER NULL ,
provider_id INTEGER NULL ,
visit_occurrence_id INTEGER NULL ,
device_source_value VARCHAR(100) NULL ,
device_source_concept_id INTEGER NULL
)
;
CREATE TABLE condition_occurrence
(
condition_occurrence_id INTEGER NOT NULL ,
person_id INTEGER NOT NULL ,
condition_concept_id INTEGER NOT NULL ,
condition_start_date DATE NOT NULL ,
condition_end_date DATE NULL ,
condition_type_concept_id INTEGER NOT NULL ,
stop_reason VARCHAR(20) NULL ,
provider_id INTEGER NULL ,
visit_occurrence_id INTEGER NULL ,
condition_source_value VARCHAR(50) NULL ,
condition_source_concept_id INTEGER NULL
)
;
CREATE TABLE measurement
(
measurement_id INTEGER NOT NULL ,
person_id INTEGER NOT NULL ,
measurement_concept_id INTEGER NOT NULL ,
measurement_date DATE NOT NULL ,
measurement_time VARCHAR(10) NULL ,
measurement_type_concept_id INTEGER NOT NULL ,
operator_concept_id INTEGER NULL ,
value_as_number FLOAT NULL ,
value_as_concept_id INTEGER NULL ,
unit_concept_id INTEGER NULL ,
range_low FLOAT NULL ,
range_high FLOAT NULL ,
provider_id INTEGER NULL ,
visit_occurrence_id INTEGER NULL ,
measurement_source_value VARCHAR(50) NULL ,
measurement_source_concept_id INTEGER NULL ,
unit_source_value VARCHAR(50) NULL ,
value_source_value VARCHAR(50) NULL
)
;
CREATE TABLE note
(
note_id INTEGER NOT NULL ,
person_id INTEGER NOT NULL ,
note_date DATE NOT NULL ,
note_time VARCHAR(10) NULL ,
note_type_concept_id INTEGER NOT NULL ,
note_text CLOB NOT NULL ,
provider_id INTEGER NULL ,
visit_occurrence_id INTEGER NULL ,
note_source_value VARCHAR(50) NULL
)
;
CREATE TABLE observation
(
observation_id INTEGER NOT NULL ,
person_id INTEGER NOT NULL ,
observation_concept_id INTEGER NOT NULL ,
observation_date DATE NOT NULL ,
observation_time VARCHAR(10) NULL ,
observation_type_concept_id INTEGER NOT NULL ,
value_as_number FLOAT NULL ,
value_as_string VARCHAR(60) NULL ,
value_as_concept_id INTEGER NULL ,
qualifier_concept_id INTEGER NULL ,
unit_concept_id INTEGER NULL ,
provider_id INTEGER NULL ,
visit_occurrence_id INTEGER NULL ,
observation_source_value VARCHAR(50) NULL ,
observation_source_concept_id INTEGER NULL ,
unit_source_value VARCHAR(50) NULL ,
qualifier_source_value VARCHAR(50) NULL
)
;
CREATE TABLE fact_relationship
(
domain_concept_id_1 INTEGER NOT NULL ,
fact_id_1 INTEGER NOT NULL ,
domain_concept_id_2 INTEGER NOT NULL ,
fact_id_2 INTEGER NOT NULL ,
relationship_concept_id INTEGER NOT NULL
)
;
/************************
Standardized health system data
************************/
CREATE TABLE location
(
location_id INTEGER NOT NULL ,
address_1 VARCHAR(50) NULL ,
address_2 VARCHAR(50) NULL ,
city VARCHAR(50) NULL ,
state VARCHAR(2) NULL ,
zip VARCHAR(9) NULL ,
county VARCHAR(20) NULL ,
location_source_value VARCHAR(50) NULL
)
;
CREATE TABLE care_site
(
care_site_id INTEGER NOT NULL ,
care_site_name VARCHAR(255) NULL ,
place_of_service_concept_id INTEGER NULL ,
location_id INTEGER NULL ,
care_site_source_value VARCHAR(50) NULL ,
place_of_service_source_value VARCHAR(50) NULL
)
;
CREATE TABLE provider
(
provider_id INTEGER NOT NULL ,
provider_name VARCHAR(255) NULL ,
NPI VARCHAR(20) NULL ,
DEA VARCHAR(20) NULL ,
specialty_concept_id INTEGER NULL ,
care_site_id INTEGER NULL ,
year_of_birth INTEGER NULL ,
gender_concept_id INTEGER NULL ,
provider_source_value VARCHAR(50) NULL ,
specialty_source_value VARCHAR(50) NULL ,
specialty_source_concept_id INTEGER NULL ,
gender_source_value VARCHAR(50) NULL ,
gender_source_concept_id INTEGER NULL
)
;
/************************
Standardized health economics
************************/
CREATE TABLE payer_plan_period
(
payer_plan_period_id INTEGER NOT NULL ,
person_id INTEGER NOT NULL ,
payer_plan_period_start_date DATE NOT NULL ,
payer_plan_period_end_date DATE NOT NULL ,
payer_source_value VARCHAR (50) NULL ,
plan_source_value VARCHAR (50) NULL ,
family_source_value VARCHAR (50) NULL
)
;
-- The individual cost tables are phased out and will be removed
/*
CREATE TABLE visit_cost
(
visit_cost_id INTEGER NOT NULL ,
visit_occurrence_id INTEGER NOT NULL ,
currency_concept_id INTEGER NULL ,
paid_copay FLOAT NULL ,
paid_coinsurance FLOAT NULL ,
paid_toward_deductible FLOAT NULL ,
paid_by_payer FLOAT NULL ,
paid_by_coordination_benefits FLOAT NULL ,
total_out_of_pocket FLOAT NULL ,
total_paid FLOAT NULL ,
payer_plan_period_id INTEGER NULL
)
;
CREATE TABLE procedure_cost
(
procedure_cost_id INTEGER NOT NULL ,
procedure_occurrence_id INTEGER NOT NULL ,
currency_concept_id INTEGER NULL ,
paid_copay FLOAT NULL ,
paid_coinsurance FLOAT NULL ,
paid_toward_deductible FLOAT NULL ,
paid_by_payer FLOAT NULL ,
paid_by_coordination_benefits FLOAT NULL ,
total_out_of_pocket FLOAT NULL ,
total_paid FLOAT NULL ,
revenue_code_concept_id INTEGER NULL ,
payer_plan_period_id INTEGER NULL ,
revenue_code_source_value VARCHAR(50) NULL
)
;
CREATE TABLE drug_cost
(
drug_cost_id INTEGER NOT NULL ,
drug_exposure_id INTEGER NOT NULL ,
currency_concept_id INTEGER NULL ,
paid_copay FLOAT NULL ,
paid_coinsurance FLOAT NULL ,
paid_toward_deductible FLOAT NULL ,
paid_by_payer FLOAT NULL ,
paid_by_coordination_benefits FLOAT NULL ,
total_out_of_pocket FLOAT NULL ,
total_paid FLOAT NULL ,
ingredient_cost FLOAT NULL ,
dispensing_fee FLOAT NULL ,
average_wholesale_price FLOAT NULL ,
payer_plan_period_id INTEGER NULL
)
;
CREATE TABLE device_cost
(
device_cost_id INTEGER NOT NULL ,
device_exposure_id INTEGER NOT NULL ,
currency_concept_id INTEGER NULL ,
paid_copay FLOAT NULL ,
paid_coinsurance FLOAT NULL ,
paid_toward_deductible FLOAT NULL ,
paid_by_payer FLOAT NULL ,
paid_by_coordination_benefits FLOAT NULL ,
total_out_of_pocket FLOAT NULL ,
total_paid FLOAT NULL ,
payer_plan_period_id INTEGER NULL
)
;
*/
CREATE TABLE cost
(
cost_id INTEGER NOT NULL ,
cost_event_id INTEGER NOT NULL ,
cost_domain_id VARCHAR2(20) NOT NULL ,
cost_type_concept_id INTEGER NOT NULL ,
currency_concept_id INTEGER NULL ,
total_charge FLOAT NULL ,
total_cost FLOAT NULL ,
total_paid FLOAT NULL ,
paid_by_payer FLOAT NULL ,
paid_by_patient FLOAT NULL ,
paid_patient_copay FLOAT NULL ,
paid_patient_coinsurance FLOAT NULL ,
paid_patient_deductible FLOAT NULL ,
paid_by_primary FLOAT NULL ,
paid_ingredient_cost FLOAT NULL ,
paid_dispensing_fee FLOAT NULL ,
payer_plan_period_id INTEGER NULL ,
amount_allowed FLOAT NULL ,
revenue_code_concept_id INTEGER NULL ,
reveue_code_source_value VARCHAR2(50) NULL
)
;
/************************
Standardized derived elements
************************/
CREATE TABLE cohort
(
cohort_definition_id INTEGER NOT NULL ,
subject_id INTEGER NOT NULL ,
cohort_start_date DATE NOT NULL ,
cohort_end_date DATE NOT NULL
)
;
CREATE TABLE cohort_attribute
(
cohort_definition_id INTEGER NOT NULL ,
cohort_start_date DATE NOT NULL ,
cohort_end_date DATE NOT NULL ,
subject_id INTEGER NOT NULL ,
attribute_definition_id INTEGER NOT NULL ,
value_as_number FLOAT NULL ,
value_as_concept_id INTEGER NULL
)
;
CREATE TABLE drug_era
(
drug_era_id INTEGER NOT NULL ,
person_id INTEGER NOT NULL ,
drug_concept_id INTEGER NOT NULL ,
drug_era_start_date DATE NOT NULL ,
drug_era_end_date DATE NOT NULL ,
drug_exposure_count INTEGER NULL ,
gap_days INTEGER NULL
)
;
CREATE TABLE dose_era
(
dose_era_id INTEGER NOT NULL ,
person_id INTEGER NOT NULL ,
drug_concept_id INTEGER NOT NULL ,
unit_concept_id INTEGER NOT NULL ,
dose_value FLOAT NOT NULL ,
dose_era_start_date DATE NOT NULL ,
dose_era_end_date DATE NOT NULL
)
;
CREATE TABLE condition_era
(
condition_era_id INTEGER NOT NULL ,
person_id INTEGER NOT NULL ,
condition_concept_id INTEGER NOT NULL ,
condition_era_start_date DATE NOT NULL ,
condition_era_end_date DATE NOT NULL ,
condition_occurrence_count INTEGER NULL
)
;

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@ -1,168 +0,0 @@
/*********************************************************************************
# Copyright 2014 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 create the required indexes within OMOP common data model, version 5.0 for Oracle database
last revised: 12 Oct 2014
author: Patrick Ryan
description: These indices are considered a minimal requirement to ensure adequate performance of analyses.
*************************/
/************************
Standardized vocabulary
************************/
CREATE INDEX idx_concept_code ON concept (concept_code ASC);
CREATE INDEX idx_concept_vocabluary_id ON concept (vocabulary_id ASC);
CREATE INDEX idx_concept_domain_id ON concept (domain_id ASC);
CREATE INDEX idx_concept_class_id ON concept (concept_class_id ASC);
CREATE INDEX idx_concept_relationship_id_1 ON concept_relationship (concept_id_1 ASC);
CREATE INDEX idx_concept_relationship_id_2 ON concept_relationship (concept_id_2 ASC);
CREATE INDEX idx_concept_relationship_id_3 ON concept_relationship (relationship_id ASC);
CREATE INDEX idx_concept_synonym_id ON concept_synonym (concept_id ASC);
CREATE INDEX idx_concept_ancestor_id_1 ON concept_ancestor (ancestor_concept_id ASC);
CREATE INDEX idx_concept_ancestor_id_2 ON concept_ancestor (descendant_concept_id ASC);
CREATE INDEX idx_source_to_concept_map_id_3 ON source_to_concept_map (target_concept_id ASC);
CREATE INDEX idx_source_to_concept_map_id_1 ON source_to_concept_map (source_vocabulary_id ASC);
CREATE INDEX idx_source_to_concept_map_id_2 ON source_to_concept_map (target_vocabulary_id ASC);
CREATE INDEX idx_source_to_concept_map_code ON source_to_concept_map (source_code ASC);
CREATE INDEX idx_drug_strength_id_1 ON drug_strength (drug_concept_id ASC);
CREATE INDEX idx_drug_strength_id_2 ON drug_strength (ingredient_concept_id ASC);
/**************************
Standardized meta-data
***************************/
/************************
Standardized clinical data
************************/
CREATE INDEX idx_observation_period_id ON observation_period (person_id ASC);
CREATE INDEX idx_specimen_person_id ON specimen (person_id ASC);
CREATE INDEX idx_specimen_concept_id ON specimen (specimen_concept_id ASC);
CREATE INDEX idx_visit_person_id ON visit_occurrence (person_id ASC);
CREATE INDEX idx_visit_concept_id ON visit_occurrence (visit_concept_id ASC);
CREATE INDEX idx_procedure_person_id ON procedure_occurrence (person_id ASC);
CREATE INDEX idx_procedure_concept_id ON procedure_occurrence (procedure_concept_id ASC);
CREATE INDEX idx_procedure_visit_id ON procedure_occurrence (visit_occurrence_id ASC);
CREATE INDEX idx_drug_person_id ON drug_exposure (person_id ASC);
CREATE INDEX idx_drug_concept_id ON drug_exposure (drug_concept_id ASC);
CREATE INDEX idx_drug_visit_id ON drug_exposure (visit_occurrence_id ASC);
CREATE INDEX idx_device_person_id ON device_exposure (person_id ASC);
CREATE INDEX idx_device_concept_id ON device_exposure (device_concept_id ASC);
CREATE INDEX idx_device_visit_id ON device_exposure (visit_occurrence_id ASC);
CREATE INDEX idx_condition_person_id ON condition_occurrence (person_id ASC);
CREATE INDEX idx_condition_concept_id ON condition_occurrence (condition_concept_id ASC);
CREATE INDEX idx_condition_visit_id ON condition_occurrence (visit_occurrence_id ASC);
CREATE INDEX idx_measurement_person_id ON measurement (person_id ASC);
CREATE INDEX idx_measurement_concept_id ON measurement (measurement_concept_id ASC);
CREATE INDEX idx_measurement_visit_id ON measurement (visit_occurrence_id ASC);
CREATE INDEX idx_note_person_id ON note (person_id ASC);
CREATE INDEX idx_note_concept_id ON note (note_type_concept_id ASC);
CREATE INDEX idx_note_visit_id ON note (visit_occurrence_id ASC);
CREATE INDEX idx_observation_person_id ON observation (person_id ASC);
CREATE INDEX idx_observation_concept_id ON observation (observation_concept_id ASC);
CREATE INDEX idx_observation_visit_id ON observation (visit_occurrence_id ASC);
CREATE INDEX idx_fact_relationship_id_1 ON fact_relationship (domain_concept_id_1 ASC);
CREATE INDEX idx_fact_relationship_id_2 ON fact_relationship (domain_concept_id_2 ASC);
CREATE INDEX idx_fact_relationship_id_3 ON fact_relationship (relationship_concept_id ASC);
/************************
Standardized health system data
************************/
/************************
Standardized health economics
************************/
CREATE INDEX idx_period_person_id ON payer_plan_period (person_id ASC);
/************************
Standardized derived elements
************************/
CREATE INDEX idx_cohort_subject_id ON cohort (subject_id ASC);
CREATE INDEX idx_cohort_c_definition_id ON cohort (cohort_definition_id ASC);
CREATE INDEX idx_ca_subject_id ON cohort_attribute (subject_id ASC);
CREATE INDEX idx_ca_definition_id ON cohort_attribute (cohort_definition_id ASC);
CREATE INDEX idx_drug_era_person_id ON drug_era (person_id ASC);
CREATE INDEX idx_drug_era_concept_id ON drug_era (drug_concept_id ASC);
CREATE INDEX idx_dose_era_person_id ON dose_era (person_id ASC);
CREATE INDEX idx_dose_era_concept_id ON dose_era (drug_concept_id ASC);
CREATE INDEX idx_condition_era_person_id ON condition_era (person_id ASC);
CREATE INDEX idx_condition_era_concept_id ON condition_era (condition_concept_id ASC);

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View File

@ -1,188 +0,0 @@
/*********************************************************************************
# Copyright 2014 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 create the required indexes within OMOP common data model, version 5.0 for Oracle database
last revised: 12 Oct 2014
author: Patrick Ryan
description: These indices are considered a minimal requirement to ensure adequate performance of analyses.
*************************/
/************************
Standardized vocabulary
************************/
CREATE UNIQUE INDEX idx_concept_concept_id ON concept (concept_id ASC);
CREATE INDEX idx_concept_code ON concept (concept_code ASC);
CREATE INDEX idx_concept_vocabluary_id ON concept (vocabulary_id ASC);
CREATE INDEX idx_concept_domain_id ON concept (domain_id ASC);
CREATE INDEX idx_concept_class_id ON concept (concept_class_id ASC);
CREATE UNIQUE INDEX idx_vocabulary_vocabulary_id ON vocabulary (vocabulary_id ASC);
CREATE UNIQUE INDEX idx_domain_domain_id ON domain (domain_id ASC);
CREATE UNIQUE INDEX idx_concept_class_class_id ON concept_class (concept_class_id ASC);
CREATE INDEX idx_concept_relationship_id_1 ON concept_relationship (concept_id_1 ASC);
CREATE INDEX idx_concept_relationship_id_2 ON concept_relationship (concept_id_2 ASC);
CREATE INDEX idx_concept_relationship_id_3 ON concept_relationship (relationship_id ASC);
CREATE UNIQUE INDEX idx_relationship_rel_id ON relationship (relationship_id ASC);
CREATE INDEX idx_concept_synonym_id ON concept_synonym (concept_id ASC);
CREATE INDEX idx_concept_ancestor_id_1 ON concept_ancestor (ancestor_concept_id ASC);
CREATE INDEX idx_concept_ancestor_id_2 ON concept_ancestor (descendant_concept_id ASC);
CREATE INDEX idx_source_to_concept_map_id_3 ON source_to_concept_map (target_concept_id ASC);
CREATE INDEX idx_source_to_concept_map_id_1 ON source_to_concept_map (source_vocabulary_id ASC);
CREATE INDEX idx_source_to_concept_map_id_2 ON source_to_concept_map (target_vocabulary_id ASC);
CREATE INDEX idx_source_to_concept_map_code ON source_to_concept_map (source_code ASC);
CREATE INDEX idx_drug_strength_id_1 ON drug_strength (drug_concept_id ASC);
CREATE INDEX idx_drug_strength_id_2 ON drug_strength (ingredient_concept_id ASC);
CREATE INDEX idx_cohort_definition_id ON cohort_definition (cohort_definition_id ASC);
CREATE INDEX idx_attribute_definition_id ON attribute_definition (attribute_definition_id ASC);
/**************************
Standardized meta-data
***************************/
/************************
Standardized clinical data
************************/
CREATE UNIQUE INDEX idx_person_id ON person (person_id ASC);
CREATE INDEX idx_observation_period_id ON observation_period (person_id ASC);
CREATE INDEX idx_specimen_person_id ON specimen (person_id ASC);
CREATE INDEX idx_specimen_concept_id ON specimen (specimen_concept_id ASC);
CREATE INDEX idx_death_person_id ON death (person_id ASC);
CREATE INDEX idx_visit_person_id ON visit_occurrence (person_id ASC);
CREATE INDEX idx_visit_concept_id ON visit_occurrence (visit_concept_id ASC);
CREATE INDEX idx_procedure_person_id ON procedure_occurrence (person_id ASC);
CREATE INDEX idx_procedure_concept_id ON procedure_occurrence (procedure_concept_id ASC);
CREATE INDEX idx_procedure_visit_id ON procedure_occurrence (visit_occurrence_id ASC);
CREATE INDEX idx_drug_person_id ON drug_exposure (person_id ASC);
CREATE INDEX idx_drug_concept_id ON drug_exposure (drug_concept_id ASC);
CREATE INDEX idx_drug_visit_id ON drug_exposure (visit_occurrence_id ASC);
CREATE INDEX idx_device_person_id ON device_exposure (person_id ASC);
CREATE INDEX idx_device_concept_id ON device_exposure (device_concept_id ASC);
CREATE INDEX idx_device_visit_id ON device_exposure (visit_occurrence_id ASC);
CREATE INDEX idx_condition_person_id ON condition_occurrence (person_id ASC);
CREATE INDEX idx_condition_concept_id ON condition_occurrence (condition_concept_id ASC);
CREATE INDEX idx_condition_visit_id ON condition_occurrence (visit_occurrence_id ASC);
CREATE INDEX idx_measurement_person_id ON measurement (person_id ASC);
CREATE INDEX idx_measurement_concept_id ON measurement (measurement_concept_id ASC);
CREATE INDEX idx_measurement_visit_id ON measurement (visit_occurrence_id ASC);
CREATE INDEX idx_note_person_id ON note (person_id ASC);
CREATE INDEX idx_note_concept_id ON note (note_type_concept_id ASC);
CREATE INDEX idx_note_visit_id ON note (visit_occurrence_id ASC);
CREATE INDEX idx_observation_person_id ON observation (person_id ASC);
CREATE INDEX idx_observation_concept_id ON observation (observation_concept_id ASC);
CREATE INDEX idx_observation_visit_id ON observation (visit_occurrence_id ASC);
CREATE INDEX idx_fact_relationship_id_1 ON fact_relationship (domain_concept_id_1 ASC);
CREATE INDEX idx_fact_relationship_id_2 ON fact_relationship (domain_concept_id_2 ASC);
CREATE INDEX idx_fact_relationship_id_3 ON fact_relationship (relationship_concept_id ASC);
/************************
Standardized health system data
************************/
/************************
Standardized health economics
************************/
CREATE INDEX idx_period_person_id ON payer_plan_period (person_id ASC);
/************************
Standardized derived elements
************************/
CREATE INDEX idx_cohort_subject_id ON cohort (subject_id ASC);
CREATE INDEX idx_cohort_c_definition_id ON cohort (cohort_definition_id ASC);
CREATE INDEX idx_ca_subject_id ON cohort_attribute (subject_id ASC);
CREATE INDEX idx_ca_definition_id ON cohort_attribute (cohort_definition_id ASC);
CREATE INDEX idx_drug_era_person_id ON drug_era (person_id ASC);
CREATE INDEX idx_drug_era_concept_id ON drug_era (drug_concept_id ASC);
CREATE INDEX idx_dose_era_person_id ON dose_era (person_id ASC);
CREATE INDEX idx_dose_era_concept_id ON dose_era (drug_concept_id ASC);
CREATE INDEX idx_condition_era_person_id ON condition_era (person_id ASC);
CREATE INDEX idx_condition_era_concept_id ON condition_era (condition_concept_id ASC);

20
Oracle/README.md
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@ -1,20 +0,0 @@
Common-Data-Model / Oracle
=================
This folder contains the SQL scripts for Oracle.
In order to create your instantiation of the Common Data Model, we recommend following these steps:
1. Create an empty schema.
2. Execute the script `OMOP CDM ddl - Oracle.sql` to create the tables and fields.
3. Load your data into the schema.
4. Execute the script `OMOP CDM constraints - Oracle.sql` to add the constraints (primary and foreign keys).
5. Execute the script `OMOP CDM indexes required - Oracle - With constraints.sql` to add the minimum set of indexes we recommend.
Note: you could also apply the constraints and/or the indexes before loading the data, but this will slow down the insertion of the data considerably.
Also note: you can apply the indexes without first applying the constraints, but then we recommend you use the script `OMOP CDM indexes required - Oracle - Without constraints.sql`. (This script will also create the indexes that would normally be automatically created by the primary key constraints.)

52
Oracle/VocabImport/OMOP CDM vocabulary load - Oracle.bat
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@ -1,52 +0,0 @@
REM *********************************************************************************
REM Copyright 2014 Observational Health Data Sciences and Informatics
REM
REM
REM Licensed under the Apache License, Version 2.0 (the "License");
REM you may not use this file except in compliance with the License.
REM You may obtain a copy of the License at
REM
REM http://www.apache.org/licenses/LICENSE-2.0
REM
REM Unless required by applicable law or agreed to in writing, software
REM distributed under the License is distributed on an "AS IS" BASIS,
REM WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
REM See the License for the specific language governing permissions and
REM limitations under the License.
REM *******************************************************************************/
REM ************************
REM
REM ####### # # ####### ###### ##### ###### # # #######
REM # # ## ## # # # # # # # # ## ## # # #
REM # # # # # # # # # # # # # # # # # # # #
REM # # # # # # # ###### # # # # # # # # ######
REM # # # # # # # # # # # # # # #
REM # # # # # # # # # # # # # # # # #
REM ####### # # ####### # ##### ###### # # ## #####
REM
REM
REM Script to load the common data model, version 5.0 vocabulary tables for PostgreSQL database on Windows (MS-DOS style file paths)
REM
REM Notes
REM
REM 1) There is no data file load for the SOURCE_TO_CONCEPT_MAP table because that table is deprecated in CDM version 5.0
REM 2) This script assumes the CDM version 5 vocabulary zip file has been unzipped into the "C:\CDMV5VOCAB" directory.
REM 3) If you unzipped your CDM version 5 vocabulary files into a different directory then replace all file paths below, with your directory path.
REM
REM last revised: 26 Nov 2014
REM
REM author: Lee Evans
REM
REM
REM *************************/
sqlldr CDMV5/<password> CONTROL=CONCEPT.ctl LOG=C:\CDMV5VOCAB\CONCEPT.log BAD=C:\CDMV5VOCAB\CONCEPT.bad
sqlldr CDMV5/<password> CONTROL=CONCEPT_ANCESTOR.ctl LOG=C:\CDMV5VOCAB\CONCEPT_ANCESTOR.log BAD=C:\CDMV5VOCAB\CONCEPT_ANCESTOR.bad
sqlldr CDMV5/<password> CONTROL=CONCEPT_CLASS.ctl LOG=C:\CDMV5VOCAB\CONCEPT_CLASS.log BAD=C:\CDMV5VOCAB\CONCEPT_CLASS.bad
sqlldr CDMV5/<password> CONTROL=CONCEPT_RELATIONSHIP.ctl LOG=C:\CDMV5VOCAB\CONCEPT_RELATIONSHIP.log BAD=C:\CDMV5VOCAB\CONCEPT_RELATIONSHIP.bad
sqlldr CDMV5/<password> CONTROL=CONCEPT_SYNONYM.ctl LOG=C:\CDMV5VOCAB\CONCEPT_SYNONYM.log BAD=C:\CDMV5VOCAB\CONCEPT_SYNONYM.bad
sqlldr CDMV5/<password> CONTROL=DOMAIN.ctl LOG=C:\CDMV5VOCAB\DOMAIN.log BAD=C:\CDMV5VOCAB\DOMAIN.bad
sqlldr CDMV5/<password> CONTROL=DRUG_STRENGTH.ctl LOG=C:\CDMV5VOCAB\DRUG_STRENGTH.log BAD=C:\CDMV5VOCAB\DRUG_STRENGTH.bad
sqlldr CDMV5/<password> CONTROL=RELATIONSHIP.ctl LOG=C:\CDMV5VOCAB\RELATIONSHIP.log BAD=C:\CDMV5VOCAB\RELATIONSHIP.bad
sqlldr CDMV5/<password> CONTROL=VOCABULARY.ctl LOG=C:\CDMV5VOCAB\VOCABULARY.log BAD=C:\CDMV5VOCAB\VOCABULARY.bad

19
Oracle/VocabImport/concept.ctl
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@ -1,19 +0,0 @@
options (skip=1)
load data
infile concept.csv
into table concept
replace
fields terminated by '\t'
trailing nullcols
(
concept_id,
concept_name,
domain_id,
vocabulary_id,
concept_class_id,
standard_concept,
concept_code,
valid_start_date DATE 'YYYYMMDD',
valid_end_date DATE 'YYYYMMDD',
invalid_reason
)

13
Oracle/VocabImport/concept_ancestor.ctl
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@ -1,13 +0,0 @@
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
)

12
Oracle/VocabImport/concept_class.ctl
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@ -1,12 +0,0 @@
options (skip=1)
load data
infile concept_class.csv
into table concept_class
replace
fields terminated by '\t'
trailing nullcols
(
concept_class_id,
concept_class_name,
concept_class_concept_id
)

15
Oracle/VocabImport/concept_relationship.ctl
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@ -1,15 +0,0 @@
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
)

12
Oracle/VocabImport/concept_synonym.ctl
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@ -1,12 +0,0 @@
options (skip=1)
load data
infile concept_synonym.csv
into table concept_synonym
replace
fields terminated by '\t'
trailing nullcols
(
concept_id,
concept_synonym_name CHAR(1000),
language_concept_id
)

12
Oracle/VocabImport/domain.ctl
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@ -1,12 +0,0 @@
options (skip=1)
load data
infile domain.csv
into table domain
replace
fields terminated by '\t'
trailing nullcols
(
domain_id,
domain_name,
domain_concept_id
)

21
Oracle/VocabImport/drug_strength.ctl
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@ -1,21 +0,0 @@
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_concept_id,
numerator_value,
numerator_unit_concept_id,
denominator_value,
denominator_unit_concept_id,
box_size,
valid_start_date DATE 'YYYYMMDD',
valid_end_date DATE 'YYYYMMDD',
invalid_reason
)

15
Oracle/VocabImport/relationship.ctl
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@ -1,15 +0,0 @@
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_id,
relationship_concept_id
)

14
Oracle/VocabImport/vocabulary.ctl
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@ -1,14 +0,0 @@
options (skip=1)
load data
infile vocabulary.csv
into table vocabulary
replace
fields terminated by '\t'
trailing nullcols
(
vocabulary_id,
vocabulary_name,
vocabulary_reference,
vocabulary_version,
vocabulary_concept_id
)

545
PostgreSQL/OMOP CDM constraints - PostgreSQL.sql
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/*********************************************************************************
# Copyright 2014 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 create constraints within OMOP common data model, version 5.0 for PostgreSQL database
last revised: 12 Oct 2014
author: Patrick Ryan
*************************/
/************************
*************************
*************************
*************************
Primary key constraints
*************************
*************************
*************************
************************/
/************************
Standardized vocabulary
************************/
ALTER TABLE concept ADD CONSTRAINT xpk_concept PRIMARY KEY (concept_id);
ALTER TABLE vocabulary ADD CONSTRAINT xpk_vocabulary PRIMARY KEY (vocabulary_id);
ALTER TABLE domain ADD CONSTRAINT xpk_domain PRIMARY KEY (domain_id);
ALTER TABLE concept_class ADD CONSTRAINT xpk_concept_class PRIMARY KEY (concept_class_id);
ALTER TABLE concept_relationship ADD CONSTRAINT xpk_concept_relationship PRIMARY KEY (concept_id_1,concept_id_2,relationship_id);
ALTER TABLE relationship ADD CONSTRAINT xpk_relationship PRIMARY KEY (relationship_id);
ALTER TABLE concept_ancestor ADD CONSTRAINT xpk_concept_ancestor PRIMARY KEY (ancestor_concept_id,descendant_concept_id);
ALTER TABLE source_to_concept_map ADD CONSTRAINT xpk_source_to_concept_map PRIMARY KEY (source_vocabulary_id,target_concept_id,source_code,valid_end_date);
ALTER TABLE drug_strength ADD CONSTRAINT xpk_drug_strength PRIMARY KEY (drug_concept_id, ingredient_concept_id);
ALTER TABLE cohort_definition ADD CONSTRAINT xpk_cohort_definition PRIMARY KEY (cohort_definition_id);
ALTER TABLE attribute_definition ADD CONSTRAINT xpk_attribute_definition PRIMARY KEY (attribute_definition_id);
/**************************
Standardized meta-data
***************************/
/************************
Standardized clinical data
************************/
/**PRIMARY KEY NONCLUSTERED constraints**/
ALTER TABLE person ADD CONSTRAINT xpk_person PRIMARY KEY ( person_id ) ;
ALTER TABLE observation_period ADD CONSTRAINT xpk_observation_period PRIMARY KEY ( observation_period_id ) ;
ALTER TABLE specimen ADD CONSTRAINT xpk_specimen PRIMARY KEY ( specimen_id ) ;
ALTER TABLE death ADD CONSTRAINT xpk_death PRIMARY KEY ( person_id ) ;
ALTER TABLE visit_occurrence ADD CONSTRAINT xpk_visit_occurrence PRIMARY KEY ( visit_occurrence_id ) ;
ALTER TABLE procedure_occurrence ADD CONSTRAINT xpk_procedure_occurrence PRIMARY KEY ( procedure_occurrence_id ) ;
ALTER TABLE drug_exposure ADD CONSTRAINT xpk_drug_exposure PRIMARY KEY ( drug_exposure_id ) ;
ALTER TABLE device_exposure ADD CONSTRAINT xpk_device_exposure PRIMARY KEY ( device_exposure_id ) ;
ALTER TABLE condition_occurrence ADD CONSTRAINT xpk_condition_occurrence PRIMARY KEY ( condition_occurrence_id ) ;
ALTER TABLE measurement ADD CONSTRAINT xpk_measurement PRIMARY KEY ( measurement_id ) ;
ALTER TABLE note ADD CONSTRAINT xpk_note PRIMARY KEY ( note_id ) ;
ALTER TABLE observation ADD CONSTRAINT xpk_observation PRIMARY KEY ( observation_id ) ;
/************************
Standardized health system data
************************/
ALTER TABLE location ADD CONSTRAINT xpk_location PRIMARY KEY ( location_id ) ;
ALTER TABLE care_site ADD CONSTRAINT xpk_care_site PRIMARY KEY ( care_site_id ) ;
ALTER TABLE provider ADD CONSTRAINT xpk_provider PRIMARY KEY ( provider_id ) ;
/************************
Standardized health economics
************************/
ALTER TABLE payer_plan_period ADD CONSTRAINT xpk_payer_plan_period PRIMARY KEY ( payer_plan_period_id ) ;
ALTER TABLE visit_cost ADD CONSTRAINT xpk_visit_cost PRIMARY KEY ( visit_cost_id ) ;
ALTER TABLE procedure_cost ADD CONSTRAINT xpk_procedure_cost PRIMARY KEY ( procedure_cost_id ) ;
ALTER TABLE drug_cost ADD CONSTRAINT xpk_drug_cost PRIMARY KEY ( drug_cost_id ) ;
ALTER TABLE device_cost ADD CONSTRAINT xpk_device_cost PRIMARY KEY ( device_cost_id ) ;
/************************
Standardized derived elements
************************/
ALTER TABLE cohort ADD CONSTRAINT xpk_cohort PRIMARY KEY ( cohort_definition_id, subject_id, cohort_start_date, cohort_end_date ) ;
ALTER TABLE cohort_attribute ADD CONSTRAINT xpk_cohort_attribute PRIMARY KEY ( cohort_definition_id, subject_id, cohort_start_date, cohort_end_date, attribute_definition_id ) ;
ALTER TABLE drug_era ADD CONSTRAINT xpk_drug_era PRIMARY KEY ( drug_era_id ) ;
ALTER TABLE dose_era ADD CONSTRAINT xpk_dose_era PRIMARY KEY ( dose_era_id ) ;
ALTER TABLE condition_era ADD CONSTRAINT xpk_condition_era PRIMARY KEY ( condition_era_id ) ;
/************************
*************************
*************************
*************************
Foreign key constraints
*************************
*************************
*************************
************************/
/************************
Standardized vocabulary
************************/
ALTER TABLE concept ADD CONSTRAINT fpk_concept_domain FOREIGN KEY (domain_id) REFERENCES domain (domain_id);
ALTER TABLE concept ADD CONSTRAINT fpk_concept_class FOREIGN KEY (concept_class_id) REFERENCES concept_class (concept_class_id);
ALTER TABLE concept ADD CONSTRAINT fpk_concept_vocabulary FOREIGN KEY (vocabulary_id) REFERENCES vocabulary (vocabulary_id);
ALTER TABLE vocabulary ADD CONSTRAINT fpk_vocabulary_concept FOREIGN KEY (vocabulary_concept_id) REFERENCES concept (concept_id);
ALTER TABLE domain ADD CONSTRAINT fpk_domain_concept FOREIGN KEY (domain_concept_id) REFERENCES concept (concept_id);
ALTER TABLE concept_class ADD CONSTRAINT fpk_concept_class_concept FOREIGN KEY (concept_class_concept_id) REFERENCES concept (concept_id);
ALTER TABLE concept_relationship ADD CONSTRAINT fpk_concept_relationship_c_1 FOREIGN KEY (concept_id_1) REFERENCES concept (concept_id);
ALTER TABLE concept_relationship ADD CONSTRAINT fpk_concept_relationship_c_2 FOREIGN KEY (concept_id_2) REFERENCES concept (concept_id);
ALTER TABLE concept_relationship ADD CONSTRAINT fpk_concept_relationship_id FOREIGN KEY (relationship_id) REFERENCES relationship (relationship_id);
ALTER TABLE relationship ADD CONSTRAINT fpk_relationship_concept FOREIGN KEY (relationship_concept_id) REFERENCES concept (concept_id);
ALTER TABLE relationship ADD CONSTRAINT fpk_relationship_reverse FOREIGN KEY (reverse_relationship_id) REFERENCES relationship (relationship_id);
ALTER TABLE concept_synonym ADD CONSTRAINT fpk_concept_synonym_concept FOREIGN KEY (concept_id) REFERENCES concept (concept_id);
ALTER TABLE concept_ancestor ADD CONSTRAINT fpk_concept_ancestor_concept_1 FOREIGN KEY (ancestor_concept_id) REFERENCES concept (concept_id);
ALTER TABLE concept_ancestor ADD CONSTRAINT fpk_concept_ancestor_concept_2 FOREIGN KEY (descendant_concept_id) REFERENCES concept (concept_id);
ALTER TABLE source_to_concept_map ADD CONSTRAINT fpk_source_to_concept_map_v_1 FOREIGN KEY (source_vocabulary_id) REFERENCES vocabulary (vocabulary_id);
ALTER TABLE source_to_concept_map ADD CONSTRAINT fpk_source_to_concept_map_v_2 FOREIGN KEY (target_vocabulary_id) REFERENCES vocabulary (vocabulary_id);
ALTER TABLE source_to_concept_map ADD CONSTRAINT fpk_source_to_concept_map_c_1 FOREIGN KEY (target_concept_id) REFERENCES concept (concept_id);
ALTER TABLE drug_strength ADD CONSTRAINT fpk_drug_strength_concept_1 FOREIGN KEY (drug_concept_id) REFERENCES concept (concept_id);
ALTER TABLE drug_strength ADD CONSTRAINT fpk_drug_strength_concept_2 FOREIGN KEY (ingredient_concept_id) REFERENCES concept (concept_id);
ALTER TABLE drug_strength ADD CONSTRAINT fpk_drug_strength_unit_1 FOREIGN KEY (amount_unit_concept_id) REFERENCES concept (concept_id);
ALTER TABLE drug_strength ADD CONSTRAINT fpk_drug_strength_unit_2 FOREIGN KEY (numerator_unit_concept_id) REFERENCES concept (concept_id);
ALTER TABLE drug_strength ADD CONSTRAINT fpk_drug_strength_unit_3 FOREIGN KEY (denominator_unit_concept_id) REFERENCES concept (concept_id);
ALTER TABLE cohort_definition ADD CONSTRAINT fpk_cohort_definition_concept FOREIGN KEY (definition_type_concept_id) REFERENCES concept (concept_id);
/**************************
Standardized meta-data
***************************/
/************************
Standardized clinical data
************************/
ALTER TABLE person ADD CONSTRAINT fpk_person_gender_concept FOREIGN KEY (gender_concept_id) REFERENCES concept (concept_id);
ALTER TABLE person ADD CONSTRAINT fpk_person_race_concept FOREIGN KEY (race_concept_id) REFERENCES concept (concept_id);
ALTER TABLE person ADD CONSTRAINT fpk_person_ethnicity_concept FOREIGN KEY (ethnicity_concept_id) REFERENCES concept (concept_id);
ALTER TABLE person ADD CONSTRAINT fpk_person_gender_concept_s FOREIGN KEY (gender_source_concept_id) REFERENCES concept (concept_id);
ALTER TABLE person ADD CONSTRAINT fpk_person_race_concept_s FOREIGN KEY (race_source_concept_id) REFERENCES concept (concept_id);
ALTER TABLE person ADD CONSTRAINT fpk_person_ethnicity_concept_s FOREIGN KEY (ethnicity_source_concept_id) REFERENCES concept (concept_id);
ALTER TABLE person ADD CONSTRAINT fpk_person_location FOREIGN KEY (location_id) REFERENCES location (location_id);
ALTER TABLE person ADD CONSTRAINT fpk_person_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
ALTER TABLE person ADD CONSTRAINT fpk_person_care_site FOREIGN KEY (care_site_id) REFERENCES care_site (care_site_id);
ALTER TABLE observation_period ADD CONSTRAINT fpk_observation_period_person FOREIGN KEY (person_id) REFERENCES person (person_id);
ALTER TABLE observation_period ADD CONSTRAINT fpk_observation_period_concept FOREIGN KEY (period_type_concept_id) REFERENCES concept (concept_id);
ALTER TABLE specimen ADD CONSTRAINT fpk_specimen_person FOREIGN KEY (person_id) REFERENCES person (person_id);
ALTER TABLE specimen ADD CONSTRAINT fpk_specimen_concept FOREIGN KEY (specimen_concept_id) REFERENCES concept (concept_id);
ALTER TABLE specimen ADD CONSTRAINT fpk_specimen_type_concept FOREIGN KEY (specimen_type_concept_id) REFERENCES concept (concept_id);
ALTER TABLE specimen ADD CONSTRAINT fpk_specimen_unit_concept FOREIGN KEY (unit_concept_id) REFERENCES concept (concept_id);
ALTER TABLE specimen ADD CONSTRAINT fpk_specimen_site_concept FOREIGN KEY (anatomic_site_concept_id) REFERENCES concept (concept_id);
ALTER TABLE specimen ADD CONSTRAINT fpk_specimen_status_concept FOREIGN KEY (disease_status_concept_id) REFERENCES concept (concept_id);
ALTER TABLE death ADD CONSTRAINT fpk_death_person FOREIGN KEY (person_id) REFERENCES person (person_id);
ALTER TABLE death ADD CONSTRAINT fpk_death_type_concept FOREIGN KEY (death_type_concept_id) REFERENCES concept (concept_id);
ALTER TABLE death ADD CONSTRAINT fpk_death_cause_concept FOREIGN KEY (cause_concept_id) REFERENCES concept (concept_id);
ALTER TABLE death ADD CONSTRAINT fpk_death_cause_concept_s FOREIGN KEY (cause_source_concept_id) REFERENCES concept (concept_id);
ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_person FOREIGN KEY (person_id) REFERENCES person (person_id);
ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_concept FOREIGN KEY (visit_concept_id) REFERENCES concept (concept_id);
ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_type_concept FOREIGN KEY (visit_type_concept_id) REFERENCES concept (concept_id);
ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_care_site FOREIGN KEY (care_site_id) REFERENCES care_site (care_site_id);
ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_concept_s FOREIGN KEY (visit_source_concept_id) REFERENCES concept (concept_id);
ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_person FOREIGN KEY (person_id) REFERENCES person (person_id);
ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_concept FOREIGN KEY (procedure_concept_id) REFERENCES concept (concept_id);
ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_type_concept FOREIGN KEY (procedure_type_concept_id) REFERENCES concept (concept_id);
ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_modifier FOREIGN KEY (modifier_concept_id) REFERENCES concept (concept_id);
ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id);
ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_concept_s FOREIGN KEY (procedure_source_concept_id) REFERENCES concept (concept_id);
ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_person FOREIGN KEY (person_id) REFERENCES person (person_id);
ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_concept FOREIGN KEY (drug_concept_id) REFERENCES concept (concept_id);
ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_type_concept FOREIGN KEY (drug_type_concept_id) REFERENCES concept (concept_id);
ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_route_concept FOREIGN KEY (route_concept_id) REFERENCES concept (concept_id);
ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_dose_unit_concept FOREIGN KEY (dose_unit_concept_id) REFERENCES concept (concept_id);
ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id);
ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_concept_s FOREIGN KEY (drug_source_concept_id) REFERENCES concept (concept_id);
ALTER TABLE device_exposure ADD CONSTRAINT fpk_device_person FOREIGN KEY (person_id) REFERENCES person (person_id);
ALTER TABLE device_exposure ADD CONSTRAINT fpk_device_concept FOREIGN KEY (device_concept_id) REFERENCES concept (concept_id);
ALTER TABLE device_exposure ADD CONSTRAINT fpk_device_type_concept FOREIGN KEY (device_type_concept_id) REFERENCES concept (concept_id);
ALTER TABLE device_exposure ADD CONSTRAINT fpk_device_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
ALTER TABLE device_exposure ADD CONSTRAINT fpk_device_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id);
ALTER TABLE device_exposure ADD CONSTRAINT fpk_device_concept_s FOREIGN KEY (device_source_concept_id) REFERENCES concept (concept_id);
ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_person FOREIGN KEY (person_id) REFERENCES person (person_id);
ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_concept FOREIGN KEY (condition_concept_id) REFERENCES concept (concept_id);
ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_type_concept FOREIGN KEY (condition_type_concept_id) REFERENCES concept (concept_id);
ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id);
ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_concept_s FOREIGN KEY (condition_source_concept_id) REFERENCES concept (concept_id);
ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_person FOREIGN KEY (person_id) REFERENCES person (person_id);
ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_concept FOREIGN KEY (measurement_concept_id) REFERENCES concept (concept_id);
ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_type_concept FOREIGN KEY (measurement_type_concept_id) REFERENCES concept (concept_id);
ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_operator FOREIGN KEY (operator_concept_id) REFERENCES concept (concept_id);
ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_value FOREIGN KEY (value_as_concept_id) REFERENCES concept (concept_id);
ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_unit FOREIGN KEY (unit_concept_id) REFERENCES concept (concept_id);
ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id);
ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_concept_s FOREIGN KEY (measurement_source_concept_id) REFERENCES concept (concept_id);
ALTER TABLE note ADD CONSTRAINT fpk_note_person FOREIGN KEY (person_id) REFERENCES person (person_id);
ALTER TABLE note ADD CONSTRAINT fpk_note_type_concept FOREIGN KEY (note_type_concept_id) REFERENCES concept (concept_id);
ALTER TABLE note ADD CONSTRAINT fpk_note_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
ALTER TABLE note ADD CONSTRAINT fpk_note_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id);
ALTER TABLE observation ADD CONSTRAINT fpk_observation_person FOREIGN KEY (person_id) REFERENCES person (person_id);
ALTER TABLE observation ADD CONSTRAINT fpk_observation_concept FOREIGN KEY (observation_concept_id) REFERENCES concept (concept_id);
ALTER TABLE observation ADD CONSTRAINT fpk_observation_type_concept FOREIGN KEY (observation_type_concept_id) REFERENCES concept (concept_id);
ALTER TABLE observation ADD CONSTRAINT fpk_observation_value FOREIGN KEY (value_as_concept_id) REFERENCES concept (concept_id);
ALTER TABLE observation ADD CONSTRAINT fpk_observation_qualifier FOREIGN KEY (qualifier_concept_id) REFERENCES concept (concept_id);
ALTER TABLE observation ADD CONSTRAINT fpk_observation_unit FOREIGN KEY (unit_concept_id) REFERENCES concept (concept_id);
ALTER TABLE observation ADD CONSTRAINT fpk_observation_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
ALTER TABLE observation ADD CONSTRAINT fpk_observation_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id);
ALTER TABLE observation ADD CONSTRAINT fpk_observation_concept_s FOREIGN KEY (observation_source_concept_id) REFERENCES concept (concept_id);
ALTER TABLE fact_relationship ADD CONSTRAINT fpk_fact_domain_1 FOREIGN KEY (domain_concept_id_1) REFERENCES concept (concept_id);
ALTER TABLE fact_relationship ADD CONSTRAINT fpk_fact_domain_2 FOREIGN KEY (domain_concept_id_2) REFERENCES concept (concept_id);
ALTER TABLE fact_relationship ADD CONSTRAINT fpk_fact_relationship FOREIGN KEY (relationship_concept_id) REFERENCES concept (concept_id);
/************************
Standardized health system data
************************/
ALTER TABLE care_site ADD CONSTRAINT fpk_care_site_location FOREIGN KEY (location_id) REFERENCES location (location_id);
ALTER TABLE care_site ADD CONSTRAINT fpk_care_site_place FOREIGN KEY (place_of_service_concept_id) REFERENCES concept (concept_id);
ALTER TABLE provider ADD CONSTRAINT fpk_provider_specialty FOREIGN KEY (specialty_concept_id) REFERENCES concept (concept_id);
ALTER TABLE provider ADD CONSTRAINT fpk_provider_care_site FOREIGN KEY (care_site_id) REFERENCES care_site (care_site_id);
ALTER TABLE provider ADD CONSTRAINT fpk_provider_gender FOREIGN KEY (gender_concept_id) REFERENCES concept (concept_id);
ALTER TABLE provider ADD CONSTRAINT fpk_provider_specialty_s FOREIGN KEY (specialty_source_concept_id) REFERENCES concept (concept_id);
ALTER TABLE provider ADD CONSTRAINT fpk_provider_gender_s FOREIGN KEY (gender_source_concept_id) REFERENCES concept (concept_id);
/************************
Standardized health economics
************************/
ALTER TABLE payer_plan_period ADD CONSTRAINT fpk_payer_plan_period FOREIGN KEY (person_id) REFERENCES person (person_id);
ALTER TABLE visit_cost ADD CONSTRAINT fpk_visit_cost_id FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id);
ALTER TABLE visit_cost ADD CONSTRAINT fpk_visit_cost_currency FOREIGN KEY (currency_concept_id) REFERENCES concept (concept_id);
ALTER TABLE visit_cost ADD CONSTRAINT fpk_visit_cost_period FOREIGN KEY (payer_plan_period_id) REFERENCES payer_plan_period (payer_plan_period_id);
ALTER TABLE procedure_cost ADD CONSTRAINT fpk_procedure_cost_id FOREIGN KEY (procedure_occurrence_id) REFERENCES procedure_occurrence (procedure_occurrence_id);
ALTER TABLE procedure_cost ADD CONSTRAINT fpk_procedure_cost_currency FOREIGN KEY (currency_concept_id) REFERENCES concept (concept_id);
ALTER TABLE procedure_cost ADD CONSTRAINT fpk_procedure_cost_period FOREIGN KEY (payer_plan_period_id) REFERENCES payer_plan_period (payer_plan_period_id);
ALTER TABLE procedure_cost ADD CONSTRAINT fpk_procedure_cost_revenue FOREIGN KEY (revenue_code_concept_id) REFERENCES concept (concept_id);
ALTER TABLE drug_cost ADD CONSTRAINT fpk_drug_cost_id FOREIGN KEY (drug_exposure_id) REFERENCES drug_exposure (drug_exposure_id);
ALTER TABLE drug_cost ADD CONSTRAINT fpk_drug_cost_currency FOREIGN KEY (currency_concept_id) REFERENCES concept (concept_id);
ALTER TABLE drug_cost ADD CONSTRAINT fpk_drug_cost_period FOREIGN KEY (payer_plan_period_id) REFERENCES payer_plan_period (payer_plan_period_id);
ALTER TABLE device_cost ADD CONSTRAINT fpk_device_cost_id FOREIGN KEY (device_exposure_id) REFERENCES device_exposure (device_exposure_id);
ALTER TABLE device_cost ADD CONSTRAINT fpk_device_cost_currency FOREIGN KEY (currency_concept_id) REFERENCES concept (concept_id);
ALTER TABLE device_cost ADD CONSTRAINT fpk_device_cost_period FOREIGN KEY (payer_plan_period_id) REFERENCES payer_plan_period (payer_plan_period_id);
/************************
Standardized derived elements
************************/
ALTER TABLE cohort ADD CONSTRAINT fpk_cohort_definition FOREIGN KEY (cohort_definition_id) REFERENCES cohort_definition (cohort_definition_id);
ALTER TABLE cohort_attribute ADD CONSTRAINT fpk_ca_cohort_definition FOREIGN KEY (cohort_definition_id) REFERENCES cohort_definition (cohort_definition_id);
ALTER TABLE cohort_attribute ADD CONSTRAINT fpk_ca_attribute_definition FOREIGN KEY (attribute_definition_id) REFERENCES attribute_definition (attribute_definition_id);
ALTER TABLE cohort_attribute ADD CONSTRAINT fpk_ca_value FOREIGN KEY (value_as_concept_id) REFERENCES concept (concept_id);
ALTER TABLE drug_era ADD CONSTRAINT fpk_drug_era_person FOREIGN KEY (person_id) REFERENCES person (person_id);
ALTER TABLE drug_era ADD CONSTRAINT fpk_drug_era_concept FOREIGN KEY (drug_concept_id) REFERENCES concept (concept_id);
ALTER TABLE dose_era ADD CONSTRAINT fpk_dose_era_person FOREIGN KEY (person_id) REFERENCES person (person_id);
ALTER TABLE dose_era ADD CONSTRAINT fpk_dose_era_concept FOREIGN KEY (drug_concept_id) REFERENCES concept (concept_id);
ALTER TABLE dose_era ADD CONSTRAINT fpk_dose_era_unit_concept FOREIGN KEY (unit_concept_id) REFERENCES concept (concept_id);
ALTER TABLE condition_era ADD CONSTRAINT fpk_condition_era_person FOREIGN KEY (person_id) REFERENCES person (person_id);
ALTER TABLE condition_era ADD CONSTRAINT fpk_condition_era_concept FOREIGN KEY (condition_concept_id) REFERENCES concept (concept_id);

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/*********************************************************************************
# Copyright 2014-6 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 create OMOP common data model, version 5.0 for PostgreSQL database
last revised: 1-May-2016
Authors: Patrick Ryan, Christian Reich
*************************/
/************************
Standardized vocabulary
************************/
CREATE TABLE concept (
concept_id INTEGER NOT NULL,
concept_name VARCHAR(255) NOT NULL,
domain_id VARCHAR(20) NOT NULL,
vocabulary_id VARCHAR(20) NOT NULL,
concept_class_id VARCHAR(20) NOT NULL,
standard_concept VARCHAR(1) NULL,
concept_code VARCHAR(50) NOT NULL,
valid_start_date DATE NOT NULL,
valid_end_date DATE NOT NULL,
invalid_reason VARCHAR(1) NULL
)
;
CREATE TABLE vocabulary (
vocabulary_id VARCHAR(20) NOT NULL,
vocabulary_name VARCHAR(255) NOT NULL,
vocabulary_reference VARCHAR(255) NULL,
vocabulary_version VARCHAR(255) NULL,
vocabulary_concept_id INTEGER NOT NULL
)
;
CREATE TABLE domain (
domain_id VARCHAR(20) NOT NULL,
domain_name VARCHAR(255) NOT NULL,
domain_concept_id INTEGER NOT NULL
)
;
CREATE TABLE concept_class (
concept_class_id VARCHAR(20) NOT NULL,
concept_class_name VARCHAR(255) NOT NULL,
concept_class_concept_id INTEGER NOT NULL
)
;
CREATE TABLE concept_relationship (
concept_id_1 INTEGER NOT NULL,
concept_id_2 INTEGER NOT NULL,
relationship_id VARCHAR(20) NOT NULL,
valid_start_date DATE NOT NULL,
valid_end_date DATE NOT NULL,
invalid_reason VARCHAR(1) NULL)
;
CREATE TABLE relationship (
relationship_id VARCHAR(20) NOT NULL,
relationship_name VARCHAR(255) NOT NULL,
is_hierarchical VARCHAR(1) NOT NULL,
defines_ancestry VARCHAR(1) NOT NULL,
reverse_relationship_id VARCHAR(20) NOT NULL,
relationship_concept_id INTEGER NOT NULL
)
;
CREATE TABLE concept_synonym (
concept_id INTEGER NOT NULL,
concept_synonym_name VARCHAR(1000) NOT NULL,
language_concept_id INTEGER NOT NULL
)
;
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 source_to_concept_map (
source_code VARCHAR(50) NOT NULL,
source_concept_id INTEGER NOT NULL,
source_vocabulary_id VARCHAR(20) NOT NULL,
source_code_description VARCHAR(255) NULL,
target_concept_id INTEGER NOT NULL,
target_vocabulary_id VARCHAR(20) NOT NULL,
valid_start_date DATE NOT NULL,
valid_end_date DATE NOT NULL,
invalid_reason VARCHAR(1) NULL
)
;
CREATE TABLE drug_strength (
drug_concept_id INTEGER NOT NULL,
ingredient_concept_id INTEGER NOT NULL,
amount_value NUMERIC NULL,
amount_unit_concept_id INTEGER NULL,
numerator_value NUMERIC NULL,
numerator_unit_concept_id INTEGER NULL,
denominator_value NUMERIC NULL,
denominator_unit_concept_id INTEGER NULL,
box_size INTEGER NULL,
valid_start_date DATE NOT NULL,
valid_end_date DATE NOT NULL,
invalid_reason VARCHAR(1) NULL
)
;
CREATE TABLE cohort_definition (
cohort_definition_id INTEGER NOT NULL,
cohort_definition_name VARCHAR(255) NOT NULL,
cohort_definition_description TEXT NULL,
definition_type_concept_id INTEGER NOT NULL,
cohort_definition_syntax TEXT NULL,
subject_concept_id INTEGER NOT NULL,
cohort_initiation_date DATE NULL
)
;
CREATE TABLE attribute_definition (
attribute_definition_id INTEGER NOT NULL,
attribute_name VARCHAR(255) NOT NULL,
attribute_description TEXT NULL,
attribute_type_concept_id INTEGER NOT NULL,
attribute_syntax TEXT NULL
)
;
/**************************
Standardized meta-data
***************************/
CREATE TABLE cdm_source
(
cdm_source_name VARCHAR(255) NOT NULL,
cdm_source_abbreviation VARCHAR(25) NULL,
cdm_holder VARCHAR(255) NULL,
source_description TEXT NULL,
source_documentation_reference VARCHAR(255) NULL,
cdm_etl_reference VARCHAR(255) NULL,
source_release_date DATE NULL,
cdm_release_date DATE NULL,
cdm_version VARCHAR(10) NULL,
vocabulary_version VARCHAR(20) NULL
)
;
/************************
Standardized clinical data
************************/
CREATE TABLE person
(
person_id INTEGER NOT NULL ,
gender_concept_id INTEGER NOT NULL ,
year_of_birth INTEGER NOT NULL ,
month_of_birth INTEGER NULL,
day_of_birth INTEGER NULL,
time_of_birth VARCHAR(10) NULL,
race_concept_id INTEGER NOT NULL,
ethnicity_concept_id INTEGER NOT NULL,
location_id INTEGER NULL,
provider_id INTEGER NULL,
care_site_id INTEGER NULL,
person_source_value VARCHAR(50) NULL,
gender_source_value VARCHAR(50) NULL,
gender_source_concept_id INTEGER NULL,
race_source_value VARCHAR(50) NULL,
race_source_concept_id INTEGER NULL,
ethnicity_source_value VARCHAR(50) NULL,
ethnicity_source_concept_id INTEGER NULL
)
;
CREATE TABLE observation_period
(
observation_period_id INTEGER NOT NULL ,
person_id INTEGER NOT NULL ,
observation_period_start_date DATE NOT NULL ,
observation_period_end_date DATE NOT NULL ,
period_type_concept_id INTEGER NOT NULL
)
;
CREATE TABLE specimen
(
specimen_id INTEGER NOT NULL ,
person_id INTEGER NOT NULL ,
specimen_concept_id INTEGER NOT NULL ,
specimen_type_concept_id INTEGER NOT NULL ,
specimen_date DATE NOT NULL ,
specimen_time VARCHAR(10) NULL ,
quantity NUMERIC NULL ,
unit_concept_id INTEGER NULL ,
anatomic_site_concept_id INTEGER NULL ,
disease_status_concept_id INTEGER NULL ,
specimen_source_id VARCHAR(50) NULL ,
specimen_source_value VARCHAR(50) NULL ,
unit_source_value VARCHAR(50) NULL ,
anatomic_site_source_value VARCHAR(50) NULL ,
disease_status_source_value VARCHAR(50) NULL
)
;
CREATE TABLE death
(
person_id INTEGER NOT NULL ,
death_date DATE NOT NULL ,
death_type_concept_id INTEGER NOT NULL ,
cause_concept_id INTEGER NULL ,
cause_source_value VARCHAR(50) NULL,
cause_source_concept_id INTEGER NULL
)
;
CREATE TABLE visit_occurrence
(
visit_occurrence_id INTEGER NOT NULL ,
person_id INTEGER NOT NULL ,
visit_concept_id INTEGER NOT NULL ,
visit_start_date DATE NOT NULL ,
visit_start_time VARCHAR(10) NULL ,
visit_end_date DATE NOT NULL ,
visit_end_time VARCHAR(10) NULL ,
visit_type_concept_id INTEGER NOT NULL ,
provider_id INTEGER NULL,
care_site_id INTEGER NULL,
visit_source_value VARCHAR(50) NULL,
visit_source_concept_id INTEGER NULL
)
;
CREATE TABLE procedure_occurrence
(
procedure_occurrence_id INTEGER NOT NULL ,
person_id INTEGER NOT NULL ,
procedure_concept_id INTEGER NOT NULL ,
procedure_date DATE NOT NULL ,
procedure_type_concept_id INTEGER NOT NULL ,
modifier_concept_id INTEGER NULL ,
quantity INTEGER NULL ,
provider_id INTEGER NULL ,
visit_occurrence_id INTEGER NULL ,
procedure_source_value VARCHAR(50) NULL ,
procedure_source_concept_id INTEGER NULL ,
qualifier_source_value VARCHAR(50) NULL
)
;
CREATE TABLE drug_exposure
(
drug_exposure_id INTEGER NOT NULL ,
person_id INTEGER NOT NULL ,
drug_concept_id INTEGER NOT NULL ,
drug_exposure_start_date DATE NOT NULL ,
drug_exposure_end_date DATE NULL ,
drug_type_concept_id INTEGER NOT NULL ,
stop_reason VARCHAR(20) NULL ,
refills INTEGER NULL ,
quantity NUMERIC NULL ,
days_supply INTEGER NULL ,
sig TEXT NULL ,
route_concept_id INTEGER NULL ,
effective_drug_dose NUMERIC NULL ,
dose_unit_concept_id INTEGER NULL ,
lot_number VARCHAR(50) NULL ,
provider_id INTEGER NULL ,
visit_occurrence_id INTEGER NULL ,
drug_source_value VARCHAR(50) NULL ,
drug_source_concept_id INTEGER NULL ,
route_source_value VARCHAR(50) NULL ,
dose_unit_source_value VARCHAR(50) NULL
)
;
CREATE TABLE device_exposure
(
device_exposure_id INTEGER NOT NULL ,
person_id INTEGER NOT NULL ,
device_concept_id INTEGER NOT NULL ,
device_exposure_start_date DATE NOT NULL ,
device_exposure_end_date DATE NULL ,
device_type_concept_id INTEGER NOT NULL ,
unique_device_id VARCHAR(50) NULL ,
quantity INTEGER NULL ,
provider_id INTEGER NULL ,
visit_occurrence_id INTEGER NULL ,
device_source_value VARCHAR(100) NULL ,
device_source_concept_id INTEGER NULL
)
;
CREATE TABLE condition_occurrence
(
condition_occurrence_id INTEGER NOT NULL ,
person_id INTEGER NOT NULL ,
condition_concept_id INTEGER NOT NULL ,
condition_start_date DATE NOT NULL ,
condition_end_date DATE NULL ,
condition_type_concept_id INTEGER NOT NULL ,
stop_reason VARCHAR(20) NULL ,
provider_id INTEGER NULL ,
visit_occurrence_id INTEGER NULL ,
condition_source_value VARCHAR(50) NULL ,
condition_source_concept_id INTEGER NULL
)
;
CREATE TABLE measurement
(
measurement_id INTEGER NOT NULL ,
person_id INTEGER NOT NULL ,
measurement_concept_id INTEGER NOT NULL ,
measurement_date DATE NOT NULL ,
measurement_time VARCHAR(10) NULL ,
measurement_type_concept_id INTEGER NOT NULL ,
operator_concept_id INTEGER NULL ,
value_as_number NUMERIC NULL ,
value_as_concept_id INTEGER NULL ,
unit_concept_id INTEGER NULL ,
range_low NUMERIC NULL ,
range_high NUMERIC NULL ,
provider_id INTEGER NULL ,
visit_occurrence_id INTEGER NULL ,
measurement_source_value VARCHAR(50) NULL ,
measurement_source_concept_id INTEGER NULL ,
unit_source_value VARCHAR(50) NULL ,
value_source_value VARCHAR(50) NULL
)
;
CREATE TABLE note
(
note_id INTEGER NOT NULL ,
person_id INTEGER NOT NULL ,
note_date DATE NOT NULL ,
note_time VARCHAR(10) NULL ,
note_type_concept_id INTEGER NOT NULL ,
note_text TEXT NOT NULL ,
provider_id INTEGER NULL ,
visit_occurrence_id INTEGER NULL ,
note_source_value VARCHAR(50) NULL
)
;
CREATE TABLE observation
(
observation_id INTEGER NOT NULL ,
person_id INTEGER NOT NULL ,
observation_concept_id INTEGER NOT NULL ,
observation_date DATE NOT NULL ,
observation_time VARCHAR(10) NULL ,
observation_type_concept_id INTEGER NOT NULL ,
value_as_number NUMERIC NULL ,
value_as_string VARCHAR(60) NULL ,
value_as_concept_id INTEGER NULL ,
qualifier_concept_id INTEGER NULL ,
unit_concept_id INTEGER NULL ,
provider_id INTEGER NULL ,
visit_occurrence_id INTEGER NULL ,
observation_source_value VARCHAR(50) NULL ,
observation_source_concept_id INTEGER NULL ,
unit_source_value VARCHAR(50) NULL ,
qualifier_source_value VARCHAR(50) NULL
)
;
CREATE TABLE fact_relationship
(
domain_concept_id_1 INTEGER NOT NULL ,
fact_id_1 INTEGER NOT NULL ,
domain_concept_id_2 INTEGER NOT NULL ,
fact_id_2 INTEGER NOT NULL ,
relationship_concept_id INTEGER NOT NULL
)
;
/************************
Standardized health system data
************************/
CREATE TABLE location
(
location_id INTEGER NOT NULL ,
address_1 VARCHAR(50) NULL ,
address_2 VARCHAR(50) NULL ,
city VARCHAR(50) NULL ,
state VARCHAR(2) NULL ,
zip VARCHAR(9) NULL ,
county VARCHAR(20) NULL ,
location_source_value VARCHAR(50) NULL
)
;
CREATE TABLE care_site
(
care_site_id INTEGER NOT NULL ,
care_site_name VARCHAR(255) NULL ,
place_of_service_concept_id INTEGER NULL ,
location_id INTEGER NULL ,
care_site_source_value VARCHAR(50) NULL ,
place_of_service_source_value VARCHAR(50) NULL
)
;
CREATE TABLE provider
(
provider_id INTEGER NOT NULL ,
provider_name VARCHAR(255) NULL ,
NPI VARCHAR(20) NULL ,
DEA VARCHAR(20) NULL ,
specialty_concept_id INTEGER NULL ,
care_site_id INTEGER NULL ,
year_of_birth INTEGER NULL ,
gender_concept_id INTEGER NULL ,
provider_source_value VARCHAR(50) NULL ,
specialty_source_value VARCHAR(50) NULL ,
specialty_source_concept_id INTEGER NULL ,
gender_source_value VARCHAR(50) NULL ,
gender_source_concept_id INTEGER NULL
)
;
/************************
Standardized health economics
************************/
CREATE TABLE payer_plan_period
(
payer_plan_period_id INTEGER NOT NULL ,
person_id INTEGER NOT NULL ,
payer_plan_period_start_date DATE NOT NULL ,
payer_plan_period_end_date DATE NOT NULL ,
payer_source_value VARCHAR (50) NULL ,
plan_source_value VARCHAR (50) NULL ,
family_source_value VARCHAR (50) NULL
)
;
/* The individual cost tables are being phased out and will disappear soon
CREATE TABLE visit_cost
(
visit_cost_id INTEGER NOT NULL ,
visit_occurrence_id INTEGER NOT NULL ,
currency_concept_id INTEGER NULL ,
paid_copay NUMERIC NULL ,
paid_coinsurance NUMERIC NULL ,
paid_toward_deductible NUMERIC NULL ,
paid_by_payer NUMERIC NULL ,
paid_by_coordination_benefits NUMERIC NULL ,
total_out_of_pocket NUMERIC NULL ,
total_paid NUMERIC NULL ,
payer_plan_period_id INTEGER NULL
)
;
CREATE TABLE procedure_cost
(
procedure_cost_id INTEGER NOT NULL ,
procedure_occurrence_id INTEGER NOT NULL ,
currency_concept_id INTEGER NULL ,
paid_copay NUMERIC NULL ,
paid_coinsurance NUMERIC NULL ,
paid_toward_deductible NUMERIC NULL ,
paid_by_payer NUMERIC NULL ,
paid_by_coordination_benefits NUMERIC NULL ,
total_out_of_pocket NUMERIC NULL ,
total_paid NUMERIC NULL ,
revenue_code_concept_id INTEGER NULL ,
payer_plan_period_id INTEGER NULL ,
revenue_code_source_value VARCHAR(50) NULL
)
;
CREATE TABLE drug_cost
(
drug_cost_id INTEGER NOT NULL ,
drug_exposure_id INTEGER NOT NULL ,
currency_concept_id INTEGER NULL ,
paid_copay NUMERIC NULL ,
paid_coinsurance NUMERIC NULL ,
paid_toward_deductible NUMERIC NULL ,
paid_by_payer NUMERIC NULL ,
paid_by_coordination_benefits NUMERIC NULL ,
total_out_of_pocket NUMERIC NULL ,
total_paid NUMERIC NULL ,
ingredient_cost NUMERIC NULL ,
dispensing_fee NUMERIC NULL ,
average_wholesale_price NUMERIC NULL ,
payer_plan_period_id INTEGER NULL
)
;
CREATE TABLE device_cost
(
device_cost_id INTEGER NOT NULL ,
device_exposure_id INTEGER NOT NULL ,
currency_concept_id INTEGER NULL ,
paid_copay NUMERIC NULL ,
paid_coinsurance NUMERIC NULL ,
paid_toward_deductible NUMERIC NULL ,
paid_by_payer NUMERIC NULL ,
paid_by_coordination_benefits NUMERIC NULL ,
total_out_of_pocket NUMERIC NULL ,
total_paid NUMERIC NULL ,
payer_plan_period_id INTEGER NULL
)
;
*/
CREATE TABLE cost
(
cost_id INTEGER NOT NULL ,
cost_event_id INTEGER NOT NULL ,
cost_domain_id VARCHAR(20) NOT NULL ,
cost_type_concept_id INTEGER NOT NULL ,
currency_concept_id INTEGER NULL ,
total_charge NUMERIC NULL ,
total_cost NUMERIC NULL ,
total_paid NUMERIC NULL ,
paid_by_payer NUMERIC NULL ,
paid_by_patient NUMERIC NULL ,
paid_patient_copay NUMERIC NULL ,
paid_patient_coinsurance NUMERIC NULL ,
paid_patient_deductible NUMERIC NULL ,
paid_by_primary NUMERIC NULL ,
paid_ingredient_cost NUMERIC NULL ,
paid_dispensing_fee NUMERIC NULL ,
payer_plan_period_id INTEGER NULL ,
amount_allowed NUMERIC NULL ,
revenue_code_concept_id INTEGER NULL ,
reveue_code_source_value VARCHAR(50) NULL
)
;
/************************
Standardized derived elements
************************/
CREATE TABLE cohort
(
cohort_definition_id INTEGER NOT NULL ,
subject_id INTEGER NOT NULL ,
cohort_start_date DATE NOT NULL ,
cohort_end_date DATE NOT NULL
)
;
CREATE TABLE cohort_attribute
(
cohort_definition_id INTEGER NOT NULL ,
cohort_start_date DATE NOT NULL ,
cohort_end_date DATE NOT NULL ,
subject_id INTEGER NOT NULL ,
attribute_definition_id INTEGER NOT NULL ,
value_as_number NUMERIC NULL ,
value_as_concept_id INTEGER NULL
)
;
CREATE TABLE drug_era
(
drug_era_id INTEGER NOT NULL ,
person_id INTEGER NOT NULL ,
drug_concept_id INTEGER NOT NULL ,
drug_era_start_date DATE NOT NULL ,
drug_era_end_date DATE NOT NULL ,
drug_exposure_count INTEGER NULL ,
gap_days INTEGER NULL
)
;
CREATE TABLE dose_era
(
dose_era_id INTEGER NOT NULL ,
person_id INTEGER NOT NULL ,
drug_concept_id INTEGER NOT NULL ,
unit_concept_id INTEGER NOT NULL ,
dose_value NUMERIC NOT NULL ,
dose_era_start_date DATE NOT NULL ,
dose_era_end_date DATE NOT NULL
)
;
CREATE TABLE condition_era
(
condition_era_id INTEGER NOT NULL ,
person_id INTEGER NOT NULL ,
condition_concept_id INTEGER NOT NULL ,
condition_era_start_date DATE NOT NULL ,
condition_era_end_date DATE NOT NULL ,
condition_occurrence_count INTEGER NULL
)
;

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/*********************************************************************************
# Copyright 2014 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 create the required indexes within OMOP common data model, version 5.0 for PostgreSQL database
last revised: 12 Oct 2014
author: Patrick Ryan
description: These indices are considered a minimal requirement to ensure adequate performance of analyses.
*************************/
/************************
Standardized vocabulary
************************/
CREATE UNIQUE INDEX idx_concept_concept_id ON concept (concept_id ASC);
CLUSTER concept USING idx_concept_concept_id ;
CREATE INDEX idx_concept_code ON concept (concept_code ASC);
CREATE INDEX idx_concept_vocabluary_id ON concept (vocabulary_id ASC);
CREATE INDEX idx_concept_domain_id ON concept (domain_id ASC);
CREATE INDEX idx_concept_class_id ON concept (concept_class_id ASC);
CREATE UNIQUE INDEX idx_vocabulary_vocabulary_id ON vocabulary (vocabulary_id ASC);
CLUSTER vocabulary USING idx_vocabulary_vocabulary_id ;
CREATE UNIQUE INDEX idx_domain_domain_id ON domain (domain_id ASC);
CLUSTER domain USING idx_domain_domain_id ;
CREATE UNIQUE INDEX idx_concept_class_class_id ON concept_class (concept_class_id ASC);
CLUSTER concept_class USING idx_concept_class_class_id ;
CREATE INDEX idx_concept_relationship_id_1 ON concept_relationship (concept_id_1 ASC);
CREATE INDEX idx_concept_relationship_id_2 ON concept_relationship (concept_id_2 ASC);
CREATE INDEX idx_concept_relationship_id_3 ON concept_relationship (relationship_id ASC);
CREATE UNIQUE INDEX idx_relationship_rel_id ON relationship (relationship_id ASC);
CLUSTER relationship USING idx_relationship_rel_id ;
CREATE INDEX idx_concept_synonym_id ON concept_synonym (concept_id ASC);
CLUSTER concept_synonym USING idx_concept_synonym_id ;
CREATE INDEX idx_concept_ancestor_id_1 ON concept_ancestor (ancestor_concept_id ASC);
CLUSTER concept_ancestor USING idx_concept_ancestor_id_1 ;
CREATE INDEX idx_concept_ancestor_id_2 ON concept_ancestor (descendant_concept_id ASC);
CREATE INDEX idx_source_to_concept_map_id_3 ON source_to_concept_map (target_concept_id ASC);
CLUSTER source_to_concept_map USING idx_source_to_concept_map_id_3 ;
CREATE INDEX idx_source_to_concept_map_id_1 ON source_to_concept_map (source_vocabulary_id ASC);
CREATE INDEX idx_source_to_concept_map_id_2 ON source_to_concept_map (target_vocabulary_id ASC);
CREATE INDEX idx_source_to_concept_map_code ON source_to_concept_map (source_code ASC);
CREATE INDEX idx_drug_strength_id_1 ON drug_strength (drug_concept_id ASC);
CLUSTER drug_strength USING idx_drug_strength_id_1 ;
CREATE INDEX idx_drug_strength_id_2 ON drug_strength (ingredient_concept_id ASC);
CREATE INDEX idx_cohort_definition_id ON cohort_definition (cohort_definition_id ASC);
CLUSTER cohort_definition USING idx_cohort_definition_id ;
CREATE INDEX idx_attribute_definition_id ON attribute_definition (attribute_definition_id ASC);
CLUSTER attribute_definition USING idx_attribute_definition_id ;
/**************************
Standardized meta-data
***************************/
/************************
Standardized clinical data
************************/
CREATE UNIQUE INDEX idx_person_id ON person (person_id ASC);
CLUSTER person USING idx_person_id ;
CREATE INDEX idx_observation_period_id ON observation_period (person_id ASC);
CLUSTER observation_period USING idx_observation_period_id ;
CREATE INDEX idx_specimen_person_id ON specimen (person_id ASC);
CLUSTER specimen USING idx_specimen_person_id ;
CREATE INDEX idx_specimen_concept_id ON specimen (specimen_concept_id ASC);
CREATE INDEX idx_death_person_id ON death (person_id ASC);
CLUSTER death USING idx_death_person_id ;
CREATE INDEX idx_visit_person_id ON visit_occurrence (person_id ASC);
CLUSTER visit_occurrence USING idx_visit_person_id ;
CREATE INDEX idx_visit_concept_id ON visit_occurrence (visit_concept_id ASC);
CREATE INDEX idx_procedure_person_id ON procedure_occurrence (person_id ASC);
CLUSTER procedure_occurrence USING idx_procedure_person_id ;
CREATE INDEX idx_procedure_concept_id ON procedure_occurrence (procedure_concept_id ASC);
CREATE INDEX idx_procedure_visit_id ON procedure_occurrence (visit_occurrence_id ASC);
CREATE INDEX idx_drug_person_id ON drug_exposure (person_id ASC);
CLUSTER drug_exposure USING idx_drug_person_id ;
CREATE INDEX idx_drug_concept_id ON drug_exposure (drug_concept_id ASC);
CREATE INDEX idx_drug_visit_id ON drug_exposure (visit_occurrence_id ASC);
CREATE INDEX idx_device_person_id ON device_exposure (person_id ASC);
CLUSTER device_exposure USING idx_device_person_id ;
CREATE INDEX idx_device_concept_id ON device_exposure (device_concept_id ASC);
CREATE INDEX idx_device_visit_id ON device_exposure (visit_occurrence_id ASC);
CREATE INDEX idx_condition_person_id ON condition_occurrence (person_id ASC);
CLUSTER condition_occurrence USING idx_condition_person_id ;
CREATE INDEX idx_condition_concept_id ON condition_occurrence (condition_concept_id ASC);
CREATE INDEX idx_condition_visit_id ON condition_occurrence (visit_occurrence_id ASC);
CREATE INDEX idx_measurement_person_id ON measurement (person_id ASC);
CLUSTER measurement USING idx_measurement_person_id ;
CREATE INDEX idx_measurement_concept_id ON measurement (measurement_concept_id ASC);
CREATE INDEX idx_measurement_visit_id ON measurement (visit_occurrence_id ASC);
CREATE INDEX idx_note_person_id ON note (person_id ASC);
CLUSTER note USING idx_note_person_id ;
CREATE INDEX idx_note_concept_id ON note (note_type_concept_id ASC);
CREATE INDEX idx_note_visit_id ON note (visit_occurrence_id ASC);
CREATE INDEX idx_observation_person_id ON observation (person_id ASC);
CLUSTER observation USING idx_observation_person_id ;
CREATE INDEX idx_observation_concept_id ON observation (observation_concept_id ASC);
CREATE INDEX idx_observation_visit_id ON observation (visit_occurrence_id ASC);
CREATE INDEX idx_fact_relationship_id_1 ON fact_relationship (domain_concept_id_1 ASC);
CREATE INDEX idx_fact_relationship_id_2 ON fact_relationship (domain_concept_id_2 ASC);
CREATE INDEX idx_fact_relationship_id_3 ON fact_relationship (relationship_concept_id ASC);
/************************
Standardized health system data
************************/
/************************
Standardized health economics
************************/
CREATE INDEX idx_period_person_id ON payer_plan_period (person_id ASC);
CLUSTER payer_plan_period USING idx_period_person_id ;
/************************
Standardized derived elements
************************/
CREATE INDEX idx_cohort_subject_id ON cohort (subject_id ASC);
CREATE INDEX idx_cohort_c_definition_id ON cohort (cohort_definition_id ASC);
CREATE INDEX idx_ca_subject_id ON cohort_attribute (subject_id ASC);
CREATE INDEX idx_ca_definition_id ON cohort_attribute (cohort_definition_id ASC);
CREATE INDEX idx_drug_era_person_id ON drug_era (person_id ASC);
CLUSTER drug_era USING idx_drug_era_person_id ;
CREATE INDEX idx_drug_era_concept_id ON drug_era (drug_concept_id ASC);
CREATE INDEX idx_dose_era_person_id ON dose_era (person_id ASC);
CLUSTER dose_era USING idx_dose_era_person_id ;
CREATE INDEX idx_dose_era_concept_id ON dose_era (drug_concept_id ASC);
CREATE INDEX idx_condition_era_person_id ON condition_era (person_id ASC);
CLUSTER condition_era USING idx_condition_era_person_id ;
CREATE INDEX idx_condition_era_concept_id ON condition_era (condition_concept_id ASC);

18
PostgreSQL/README.md
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@ -1,18 +0,0 @@
Common-Data-Model / PostgreSQL
=================
This folder contains the SQL scripts for PostgreSQL.
In order to create your instantiation of the Common Data Model, we recommend following these steps:
1. Create an empty schema.
2. Execute the script `OMOP CDM ddl - PostgreSQL.sql` to create the tables and fields.
3. Load your data into the schema.
4. Execute the script `OMOP CDM constraints - PostgreSQL.sql` to add the constraints (primary and foreign keys).
5. Execute the script `OMOP CDM indexes required - PostgreSQL.sql` to add the minimum set of indexes we recommend.
Note: you could also apply the constraints and/or the indexes before loading the data, but this will slow down the insertion of the data considerably.

63
PostgreSQL/VocabImport/OMOP CDM vocabulary load - PostgreSQL.sql
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@ -1,63 +0,0 @@
/*********************************************************************************
# Copyright 2014 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 5.0 vocabulary tables for PostgreSQL database on Windows (MS-DOS style file paths)
The database account running this script must have the "superuser" permission in the 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:\CDMV5VOCAB" 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) Truncate each table that will be lodaed below, before running this script.
last revised: 5 Dec 2014
author: Lee Evans
*************************/
COPY DRUG_STRENGTH FROM 'C:\CDMV5VOCAB\DRUG_STRENGTH.csv' WITH DELIMITER E'\t' CSV HEADER QUOTE E'\b' ;
COPY CONCEPT FROM 'C:\CDMV5VOCAB\CONCEPT.csv' WITH DELIMITER E'\t' CSV HEADER QUOTE E'\b' ;
COPY CONCEPT_RELATIONSHIP FROM 'C:\CDMV5VOCAB\CONCEPT_RELATIONSHIP.csv' WITH DELIMITER E'\t' CSV HEADER QUOTE E'\b' ;
COPY CONCEPT_ANCESTOR FROM 'C:\CDMV5VOCAB\CONCEPT_ANCESTOR.csv' WITH DELIMITER E'\t' CSV HEADER QUOTE E'\b' ;
COPY CONCEPT_SYNONYM FROM 'C:\CDMV5VOCAB\CONCEPT_SYNONYM.csv' WITH DELIMITER E'\t' CSV HEADER QUOTE E'\b' ;
COPY VOCABULARY FROM 'C:\CDMV5VOCAB\VOCABULARY.csv' WITH DELIMITER E'\t' CSV HEADER QUOTE E'\b' ;
COPY RELATIONSHIP FROM 'C:\CDMV5VOCAB\RELATIONSHIP.csv' WITH DELIMITER E'\t' CSV HEADER QUOTE E'\b' ;
COPY CONCEPT_CLASS FROM 'C:\CDMV5VOCAB\CONCEPT_CLASS.csv' WITH DELIMITER E'\t' CSV HEADER QUOTE E'\b' ;
COPY DOMAIN FROM 'C:\CDMV5VOCAB\DOMAIN.csv' WITH DELIMITER E'\t' CSV HEADER QUOTE E'\b' ;

545
Sql Server/OMOP CDM constraints - SQL Server.sql
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@ -1,545 +0,0 @@
/*********************************************************************************
# Copyright 2014 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 create constraints within OMOP common data model, version 5.0 for SQL Server database
last revised: 12 Oct 2014
author: Patrick Ryan
*************************/
/************************
*************************
*************************
*************************
Primary key constraints
*************************
*************************
*************************
************************/
/************************
Standardized vocabulary
************************/
ALTER TABLE concept ADD CONSTRAINT xpk_concept PRIMARY KEY NONCLUSTERED (concept_id);
ALTER TABLE vocabulary ADD CONSTRAINT xpk_vocabulary PRIMARY KEY NONCLUSTERED (vocabulary_id);
ALTER TABLE domain ADD CONSTRAINT xpk_domain PRIMARY KEY NONCLUSTERED (domain_id);
ALTER TABLE concept_class ADD CONSTRAINT xpk_concept_class PRIMARY KEY NONCLUSTERED (concept_class_id);
ALTER TABLE concept_relationship ADD CONSTRAINT xpk_concept_relationship PRIMARY KEY NONCLUSTERED (concept_id_1,concept_id_2,relationship_id);
ALTER TABLE relationship ADD CONSTRAINT xpk_relationship PRIMARY KEY NONCLUSTERED (relationship_id);
ALTER TABLE concept_ancestor ADD CONSTRAINT xpk_concept_ancestor PRIMARY KEY NONCLUSTERED (ancestor_concept_id,descendant_concept_id);
ALTER TABLE source_to_concept_map ADD CONSTRAINT xpk_source_to_concept_map PRIMARY KEY NONCLUSTERED (source_vocabulary_id,target_concept_id,source_code,valid_end_date);
ALTER TABLE drug_strength ADD CONSTRAINT xpk_drug_strength PRIMARY KEY NONCLUSTERED (drug_concept_id, ingredient_concept_id);
ALTER TABLE cohort_definition ADD CONSTRAINT xpk_cohort_definition PRIMARY KEY NONCLUSTERED (cohort_definition_id);
ALTER TABLE attribute_definition ADD CONSTRAINT xpk_attribute_definition PRIMARY KEY NONCLUSTERED (attribute_definition_id);
/**************************
Standardized meta-data
***************************/
/************************
Standardized clinical data
************************/
/**PRIMARY KEY NONCLUSTERED constraints**/
ALTER TABLE person ADD CONSTRAINT xpk_person PRIMARY KEY NONCLUSTERED ( person_id ) ;
ALTER TABLE observation_period ADD CONSTRAINT xpk_observation_period PRIMARY KEY NONCLUSTERED ( observation_period_id ) ;
ALTER TABLE specimen ADD CONSTRAINT xpk_specimen PRIMARY KEY NONCLUSTERED ( specimen_id ) ;
ALTER TABLE death ADD CONSTRAINT xpk_death PRIMARY KEY NONCLUSTERED ( person_id ) ;
ALTER TABLE visit_occurrence ADD CONSTRAINT xpk_visit_occurrence PRIMARY KEY NONCLUSTERED ( visit_occurrence_id ) ;
ALTER TABLE procedure_occurrence ADD CONSTRAINT xpk_procedure_occurrence PRIMARY KEY NONCLUSTERED ( procedure_occurrence_id ) ;
ALTER TABLE drug_exposure ADD CONSTRAINT xpk_drug_exposure PRIMARY KEY NONCLUSTERED ( drug_exposure_id ) ;
ALTER TABLE device_exposure ADD CONSTRAINT xpk_device_exposure PRIMARY KEY NONCLUSTERED ( device_exposure_id ) ;
ALTER TABLE condition_occurrence ADD CONSTRAINT xpk_condition_occurrence PRIMARY KEY NONCLUSTERED ( condition_occurrence_id ) ;
ALTER TABLE measurement ADD CONSTRAINT xpk_measurement PRIMARY KEY NONCLUSTERED ( measurement_id ) ;
ALTER TABLE note ADD CONSTRAINT xpk_note PRIMARY KEY NONCLUSTERED ( note_id ) ;
ALTER TABLE observation ADD CONSTRAINT xpk_observation PRIMARY KEY NONCLUSTERED ( observation_id ) ;
/************************
Standardized health system data
************************/
ALTER TABLE location ADD CONSTRAINT xpk_location PRIMARY KEY NONCLUSTERED ( location_id ) ;
ALTER TABLE care_site ADD CONSTRAINT xpk_care_site PRIMARY KEY NONCLUSTERED ( care_site_id ) ;
ALTER TABLE provider ADD CONSTRAINT xpk_provider PRIMARY KEY NONCLUSTERED ( provider_id ) ;
/************************
Standardized health economics
************************/
ALTER TABLE payer_plan_period ADD CONSTRAINT xpk_payer_plan_period PRIMARY KEY NONCLUSTERED ( payer_plan_period_id ) ;
ALTER TABLE visit_cost ADD CONSTRAINT xpk_visit_cost PRIMARY KEY NONCLUSTERED ( visit_cost_id ) ;
ALTER TABLE procedure_cost ADD CONSTRAINT xpk_procedure_cost PRIMARY KEY NONCLUSTERED ( procedure_cost_id ) ;
ALTER TABLE drug_cost ADD CONSTRAINT xpk_drug_cost PRIMARY KEY NONCLUSTERED ( drug_cost_id ) ;
ALTER TABLE device_cost ADD CONSTRAINT xpk_device_cost PRIMARY KEY NONCLUSTERED ( device_cost_id ) ;
/************************
Standardized derived elements
************************/
ALTER TABLE cohort ADD CONSTRAINT xpk_cohort PRIMARY KEY NONCLUSTERED ( cohort_definition_id, subject_id, cohort_start_date, cohort_end_date ) ;
ALTER TABLE cohort_attribute ADD CONSTRAINT xpk_cohort_attribute PRIMARY KEY NONCLUSTERED ( cohort_definition_id, subject_id, cohort_start_date, cohort_end_date, attribute_definition_id ) ;
ALTER TABLE drug_era ADD CONSTRAINT xpk_drug_era PRIMARY KEY NONCLUSTERED ( drug_era_id ) ;
ALTER TABLE dose_era ADD CONSTRAINT xpk_dose_era PRIMARY KEY NONCLUSTERED ( dose_era_id ) ;
ALTER TABLE condition_era ADD CONSTRAINT xpk_condition_era PRIMARY KEY NONCLUSTERED ( condition_era_id ) ;
/************************
*************************
*************************
*************************
Foreign key constraints
*************************
*************************
*************************
************************/
/************************
Standardized vocabulary
************************/
ALTER TABLE concept ADD CONSTRAINT fpk_concept_domain FOREIGN KEY (domain_id) REFERENCES domain (domain_id);
ALTER TABLE concept ADD CONSTRAINT fpk_concept_class FOREIGN KEY (concept_class_id) REFERENCES concept_class (concept_class_id);
ALTER TABLE concept ADD CONSTRAINT fpk_concept_vocabulary FOREIGN KEY (vocabulary_id) REFERENCES vocabulary (vocabulary_id);
ALTER TABLE vocabulary ADD CONSTRAINT fpk_vocabulary_concept FOREIGN KEY (vocabulary_concept_id) REFERENCES concept (concept_id);
ALTER TABLE domain ADD CONSTRAINT fpk_domain_concept FOREIGN KEY (domain_concept_id) REFERENCES concept (concept_id);
ALTER TABLE concept_class ADD CONSTRAINT fpk_concept_class_concept FOREIGN KEY (concept_class_concept_id) REFERENCES concept (concept_id);
ALTER TABLE concept_relationship ADD CONSTRAINT fpk_concept_relationship_c_1 FOREIGN KEY (concept_id_1) REFERENCES concept (concept_id);
ALTER TABLE concept_relationship ADD CONSTRAINT fpk_concept_relationship_c_2 FOREIGN KEY (concept_id_2) REFERENCES concept (concept_id);
ALTER TABLE concept_relationship ADD CONSTRAINT fpk_concept_relationship_id FOREIGN KEY (relationship_id) REFERENCES relationship (relationship_id);
ALTER TABLE relationship ADD CONSTRAINT fpk_relationship_concept FOREIGN KEY (relationship_concept_id) REFERENCES concept (concept_id);
ALTER TABLE relationship ADD CONSTRAINT fpk_relationship_reverse FOREIGN KEY (reverse_relationship_id) REFERENCES relationship (relationship_id);
ALTER TABLE concept_synonym ADD CONSTRAINT fpk_concept_synonym_concept FOREIGN KEY (concept_id) REFERENCES concept (concept_id);
ALTER TABLE concept_ancestor ADD CONSTRAINT fpk_concept_ancestor_concept_1 FOREIGN KEY (ancestor_concept_id) REFERENCES concept (concept_id);
ALTER TABLE concept_ancestor ADD CONSTRAINT fpk_concept_ancestor_concept_2 FOREIGN KEY (descendant_concept_id) REFERENCES concept (concept_id);
ALTER TABLE source_to_concept_map ADD CONSTRAINT fpk_source_to_concept_map_v_1 FOREIGN KEY (source_vocabulary_id) REFERENCES vocabulary (vocabulary_id);
ALTER TABLE source_to_concept_map ADD CONSTRAINT fpk_source_to_concept_map_v_2 FOREIGN KEY (target_vocabulary_id) REFERENCES vocabulary (vocabulary_id);
ALTER TABLE source_to_concept_map ADD CONSTRAINT fpk_source_to_concept_map_c_1 FOREIGN KEY (target_concept_id) REFERENCES concept (concept_id);
ALTER TABLE drug_strength ADD CONSTRAINT fpk_drug_strength_concept_1 FOREIGN KEY (drug_concept_id) REFERENCES concept (concept_id);
ALTER TABLE drug_strength ADD CONSTRAINT fpk_drug_strength_concept_2 FOREIGN KEY (ingredient_concept_id) REFERENCES concept (concept_id);
ALTER TABLE drug_strength ADD CONSTRAINT fpk_drug_strength_unit_1 FOREIGN KEY (amount_unit_concept_id) REFERENCES concept (concept_id);
ALTER TABLE drug_strength ADD CONSTRAINT fpk_drug_strength_unit_2 FOREIGN KEY (numerator_unit_concept_id) REFERENCES concept (concept_id);
ALTER TABLE drug_strength ADD CONSTRAINT fpk_drug_strength_unit_3 FOREIGN KEY (denominator_unit_concept_id) REFERENCES concept (concept_id);
ALTER TABLE cohort_definition ADD CONSTRAINT fpk_cohort_definition_concept FOREIGN KEY (definition_type_concept_id) REFERENCES concept (concept_id);
/**************************
Standardized meta-data
***************************/
/************************
Standardized clinical data
************************/
ALTER TABLE person ADD CONSTRAINT fpk_person_gender_concept FOREIGN KEY (gender_concept_id) REFERENCES concept (concept_id);
ALTER TABLE person ADD CONSTRAINT fpk_person_race_concept FOREIGN KEY (race_concept_id) REFERENCES concept (concept_id);
ALTER TABLE person ADD CONSTRAINT fpk_person_ethnicity_concept FOREIGN KEY (ethnicity_concept_id) REFERENCES concept (concept_id);
ALTER TABLE person ADD CONSTRAINT fpk_person_gender_concept_s FOREIGN KEY (gender_source_concept_id) REFERENCES concept (concept_id);
ALTER TABLE person ADD CONSTRAINT fpk_person_race_concept_s FOREIGN KEY (race_source_concept_id) REFERENCES concept (concept_id);
ALTER TABLE person ADD CONSTRAINT fpk_person_ethnicity_concept_s FOREIGN KEY (ethnicity_source_concept_id) REFERENCES concept (concept_id);
ALTER TABLE person ADD CONSTRAINT fpk_person_location FOREIGN KEY (location_id) REFERENCES location (location_id);
ALTER TABLE person ADD CONSTRAINT fpk_person_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
ALTER TABLE person ADD CONSTRAINT fpk_person_care_site FOREIGN KEY (care_site_id) REFERENCES care_site (care_site_id);
ALTER TABLE observation_period ADD CONSTRAINT fpk_observation_period_person FOREIGN KEY (person_id) REFERENCES person (person_id);
ALTER TABLE observation_period ADD CONSTRAINT fpk_observation_period_concept FOREIGN KEY (period_type_concept_id) REFERENCES concept (concept_id);
ALTER TABLE specimen ADD CONSTRAINT fpk_specimen_person FOREIGN KEY (person_id) REFERENCES person (person_id);
ALTER TABLE specimen ADD CONSTRAINT fpk_specimen_concept FOREIGN KEY (specimen_concept_id) REFERENCES concept (concept_id);
ALTER TABLE specimen ADD CONSTRAINT fpk_specimen_type_concept FOREIGN KEY (specimen_type_concept_id) REFERENCES concept (concept_id);
ALTER TABLE specimen ADD CONSTRAINT fpk_specimen_unit_concept FOREIGN KEY (unit_concept_id) REFERENCES concept (concept_id);
ALTER TABLE specimen ADD CONSTRAINT fpk_specimen_site_concept FOREIGN KEY (anatomic_site_concept_id) REFERENCES concept (concept_id);
ALTER TABLE specimen ADD CONSTRAINT fpk_specimen_status_concept FOREIGN KEY (disease_status_concept_id) REFERENCES concept (concept_id);
ALTER TABLE death ADD CONSTRAINT fpk_death_person FOREIGN KEY (person_id) REFERENCES person (person_id);
ALTER TABLE death ADD CONSTRAINT fpk_death_type_concept FOREIGN KEY (death_type_concept_id) REFERENCES concept (concept_id);
ALTER TABLE death ADD CONSTRAINT fpk_death_cause_concept FOREIGN KEY (cause_concept_id) REFERENCES concept (concept_id);
ALTER TABLE death ADD CONSTRAINT fpk_death_cause_concept_s FOREIGN KEY (cause_source_concept_id) REFERENCES concept (concept_id);
ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_person FOREIGN KEY (person_id) REFERENCES person (person_id);
ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_concept FOREIGN KEY (visit_concept_id) REFERENCES concept (concept_id);
ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_type_concept FOREIGN KEY (visit_type_concept_id) REFERENCES concept (concept_id);
ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_care_site FOREIGN KEY (care_site_id) REFERENCES care_site (care_site_id);
ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_concept_s FOREIGN KEY (visit_source_concept_id) REFERENCES concept (concept_id);
ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_person FOREIGN KEY (person_id) REFERENCES person (person_id);
ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_concept FOREIGN KEY (procedure_concept_id) REFERENCES concept (concept_id);
ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_type_concept FOREIGN KEY (procedure_type_concept_id) REFERENCES concept (concept_id);
ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_modifier FOREIGN KEY (modifier_concept_id) REFERENCES concept (concept_id);
ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id);
ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_concept_s FOREIGN KEY (procedure_source_concept_id) REFERENCES concept (concept_id);
ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_person FOREIGN KEY (person_id) REFERENCES person (person_id);
ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_concept FOREIGN KEY (drug_concept_id) REFERENCES concept (concept_id);
ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_type_concept FOREIGN KEY (drug_type_concept_id) REFERENCES concept (concept_id);
ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_route_concept FOREIGN KEY (route_concept_id) REFERENCES concept (concept_id);
ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_dose_unit_concept FOREIGN KEY (dose_unit_concept_id) REFERENCES concept (concept_id);
ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id);
ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_concept_s FOREIGN KEY (drug_source_concept_id) REFERENCES concept (concept_id);
ALTER TABLE device_exposure ADD CONSTRAINT fpk_device_person FOREIGN KEY (person_id) REFERENCES person (person_id);
ALTER TABLE device_exposure ADD CONSTRAINT fpk_device_concept FOREIGN KEY (device_concept_id) REFERENCES concept (concept_id);
ALTER TABLE device_exposure ADD CONSTRAINT fpk_device_type_concept FOREIGN KEY (device_type_concept_id) REFERENCES concept (concept_id);
ALTER TABLE device_exposure ADD CONSTRAINT fpk_device_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
ALTER TABLE device_exposure ADD CONSTRAINT fpk_device_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id);
ALTER TABLE device_exposure ADD CONSTRAINT fpk_device_concept_s FOREIGN KEY (device_source_concept_id) REFERENCES concept (concept_id);
ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_person FOREIGN KEY (person_id) REFERENCES person (person_id);
ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_concept FOREIGN KEY (condition_concept_id) REFERENCES concept (concept_id);
ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_type_concept FOREIGN KEY (condition_type_concept_id) REFERENCES concept (concept_id);
ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id);
ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_concept_s FOREIGN KEY (condition_source_concept_id) REFERENCES concept (concept_id);
ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_person FOREIGN KEY (person_id) REFERENCES person (person_id);
ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_concept FOREIGN KEY (measurement_concept_id) REFERENCES concept (concept_id);
ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_type_concept FOREIGN KEY (measurement_type_concept_id) REFERENCES concept (concept_id);
ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_operator FOREIGN KEY (operator_concept_id) REFERENCES concept (concept_id);
ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_value FOREIGN KEY (value_as_concept_id) REFERENCES concept (concept_id);
ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_unit FOREIGN KEY (unit_concept_id) REFERENCES concept (concept_id);
ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id);
ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_concept_s FOREIGN KEY (measurement_source_concept_id) REFERENCES concept (concept_id);
ALTER TABLE note ADD CONSTRAINT fpk_note_person FOREIGN KEY (person_id) REFERENCES person (person_id);
ALTER TABLE note ADD CONSTRAINT fpk_note_type_concept FOREIGN KEY (note_type_concept_id) REFERENCES concept (concept_id);
ALTER TABLE note ADD CONSTRAINT fpk_note_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
ALTER TABLE note ADD CONSTRAINT fpk_note_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id);
ALTER TABLE observation ADD CONSTRAINT fpk_observation_person FOREIGN KEY (person_id) REFERENCES person (person_id);
ALTER TABLE observation ADD CONSTRAINT fpk_observation_concept FOREIGN KEY (observation_concept_id) REFERENCES concept (concept_id);
ALTER TABLE observation ADD CONSTRAINT fpk_observation_type_concept FOREIGN KEY (observation_type_concept_id) REFERENCES concept (concept_id);
ALTER TABLE observation ADD CONSTRAINT fpk_observation_value FOREIGN KEY (value_as_concept_id) REFERENCES concept (concept_id);
ALTER TABLE observation ADD CONSTRAINT fpk_observation_qualifier FOREIGN KEY (qualifier_concept_id) REFERENCES concept (concept_id);
ALTER TABLE observation ADD CONSTRAINT fpk_observation_unit FOREIGN KEY (unit_concept_id) REFERENCES concept (concept_id);
ALTER TABLE observation ADD CONSTRAINT fpk_observation_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
ALTER TABLE observation ADD CONSTRAINT fpk_observation_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id);
ALTER TABLE observation ADD CONSTRAINT fpk_observation_concept_s FOREIGN KEY (observation_source_concept_id) REFERENCES concept (concept_id);
ALTER TABLE fact_relationship ADD CONSTRAINT fpk_fact_domain_1 FOREIGN KEY (domain_concept_id_1) REFERENCES concept (concept_id);
ALTER TABLE fact_relationship ADD CONSTRAINT fpk_fact_domain_2 FOREIGN KEY (domain_concept_id_2) REFERENCES concept (concept_id);
ALTER TABLE fact_relationship ADD CONSTRAINT fpk_fact_relationship FOREIGN KEY (relationship_concept_id) REFERENCES concept (concept_id);
/************************
Standardized health system data
************************/
ALTER TABLE care_site ADD CONSTRAINT fpk_care_site_location FOREIGN KEY (location_id) REFERENCES location (location_id);
ALTER TABLE care_site ADD CONSTRAINT fpk_care_site_place FOREIGN KEY (place_of_service_concept_id) REFERENCES concept (concept_id);
ALTER TABLE provider ADD CONSTRAINT fpk_provider_specialty FOREIGN KEY (specialty_concept_id) REFERENCES concept (concept_id);
ALTER TABLE provider ADD CONSTRAINT fpk_provider_care_site FOREIGN KEY (care_site_id) REFERENCES care_site (care_site_id);
ALTER TABLE provider ADD CONSTRAINT fpk_provider_gender FOREIGN KEY (gender_concept_id) REFERENCES concept (concept_id);
ALTER TABLE provider ADD CONSTRAINT fpk_provider_specialty_s FOREIGN KEY (specialty_source_concept_id) REFERENCES concept (concept_id);
ALTER TABLE provider ADD CONSTRAINT fpk_provider_gender_s FOREIGN KEY (gender_source_concept_id) REFERENCES concept (concept_id);
/************************
Standardized health economics
************************/
ALTER TABLE payer_plan_period ADD CONSTRAINT fpk_payer_plan_period FOREIGN KEY (person_id) REFERENCES person (person_id);
ALTER TABLE visit_cost ADD CONSTRAINT fpk_visit_cost_id FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id);
ALTER TABLE visit_cost ADD CONSTRAINT fpk_visit_cost_currency FOREIGN KEY (currency_concept_id) REFERENCES concept (concept_id);
ALTER TABLE visit_cost ADD CONSTRAINT fpk_visit_cost_period FOREIGN KEY (payer_plan_period_id) REFERENCES payer_plan_period (payer_plan_period_id);
ALTER TABLE procedure_cost ADD CONSTRAINT fpk_procedure_cost_id FOREIGN KEY (procedure_occurrence_id) REFERENCES procedure_occurrence (procedure_occurrence_id);
ALTER TABLE procedure_cost ADD CONSTRAINT fpk_procedure_cost_currency FOREIGN KEY (currency_concept_id) REFERENCES concept (concept_id);
ALTER TABLE procedure_cost ADD CONSTRAINT fpk_procedure_cost_period FOREIGN KEY (payer_plan_period_id) REFERENCES payer_plan_period (payer_plan_period_id);
ALTER TABLE procedure_cost ADD CONSTRAINT fpk_procedure_cost_revenue FOREIGN KEY (revenue_code_concept_id) REFERENCES concept (concept_id);
ALTER TABLE drug_cost ADD CONSTRAINT fpk_drug_cost_id FOREIGN KEY (drug_exposure_id) REFERENCES drug_exposure (drug_exposure_id);
ALTER TABLE drug_cost ADD CONSTRAINT fpk_drug_cost_currency FOREIGN KEY (currency_concept_id) REFERENCES concept (concept_id);
ALTER TABLE drug_cost ADD CONSTRAINT fpk_drug_cost_period FOREIGN KEY (payer_plan_period_id) REFERENCES payer_plan_period (payer_plan_period_id);
ALTER TABLE device_cost ADD CONSTRAINT fpk_device_cost_id FOREIGN KEY (device_exposure_id) REFERENCES device_exposure (device_exposure_id);
ALTER TABLE device_cost ADD CONSTRAINT fpk_device_cost_currency FOREIGN KEY (currency_concept_id) REFERENCES concept (concept_id);
ALTER TABLE device_cost ADD CONSTRAINT fpk_device_cost_period FOREIGN KEY (payer_plan_period_id) REFERENCES payer_plan_period (payer_plan_period_id);
/************************
Standardized derived elements
************************/
ALTER TABLE cohort ADD CONSTRAINT fpk_cohort_definition FOREIGN KEY (cohort_definition_id) REFERENCES cohort_definition (cohort_definition_id);
ALTER TABLE cohort_attribute ADD CONSTRAINT fpk_ca_cohort_definition FOREIGN KEY (cohort_definition_id) REFERENCES cohort_definition (cohort_definition_id);
ALTER TABLE cohort_attribute ADD CONSTRAINT fpk_ca_attribute_definition FOREIGN KEY (attribute_definition_id) REFERENCES attribute_definition (attribute_definition_id);
ALTER TABLE cohort_attribute ADD CONSTRAINT fpk_ca_value FOREIGN KEY (value_as_concept_id) REFERENCES concept (concept_id);
ALTER TABLE drug_era ADD CONSTRAINT fpk_drug_era_person FOREIGN KEY (person_id) REFERENCES person (person_id);
ALTER TABLE drug_era ADD CONSTRAINT fpk_drug_era_concept FOREIGN KEY (drug_concept_id) REFERENCES concept (concept_id);
ALTER TABLE dose_era ADD CONSTRAINT fpk_dose_era_person FOREIGN KEY (person_id) REFERENCES person (person_id);
ALTER TABLE dose_era ADD CONSTRAINT fpk_dose_era_concept FOREIGN KEY (drug_concept_id) REFERENCES concept (concept_id);
ALTER TABLE dose_era ADD CONSTRAINT fpk_dose_era_unit_concept FOREIGN KEY (unit_concept_id) REFERENCES concept (concept_id);
ALTER TABLE condition_era ADD CONSTRAINT fpk_condition_era_person FOREIGN KEY (person_id) REFERENCES person (person_id);
ALTER TABLE condition_era ADD CONSTRAINT fpk_condition_era_concept FOREIGN KEY (condition_concept_id) REFERENCES concept (concept_id);

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Sql Server/OMOP CDM ddl - SQL Server.sql
View File

@ -1,738 +0,0 @@
/*********************************************************************************
# Copyright 2014-6 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 create OMOP common data model, version 5.0 for SQL Server database
last revised: 1-May-2016
Authors: Patrick Ryan, Christian Reich
*************************/
/************************
Standardized vocabulary
************************/
CREATE TABLE concept (
concept_id INTEGER NOT NULL,
concept_name VARCHAR(255) NOT NULL,
domain_id VARCHAR(20) NOT NULL,
vocabulary_id VARCHAR(20) NOT NULL,
concept_class_id VARCHAR(20) NOT NULL,
standard_concept VARCHAR(1) NULL,
concept_code VARCHAR(50) NOT NULL,
valid_start_date DATE NOT NULL,
valid_end_date DATE NOT NULL,
invalid_reason VARCHAR(1) NULL
)
;
CREATE TABLE vocabulary (
vocabulary_id VARCHAR(20) NOT NULL,
vocabulary_name VARCHAR(255) NOT NULL,
vocabulary_reference VARCHAR(255) NULL,
vocabulary_version VARCHAR(255) NULL,
vocabulary_concept_id INTEGER NOT NULL
)
;
CREATE TABLE domain (
domain_id VARCHAR(20) NOT NULL,
domain_name VARCHAR(255) NOT NULL,
domain_concept_id INTEGER NOT NULL
)
;
CREATE TABLE concept_class (
concept_class_id VARCHAR(20) NOT NULL,
concept_class_name VARCHAR(255) NOT NULL,
concept_class_concept_id INTEGER NOT NULL
)
;
CREATE TABLE concept_relationship (
concept_id_1 INTEGER NOT NULL,
concept_id_2 INTEGER NOT NULL,
relationship_id VARCHAR(20) NOT NULL,
valid_start_date DATE NOT NULL,
valid_end_date DATE NOT NULL,
invalid_reason VARCHAR(1) NULL)
;
CREATE TABLE relationship (
relationship_id VARCHAR(20) NOT NULL,
relationship_name VARCHAR(255) NOT NULL,
is_hierarchical VARCHAR(1) NOT NULL,
defines_ancestry VARCHAR(1) NOT NULL,
reverse_relationship_id VARCHAR(20) NOT NULL,
relationship_concept_id INTEGER NOT NULL
)
;
CREATE TABLE concept_synonym (
concept_id INTEGER NOT NULL,
concept_synonym_name VARCHAR(1000) NOT NULL,
language_concept_id INTEGER NOT NULL
)
;
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 source_to_concept_map (
source_code VARCHAR(50) NOT NULL,
source_concept_id INTEGER NOT NULL,
source_vocabulary_id VARCHAR(20) NOT NULL,
source_code_description VARCHAR(255) NULL,
target_concept_id INTEGER NOT NULL,
target_vocabulary_id VARCHAR(20) NOT NULL,
valid_start_date DATE NOT NULL,
valid_end_date DATE NOT NULL,
invalid_reason VARCHAR(1) NULL
)
;
CREATE TABLE drug_strength (
drug_concept_id INTEGER NOT NULL,
ingredient_concept_id INTEGER NOT NULL,
amount_value FLOAT NULL,
amount_unit_concept_id INTEGER NULL,
numerator_value FLOAT NULL,
numerator_unit_concept_id INTEGER NULL,
denominator_value FLOAT NULL,
denominator_unit_concept_id INTEGER NULL,
box_size INTEGER NULL,
valid_start_date DATE NOT NULL,
valid_end_date DATE NOT NULL,
invalid_reason VARCHAR(1) NULL
)
;
CREATE TABLE cohort_definition (
cohort_definition_id INTEGER NOT NULL,
cohort_definition_name VARCHAR(255) NOT NULL,
cohort_definition_description VARCHAR(MAX) NULL,
definition_type_concept_id INTEGER NOT NULL,
cohort_definition_syntax VARCHAR(MAX) NULL,
subject_concept_id INTEGER NOT NULL,
cohort_initiation_date DATE NULL
)
;
CREATE TABLE attribute_definition (
attribute_definition_id INTEGER NOT NULL,
attribute_name VARCHAR(255) NOT NULL,
attribute_description VARCHAR(MAX) NULL,
attribute_type_concept_id INTEGER NOT NULL,
attribute_syntax VARCHAR(MAX) NULL
)
;
/**************************
Standardized meta-data
***************************/
CREATE TABLE cdm_source
(
cdm_source_name VARCHAR(255) NOT NULL,
cdm_source_abbreviation VARCHAR(25) NULL,
cdm_holder VARCHAR(255) NULL,
source_description VARCHAR(MAX) NULL,
source_documentation_reference VARCHAR(255) NULL,
cdm_etl_reference VARCHAR(255) NULL,
source_release_date DATE NULL,
cdm_release_date DATE NULL,
cdm_version VARCHAR(10) NULL,
vocabulary_version VARCHAR(20) NULL
)
;
/************************
Standardized clinical data
************************/
CREATE TABLE person
(
person_id INTEGER NOT NULL ,
gender_concept_id INTEGER NOT NULL ,
year_of_birth INTEGER NOT NULL ,
month_of_birth INTEGER NULL,
day_of_birth INTEGER NULL,
time_of_birth VARCHAR(10) NULL,
race_concept_id INTEGER NOT NULL,
ethnicity_concept_id INTEGER NOT NULL,
location_id INTEGER NULL,
provider_id INTEGER NULL,
care_site_id INTEGER NULL,
person_source_value VARCHAR(50) NULL,
gender_source_value VARCHAR(50) NULL,
gender_source_concept_id INTEGER NULL,
race_source_value VARCHAR(50) NULL,
race_source_concept_id INTEGER NULL,
ethnicity_source_value VARCHAR(50) NULL,
ethnicity_source_concept_id INTEGER NULL
)
;
CREATE TABLE observation_period
(
observation_period_id INTEGER NOT NULL ,
person_id INTEGER NOT NULL ,
observation_period_start_date DATE NOT NULL ,
observation_period_end_date DATE NOT NULL ,
period_type_concept_id INTEGER NOT NULL
)
;
CREATE TABLE specimen
(
specimen_id INTEGER NOT NULL ,
person_id INTEGER NOT NULL ,
specimen_concept_id INTEGER NOT NULL ,
specimen_type_concept_id INTEGER NOT NULL ,
specimen_date DATE NOT NULL ,
specimen_time VARCHAR(10) NULL ,
quantity FLOAT NULL ,
unit_concept_id INTEGER NULL ,
anatomic_site_concept_id INTEGER NULL ,
disease_status_concept_id INTEGER NULL ,
specimen_source_id VARCHAR(50) NULL ,
specimen_source_value VARCHAR(50) NULL ,
unit_source_value VARCHAR(50) NULL ,
anatomic_site_source_value VARCHAR(50) NULL ,
disease_status_source_value VARCHAR(50) NULL
)
;
CREATE TABLE death
(
person_id INTEGER NOT NULL ,
death_date DATE NOT NULL ,
death_type_concept_id INTEGER NOT NULL ,
cause_concept_id INTEGER NULL ,
cause_source_value VARCHAR(50) NULL,
cause_source_concept_id INTEGER NULL
)
;
CREATE TABLE visit_occurrence
(
visit_occurrence_id INTEGER NOT NULL ,
person_id INTEGER NOT NULL ,
visit_concept_id INTEGER NOT NULL ,
visit_start_date DATE NOT NULL ,
visit_start_time VARCHAR(10) NULL ,
visit_end_date DATE NOT NULL ,
visit_end_time VARCHAR(10) NULL ,
visit_type_concept_id INTEGER NOT NULL ,
provider_id INTEGER NULL,
care_site_id INTEGER NULL,
visit_source_value VARCHAR(50) NULL,
visit_source_concept_id INTEGER NULL
)
;
CREATE TABLE procedure_occurrence
(
procedure_occurrence_id INTEGER NOT NULL ,
person_id INTEGER NOT NULL ,
procedure_concept_id INTEGER NOT NULL ,
procedure_date DATE NOT NULL ,
procedure_type_concept_id INTEGER NOT NULL ,
modifier_concept_id INTEGER NULL ,
quantity INTEGER NULL ,
provider_id INTEGER NULL ,
visit_occurrence_id INTEGER NULL ,
procedure_source_value VARCHAR(50) NULL ,
procedure_source_concept_id INTEGER NULL ,
qualifier_source_value VARCHAR(50) NULL
)
;
CREATE TABLE drug_exposure
(
drug_exposure_id INTEGER NOT NULL ,
person_id INTEGER NOT NULL ,
drug_concept_id INTEGER NOT NULL ,
drug_exposure_start_date DATE NOT NULL ,
drug_exposure_end_date DATE NULL ,
drug_type_concept_id INTEGER NOT NULL ,
stop_reason VARCHAR(20) NULL ,
refills INTEGER NULL ,
quantity FLOAT NULL ,
days_supply INTEGER NULL ,
sig VARCHAR(MAX) NULL ,
route_concept_id INTEGER NULL ,
effective_drug_dose FLOAT NULL ,
dose_unit_concept_id INTEGER NULL ,
lot_number VARCHAR(50) NULL ,
provider_id INTEGER NULL ,
visit_occurrence_id INTEGER NULL ,
drug_source_value VARCHAR(50) NULL ,
drug_source_concept_id INTEGER NULL ,
route_source_value VARCHAR(50) NULL ,
dose_unit_source_value VARCHAR(50) NULL
)
;
CREATE TABLE device_exposure
(
device_exposure_id INTEGER NOT NULL ,
person_id INTEGER NOT NULL ,
device_concept_id INTEGER NOT NULL ,
device_exposure_start_date DATE NOT NULL ,
device_exposure_end_date DATE NULL ,
device_type_concept_id INTEGER NOT NULL ,
unique_device_id VARCHAR(50) NULL ,
quantity INTEGER NULL ,
provider_id INTEGER NULL ,
visit_occurrence_id INTEGER NULL ,
device_source_value VARCHAR(100) NULL ,
device_source_concept_id INTEGER NULL
)
;
CREATE TABLE condition_occurrence
(
condition_occurrence_id INTEGER NOT NULL ,
person_id INTEGER NOT NULL ,
condition_concept_id INTEGER NOT NULL ,
condition_start_date DATE NOT NULL ,
condition_end_date DATE NULL ,
condition_type_concept_id INTEGER NOT NULL ,
stop_reason VARCHAR(20) NULL ,
provider_id INTEGER NULL ,
visit_occurrence_id INTEGER NULL ,
condition_source_value VARCHAR(50) NULL ,
condition_source_concept_id INTEGER NULL
)
;
CREATE TABLE measurement
(
measurement_id INTEGER NOT NULL ,
person_id INTEGER NOT NULL ,
measurement_concept_id INTEGER NOT NULL ,
measurement_date DATE NOT NULL ,
measurement_time VARCHAR(10) NULL ,
measurement_type_concept_id INTEGER NOT NULL ,
operator_concept_id INTEGER NULL ,
value_as_number FLOAT NULL ,
value_as_concept_id INTEGER NULL ,
unit_concept_id INTEGER NULL ,
range_low FLOAT NULL ,
range_high FLOAT NULL ,
provider_id INTEGER NULL ,
visit_occurrence_id INTEGER NULL ,
measurement_source_value VARCHAR(50) NULL ,
measurement_source_concept_id INTEGER NULL ,
unit_source_value VARCHAR(50) NULL ,
value_source_value VARCHAR(50) NULL
)
;
CREATE TABLE note
(
note_id INTEGER NOT NULL ,
person_id INTEGER NOT NULL ,
note_date DATE NOT NULL ,
note_time VARCHAR(10) NULL ,
note_type_concept_id INTEGER NOT NULL ,
note_text VARCHAR(MAX) NOT NULL ,
provider_id INTEGER NULL ,
visit_occurrence_id INTEGER NULL ,
note_source_value VARCHAR(50) NULL
)
;
CREATE TABLE observation
(
observation_id INTEGER NOT NULL ,
person_id INTEGER NOT NULL ,
observation_concept_id INTEGER NOT NULL ,
observation_date DATE NOT NULL ,
observation_time VARCHAR(10) NULL ,
observation_type_concept_id INTEGER NOT NULL ,
value_as_number FLOAT NULL ,
value_as_string VARCHAR(60) NULL ,
value_as_concept_id INTEGER NULL ,
qualifier_concept_id INTEGER NULL ,
unit_concept_id INTEGER NULL ,
provider_id INTEGER NULL ,
visit_occurrence_id INTEGER NULL ,
observation_source_value VARCHAR(50) NULL ,
observation_source_concept_id INTEGER NULL ,
unit_source_value VARCHAR(50) NULL ,
qualifier_source_value VARCHAR(50) NULL
)
;
CREATE TABLE fact_relationship
(
domain_concept_id_1 INTEGER NOT NULL ,
fact_id_1 INTEGER NOT NULL ,
domain_concept_id_2 INTEGER NOT NULL ,
fact_id_2 INTEGER NOT NULL ,
relationship_concept_id INTEGER NOT NULL
)
;
/************************
Standardized health system data
************************/
CREATE TABLE location
(
location_id INTEGER NOT NULL ,
address_1 VARCHAR(50) NULL ,
address_2 VARCHAR(50) NULL ,
city VARCHAR(50) NULL ,
state VARCHAR(2) NULL ,
zip VARCHAR(9) NULL ,
county VARCHAR(20) NULL ,
location_source_value VARCHAR(50) NULL
)
;
CREATE TABLE care_site
(
care_site_id INTEGER NOT NULL ,
care_site_name VARCHAR(255) NULL ,
place_of_service_concept_id INTEGER NULL ,
location_id INTEGER NULL ,
care_site_source_value VARCHAR(50) NULL ,
place_of_service_source_value VARCHAR(50) NULL
)
;
CREATE TABLE provider
(
provider_id INTEGER NOT NULL ,
provider_name VARCHAR(255) NULL ,
NPI VARCHAR(20) NULL ,
DEA VARCHAR(20) NULL ,
specialty_concept_id INTEGER NULL ,
care_site_id INTEGER NULL ,
year_of_birth INTEGER NULL ,
gender_concept_id INTEGER NULL ,
provider_source_value VARCHAR(50) NULL ,
specialty_source_value VARCHAR(50) NULL ,
specialty_source_concept_id INTEGER NULL ,
gender_source_value VARCHAR(50) NULL ,
gender_source_concept_id INTEGER NULL
)
;
/************************
Standardized health economics
************************/
CREATE TABLE payer_plan_period
(
payer_plan_period_id INTEGER NOT NULL ,
person_id INTEGER NOT NULL ,
payer_plan_period_start_date DATE NOT NULL ,
payer_plan_period_end_date DATE NOT NULL ,
payer_source_value VARCHAR (50) NULL ,
plan_source_value VARCHAR (50) NULL ,
family_source_value VARCHAR (50) NULL
)
;
/* The individual cost tables are being phased out and will disappear
CREATE TABLE visit_cost
(
visit_cost_id INTEGER NOT NULL ,
visit_occurrence_id INTEGER NOT NULL ,
currency_concept_id INTEGER NULL ,
paid_copay FLOAT NULL ,
paid_coinsurance FLOAT NULL ,
paid_toward_deductible FLOAT NULL ,
paid_by_payer FLOAT NULL ,
paid_by_coordination_benefits FLOAT NULL ,
total_out_of_pocket FLOAT NULL ,
total_paid FLOAT NULL ,
payer_plan_period_id INTEGER NULL
)
;
CREATE TABLE procedure_cost
(
procedure_cost_id INTEGER NOT NULL ,
procedure_occurrence_id INTEGER NOT NULL ,
currency_concept_id INTEGER NULL ,
paid_copay FLOAT NULL ,
paid_coinsurance FLOAT NULL ,
paid_toward_deductible FLOAT NULL ,
paid_by_payer FLOAT NULL ,
paid_by_coordination_benefits FLOAT NULL ,
total_out_of_pocket FLOAT NULL ,
total_paid FLOAT NULL ,
revenue_code_concept_id INTEGER NULL ,
payer_plan_period_id INTEGER NULL ,
revenue_code_source_value VARCHAR(50) NULL
)
;
CREATE TABLE drug_cost
(
drug_cost_id INTEGER NOT NULL ,
drug_exposure_id INTEGER NOT NULL ,
currency_concept_id INTEGER NULL ,
paid_copay FLOAT NULL ,
paid_coinsurance FLOAT NULL ,
paid_toward_deductible FLOAT NULL ,
paid_by_payer FLOAT NULL ,
paid_by_coordination_benefits FLOAT NULL ,
total_out_of_pocket FLOAT NULL ,
total_paid FLOAT NULL ,
ingredient_cost FLOAT NULL ,
dispensing_fee FLOAT NULL ,
average_wholesale_price FLOAT NULL ,
payer_plan_period_id INTEGER NULL
)
;
CREATE TABLE device_cost
(
device_cost_id INTEGER NOT NULL ,
device_exposure_id INTEGER NOT NULL ,
currency_concept_id INTEGER NULL ,
paid_copay FLOAT NULL ,
paid_coinsurance FLOAT NULL ,
paid_toward_deductible FLOAT NULL ,
paid_by_payer FLOAT NULL ,
paid_by_coordination_benefits FLOAT NULL ,
total_out_of_pocket FLOAT NULL ,
total_paid FLOAT NULL ,
payer_plan_period_id INTEGER NULL
)
;
*/
CREATE TABLE cost
(
cost_id INTEGER NOT NULL ,
cost_event_id INTEGER NOT NULL ,
cost_domain_id VARCHAR(20) NOT NULL ,
cost_type_concept_id INTEGER NOT NULL ,
currency_concept_id INTEGER NULL ,
total_charge FLOAT NULL ,
total_cost FLOAT NULL ,
total_paid FLOAT NULL ,
paid_by_payer FLOAT NULL ,
paid_by_patient FLOAT NULL ,
paid_patient_copay FLOAT NULL ,
paid_patient_coinsurance FLOAT NULL ,
paid_patient_deductible FLOAT NULL ,
paid_by_primary FLOAT NULL ,
paid_ingredient_cost FLOAT NULL ,
paid_dispensing_fee FLOAT NULL ,
payer_plan_period_id INTEGER NULL ,
amount_allowed FLOAT NULL ,
revenue_code_concept_id INTEGER NULL ,
reveue_code_source_value VARCHAR(50) NULL
)
;
/************************
Standardized derived elements
************************/
CREATE TABLE cohort
(
cohort_definition_id INTEGER NOT NULL ,
subject_id INTEGER NOT NULL ,
cohort_start_date DATE NOT NULL ,
cohort_end_date DATE NOT NULL
)
;
CREATE TABLE cohort_attribute
(
cohort_definition_id INTEGER NOT NULL ,
cohort_start_date DATE NOT NULL ,
cohort_end_date DATE NOT NULL ,
subject_id INTEGER NOT NULL ,
attribute_definition_id INTEGER NOT NULL ,
value_as_number FLOAT NULL ,
value_as_concept_id INTEGER NULL
)
;
CREATE TABLE drug_era
(
drug_era_id INTEGER NOT NULL ,
person_id INTEGER NOT NULL ,
drug_concept_id INTEGER NOT NULL ,
drug_era_start_date DATE NOT NULL ,
drug_era_end_date DATE NOT NULL ,
drug_exposure_count INTEGER NULL ,
gap_days INTEGER NULL
)
;
CREATE TABLE dose_era
(
dose_era_id INTEGER NOT NULL ,
person_id INTEGER NOT NULL ,
drug_concept_id INTEGER NOT NULL ,
unit_concept_id INTEGER NOT NULL ,
dose_value FLOAT NOT NULL ,
dose_era_start_date DATE NOT NULL ,
dose_era_end_date DATE NOT NULL
)
;
CREATE TABLE condition_era
(
condition_era_id INTEGER NOT NULL ,
person_id INTEGER NOT NULL ,
condition_concept_id INTEGER NOT NULL ,
condition_era_start_date DATE NOT NULL ,
condition_era_end_date DATE NOT NULL ,
condition_occurrence_count INTEGER NULL
)
;

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Sql Server/OMOP CDM indexes required - SQL Server.sql
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/*********************************************************************************
# Copyright 2014 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 create the required indexes within OMOP common data model, version 5.0 for SQL Server database
last revised: 12 Oct 2014
author: Patrick Ryan
description: These indices are considered a minimal requirement to ensure adequate performance of analyses.
*************************/
/************************
Standardized vocabulary
************************/
CREATE UNIQUE CLUSTERED INDEX idx_concept_concept_id ON concept (concept_id ASC);
CREATE INDEX idx_concept_code ON concept (concept_code ASC);
CREATE INDEX idx_concept_vocabluary_id ON concept (vocabulary_id ASC);
CREATE INDEX idx_concept_domain_id ON concept (domain_id ASC);
CREATE INDEX idx_concept_class_id ON concept (concept_class_id ASC);
CREATE UNIQUE CLUSTERED INDEX idx_vocabulary_vocabulary_id ON vocabulary (vocabulary_id ASC);
CREATE UNIQUE CLUSTERED INDEX idx_domain_domain_id ON domain (domain_id ASC);
CREATE UNIQUE CLUSTERED INDEX idx_concept_class_class_id ON concept_class (concept_class_id ASC);
CREATE INDEX idx_concept_relationship_id_1 ON concept_relationship (concept_id_1 ASC);
CREATE INDEX idx_concept_relationship_id_2 ON concept_relationship (concept_id_2 ASC);
CREATE INDEX idx_concept_relationship_id_3 ON concept_relationship (relationship_id ASC);
CREATE UNIQUE CLUSTERED INDEX idx_relationship_rel_id ON relationship (relationship_id ASC);
CREATE CLUSTERED INDEX idx_concept_synonym_id ON concept_synonym (concept_id ASC);
CREATE CLUSTERED INDEX idx_concept_ancestor_id_1 ON concept_ancestor (ancestor_concept_id ASC);
CREATE INDEX idx_concept_ancestor_id_2 ON concept_ancestor (descendant_concept_id ASC);
CREATE CLUSTERED INDEX idx_source_to_concept_map_id_3 ON source_to_concept_map (target_concept_id ASC);
CREATE INDEX idx_source_to_concept_map_id_1 ON source_to_concept_map (source_vocabulary_id ASC);
CREATE INDEX idx_source_to_concept_map_id_2 ON source_to_concept_map (target_vocabulary_id ASC);
CREATE INDEX idx_source_to_concept_map_code ON source_to_concept_map (source_code ASC);
CREATE CLUSTERED INDEX idx_drug_strength_id_1 ON drug_strength (drug_concept_id ASC);
CREATE INDEX idx_drug_strength_id_2 ON drug_strength (ingredient_concept_id ASC);
CREATE CLUSTERED INDEX idx_cohort_definition_id ON cohort_definition (cohort_definition_id ASC);
CREATE CLUSTERED INDEX idx_attribute_definition_id ON attribute_definition (attribute_definition_id ASC);
/**************************
Standardized meta-data
***************************/
/************************
Standardized clinical data
************************/
CREATE UNIQUE CLUSTERED INDEX idx_person_id ON person (person_id ASC);
CREATE CLUSTERED INDEX idx_observation_period_id ON observation_period (person_id ASC);
CREATE CLUSTERED INDEX idx_specimen_person_id ON specimen (person_id ASC);
CREATE INDEX idx_specimen_concept_id ON specimen (specimen_concept_id ASC);
CREATE CLUSTERED INDEX idx_death_person_id ON death (person_id ASC);
CREATE CLUSTERED INDEX idx_visit_person_id ON visit_occurrence (person_id ASC);
CREATE INDEX idx_visit_concept_id ON visit_occurrence (visit_concept_id ASC);
CREATE CLUSTERED INDEX idx_procedure_person_id ON procedure_occurrence (person_id ASC);
CREATE INDEX idx_procedure_concept_id ON procedure_occurrence (procedure_concept_id ASC);
CREATE INDEX idx_procedure_visit_id ON procedure_occurrence (visit_occurrence_id ASC);
CREATE CLUSTERED INDEX idx_drug_person_id ON drug_exposure (person_id ASC);
CREATE INDEX idx_drug_concept_id ON drug_exposure (drug_concept_id ASC);
CREATE INDEX idx_drug_visit_id ON drug_exposure (visit_occurrence_id ASC);
CREATE CLUSTERED INDEX idx_device_person_id ON device_exposure (person_id ASC);
CREATE INDEX idx_device_concept_id ON device_exposure (device_concept_id ASC);
CREATE INDEX idx_device_visit_id ON device_exposure (visit_occurrence_id ASC);
CREATE CLUSTERED INDEX idx_condition_person_id ON condition_occurrence (person_id ASC);
CREATE INDEX idx_condition_concept_id ON condition_occurrence (condition_concept_id ASC);
CREATE INDEX idx_condition_visit_id ON condition_occurrence (visit_occurrence_id ASC);
CREATE CLUSTERED INDEX idx_measurement_person_id ON measurement (person_id ASC);
CREATE INDEX idx_measurement_concept_id ON measurement (measurement_concept_id ASC);
CREATE INDEX idx_measurement_visit_id ON measurement (visit_occurrence_id ASC);
CREATE CLUSTERED INDEX idx_note_person_id ON note (person_id ASC);
CREATE INDEX idx_note_concept_id ON note (note_type_concept_id ASC);
CREATE INDEX idx_note_visit_id ON note (visit_occurrence_id ASC);
CREATE CLUSTERED INDEX idx_observation_person_id ON observation (person_id ASC);
CREATE INDEX idx_observation_concept_id ON observation (observation_concept_id ASC);
CREATE INDEX idx_observation_visit_id ON observation (visit_occurrence_id ASC);
CREATE INDEX idx_fact_relationship_id_1 ON fact_relationship (domain_concept_id_1 ASC);
CREATE INDEX idx_fact_relationship_id_2 ON fact_relationship (domain_concept_id_2 ASC);
CREATE INDEX idx_fact_relationship_id_3 ON fact_relationship (relationship_concept_id ASC);
/************************
Standardized health system data
************************/
/************************
Standardized health economics
************************/
CREATE CLUSTERED INDEX idx_period_person_id ON payer_plan_period (person_id ASC);
/************************
Standardized derived elements
************************/
CREATE INDEX idx_cohort_subject_id ON cohort (subject_id ASC);
CREATE INDEX idx_cohort_c_definition_id ON cohort (cohort_definition_id ASC);
CREATE INDEX idx_ca_subject_id ON cohort_attribute (subject_id ASC);
CREATE INDEX idx_ca_definition_id ON cohort_attribute (cohort_definition_id ASC);
CREATE CLUSTERED INDEX idx_drug_era_person_id ON drug_era (person_id ASC);
CREATE INDEX idx_drug_era_concept_id ON drug_era (drug_concept_id ASC);
CREATE CLUSTERED INDEX idx_dose_era_person_id ON dose_era (person_id ASC);
CREATE INDEX idx_dose_era_concept_id ON dose_era (drug_concept_id ASC);
CREATE CLUSTERED INDEX idx_condition_era_person_id ON condition_era (person_id ASC);
CREATE INDEX idx_condition_era_concept_id ON condition_era (condition_concept_id ASC);

18
Sql Server/README.md
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Common-Data-Model / SQL Server
=================
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:
1. Create an empty schema.
2. Execute the script `OMOP CDM ddl - SQL Server.sql` to create the tables and fields.
3. Load your data into the schema.
4. Execute the script `OMOP CDM constraints - SQL Server.sql` to add the constraints (primary and foreign keys).
5. Execute the script `OMOP CDM indexes required - SQL Server.sql` to add the minimum set of indexes we recommend.
Note: you could also apply the constraints and/or the indexes before loading the data, but this will slow down the insertion of the data considerably.

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Sql Server/VocabImport/OMOP CDM vocabulary load - SQL Server.sql
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/*********************************************************************************
# Copyright 2014 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 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
*************************/
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
);

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Version4/Oracle/CDM V4 DDL.sql
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@ -1,310 +0,0 @@
/*********************************************************************************
# 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 5.0 for Oracle database
last revised: 1 Mar 2015
author: Christian Reich
*************************/
CREATE TABLE concept
(
concept_id INTEGER NOT NULL,
concept_name VARCHAR2(256 BYTE) NOT NULL,
concept_level NUMBER NOT NULL,
concept_class VARCHAR2(60 BYTE) NOT NULL,
vocabulary_id INTEGER NOT NULL,
concept_code VARCHAR2(40 BYTE) NOT NULL,
valid_start_date DATE NOT NULL,
valid_end_date DATE DEFAULT '31-Dec-2099' NOT NULL,
invalid_reason CHAR(1 BYTE)
) NOLOGGING;
COMMENT ON TABLE concept IS 'A list of all valid terminology concepts across domains and their attributes. Concepts are derived from existing standards.';
COMMENT ON COLUMN concept.concept_id IS 'A system-generated identifier to uniquely identify each concept across all concept types.';
COMMENT ON COLUMN concept.concept_name IS 'An unambiguous, meaningful and descriptive name for the concept.';
COMMENT ON COLUMN concept.concept_level IS 'The level of hierarchy associated with the concept. Different concept levels are assigned to concepts to depict their seniority in a clearly defined hierarchy, such as drugs, conditions, etc. A concept level of 0 is assigned to concepts that are not part of a standard vocabulary, but are part of the vocabulary for reference purposes (e.g. drug form).';
COMMENT ON COLUMN concept.concept_class IS 'The category or class of the concept along both the hierarchical tree as well as different domains within a vocabulary. Examples are ''Clinical Drug'', ''Ingredient'', ''Clinical Finding'' etc.';
COMMENT ON COLUMN concept.vocabulary_id IS 'A foreign key to the vocabulary table indicating from which source the concept has been adapted.';
COMMENT ON COLUMN concept.concept_code IS 'The concept code represents the identifier of the concept in the source data it originates from, such as SNOMED-CT concept IDs, RxNorm RXCUIs etc. Note that concept codes are not unique across vocabularies.';
COMMENT ON COLUMN concept.valid_start_date IS 'The date when the was first recorded.';
COMMENT ON COLUMN concept.valid_end_date IS 'The date when the concept became invalid because it was deleted or superseded (updated) by a new concept. The default value is 31-Dec-2099.';
COMMENT ON COLUMN concept.invalid_reason IS 'Concepts that are replaced with a new concept are designated "Updated" (U) and concepts that are removed without replacement are "Deprecated" (D).';
CREATE INDEX concept_code ON concept (concept_code, vocabulary_id);
CREATE UNIQUE INDEX XPKconcept ON concept (concept_id);
ALTER TABLE concept ADD (
CHECK ( invalid_reason IN ('D', 'U'))
ENABLE VALIDATE,
CONSTRAINT XPKCONCEPT
PRIMARY KEY
(concept_id)
USING INDEX XPKCONCEPT
ENABLE VALIDATE);
--add table RELATIONSHIP
CREATE TABLE relationship
(
relationship_id INTEGER NOT NULL,
relationship_name VARCHAR2(256 BYTE) NOT NULL,
is_hierarchical INTEGER NOT NULL,
defines_ancestry INTEGER DEFAULT 1 NOT NULL,
reverse_relationship INTEGER
) NOLOGGING;
COMMENT ON TABLE relationship IS 'A list of relationship between concepts. Some of these relationships are generic (e.g. "Subsumes" relationship), others are domain-specific.';
COMMENT ON COLUMN relationship.relationship_id IS 'The type of relationship captured by the relationship record.';
COMMENT ON COLUMN relationship.relationship_name IS 'The text that describes the relationship type.';
COMMENT ON COLUMN relationship.is_hierarchical IS 'Defines whether a relationship defines concepts into classes or hierarchies. Values are Y for hierarchical relationship or NULL if not';
COMMENT ON COLUMN relationship.defines_ancestry IS 'Defines whether a hierarchical relationship contributes to the concept_ancestor table. These are subsets of the hierarchical relationships. Valid values are Y or NULL.';
COMMENT ON COLUMN relationship.reverse_relationship IS 'relationship ID of the reverse relationship to this one. Corresponding records of reverse relationships have their concept_id_1 and concept_id_2 swapped.';
CREATE UNIQUE INDEX XPKRELATIONHIP_TYPE ON relationship
(relationship_id);
ALTER TABLE relationship ADD (
CONSTRAINT xpkrelationship_type
PRIMARY KEY
(relationship_id)
USING INDEX xpkrelationship_type
ENABLE VALIDATE);
--add table concept_relationship
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 DEFAULT '31-Dec-2099' NOT NULL,
invalid_reason CHAR(1 BYTE)
) NOLOGGING;
COMMENT ON TABLE concept_relationship IS 'A list of relationship between concepts. Some of these relationships are generic (e.g. ''Subsumes'' relationship), others are domain-specific.';
COMMENT ON COLUMN concept_relationship.concept_id_1 IS 'A foreign key to the concept in the concept table associated with the relationship. relationships are directional, and this field represents the source concept designation.';
COMMENT ON COLUMN concept_relationship.concept_id_2 IS 'A foreign key to the concept in the concept table associated with the relationship. relationships are directional, and this field represents the destination concept designation.';
COMMENT ON COLUMN concept_relationship.relationship_id IS 'The type of relationship as defined in the relationship table.';
COMMENT ON COLUMN concept_relationship.valid_start_date IS 'The date when the the relationship was first recorded.';
COMMENT ON COLUMN concept_relationship.valid_end_date IS 'The date when the relationship became invalid because it was deleted or superseded (updated) by a new relationship. Default value is 31-Dec-2099.';
COMMENT ON COLUMN concept_relationship.invalid_reason IS 'Reason the relationship was invalidated. Possible values are D (deleted), U (replaced with an update) or NULL when valid_end_date has the default value.';
CREATE UNIQUE INDEX xpkconcept_relationship ON concept_relationship
(concept_id_1, concept_id_2, relationship_id);
ALTER TABLE concept_relationship ADD (
CHECK ( invalid_reason IN ('D', 'U'))
ENABLE VALIDATE,
CHECK ( invalid_reason IN ('D', 'U'))
ENABLE VALIDATE,
CHECK (invalid_reason in ('D', 'U'))
ENABLE VALIDATE,
CONSTRAINT xpkconcept_relationship
PRIMARY KEY
(concept_id_1, concept_id_2, relationship_id)
USING INDEX xpkconcept_relationship
ENABLE VALIDATE);
ALTER TABLE concept_relationship ADD (
CONSTRAINT concept_REL_CHILD_FK
FOREIGN KEY (concept_id_2)
REFERENCES concept (concept_id)
ENABLE VALIDATE,
CONSTRAINT concept_REL_PARENT_FK
FOREIGN KEY (concept_id_1)
REFERENCES concept (concept_id)
ENABLE VALIDATE,
CONSTRAINT concept_REL_REL_type_FK
FOREIGN KEY (relationship_id)
REFERENCES relationship (relationship_id)
ENABLE VALIDATE);
--add table concept_ancestor
CREATE TABLE concept_ancestor
(
ancestor_concept_id INTEGER NOT NULL,
descendant_concept_id INTEGER NOT NULL,
max_levels_of_separation NUMBER,
min_levels_of_separation NUMBER
) NOLOGGING;
COMMENT ON TABLE concept_ancestor IS 'A specialized table containing only hierarchical relationship between concepts that may span several generations.';
COMMENT ON COLUMN concept_ancestor.ancestor_concept_id IS 'A foreign key to the concept code in the concept table for the higher-level concept that forms the ancestor in the relationship.';
COMMENT ON COLUMN concept_ancestor.descendant_concept_id IS 'A foreign key to the concept code in the concept table for the lower-level concept that forms the descendant in the relationship.';
COMMENT ON COLUMN concept_ancestor.max_levels_of_separation IS 'The maximum separation in number of levels of hierarchy between ancestor and descendant concepts. This is an optional attribute that is used to simplify hierarchic analysis. ';
COMMENT ON COLUMN concept_ancestor.min_levels_of_separation IS 'The minimum separation in number of levels of hierarchy between ancestor and descendant concepts. This is an optional attribute that is used to simplify hierarchic analysis.';
CREATE UNIQUE INDEX xpkconcept_ancestor ON concept_ancestor
(ancestor_concept_id, descendant_concept_id);
ALTER TABLE concept_ancestor ADD (
CONSTRAINT xpkconcept_ancestor
PRIMARY KEY
(ancestor_concept_id, descendant_concept_id)
USING INDEX xpkconcept_ancestor
ENABLE VALIDATE);
ALTER TABLE concept_ancestor ADD (
CONSTRAINT concept_ancestor_FK
FOREIGN KEY (ancestor_concept_id)
REFERENCES concept (concept_id)
ENABLE VALIDATE,
CONSTRAINT concept_descendant_FK
FOREIGN KEY (descendant_concept_id)
REFERENCES concept (concept_id)
ENABLE VALIDATE);
--add table concept_synonym
CREATE TABLE concept_synonym
(
concept_synonym_id INTEGER NOT NULL,
concept_id INTEGER NOT NULL,
concept_synonym_name VARCHAR2(1000 BYTE) NOT NULL
) NOLOGGING;
COMMENT ON TABLE concept_synonym IS 'A table with synonyms for concepts that have more than one valid name or description.';
COMMENT ON COLUMN concept_synonym.concept_synonym_id IS 'A system-generated unique identifier for each concept synonym.';
COMMENT ON COLUMN concept_synonym.concept_id IS 'A foreign key to the concept in the concept table. ';
COMMENT ON COLUMN concept_synonym.concept_synonym_name IS 'The alternative name for the concept.';
CREATE UNIQUE INDEX xpkconcept_synonym ON concept_synonym
(concept_synonym_id);
ALTER TABLE concept_synonym ADD (
CONSTRAINT xpkconcept_synonym
PRIMARY KEY
(concept_synonym_id)
USING INDEX xpkconcept_synonym
ENABLE VALIDATE);
ALTER TABLE concept_synonym ADD (
CONSTRAINT concept_synonym_concept_FK
FOREIGN KEY (concept_id)
REFERENCES concept (concept_id)
ENABLE VALIDATE);
--add table source_to_concept_map
CREATE TABLE source_to_concept_map
(
source_code VARCHAR2(40 BYTE) NOT NULL,
source_vocabulary_id INTEGER NOT NULL,
source_code_description VARCHAR2(256 BYTE),
target_concept_id INTEGER NOT NULL,
target_vocabulary_id INTEGER NOT NULL,
mapping_type VARCHAR2(256 BYTE),
primary_map CHAR(1 BYTE),
valid_start_date DATE NOT NULL,
valid_end_date DATE NOT NULL,
invalid_reason CHAR(1 BYTE)
) NOLOGGING;
CREATE INDEX SOURCE_TO_concept_SOURCE_idX ON source_to_concept_map
(SOURCE_CODE);
CREATE UNIQUE INDEX xpksource_to_concept_map ON source_to_concept_map
(SOURCE_vocabulary_id, TARGET_concept_id, SOURCE_CODE, valid_end_date);
ALTER TABLE source_to_concept_map ADD (
CHECK (primary_map in ('Y'))
ENABLE VALIDATE,
CHECK (invalid_reason in ('D', 'U'))
ENABLE VALIDATE,
CONSTRAINT xpksource_to_concept_map
PRIMARY KEY
(SOURCE_vocabulary_id, TARGET_concept_id, SOURCE_CODE, valid_end_date)
USING INDEX xpksource_to_concept_map
ENABLE VALIDATE);
ALTER TABLE source_to_concept_map ADD (
CONSTRAINT SOURCE_TO_concept_concept
FOREIGN KEY (TARGET_concept_id)
REFERENCES concept (concept_id)
ENABLE VALIDATE);
--add table drug_strength
CREATE TABLE drug_strength
(
drug_concept_id INTEGER NOT NULL,
ingredient_concept_id INTEGER NOT NULL,
amount_value NUMBER,
amount_unit VARCHAR2 (60 BYTE),
concentration_value NUMBER,
concentration_enum_unit VARCHAR2 (60 BYTE),
concentration_denom_unit VARCHAR2 (60 BYTE),
valid_start_date DATE NOT NULL,
valid_end_date DATE NOT NULL,
invalid_reason VARCHAR2 (1 BYTE)
);
--add table vocabulary
CREATE TABLE VOCABULARY
(
VOCABULARY_ID INTEGER NOT NULL,
VOCABULARY_NAME VARCHAR2 (256 BYTE) NOT NULL
);

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Common-Data-Model / Oracle
=================
This folder contains the SQL scripts for Oracle.
In order to create your instantiation of the Common Data Model, we recommend following these steps:
1. Create an empty schema.
2. Execute the script `CDM V4 ddl.sql` to create the tables and fields.
3. Load your data into the schema using the loading scripts in VocabImport
Note: you could also apply the constraints and the indexes after loading the data, this will speed up the insertion of the data considerably.

51
Version4/Oracle/VocabImport/OMOP CDM vocabulary load - Oracle.bat
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@ -1,51 +0,0 @@
/*********************************************************************************
# 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

18
Version4/Oracle/VocabImport/concept.ctl
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@ -1,18 +0,0 @@
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
)

13
Version4/Oracle/VocabImport/concept_ancestor.ctl
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@ -1,13 +0,0 @@
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
)

15
Version4/Oracle/VocabImport/concept_relationship.ctl
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@ -1,15 +0,0 @@
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
)

12
Version4/Oracle/VocabImport/concept_synonym.ctl
View File

@ -1,12 +0,0 @@
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)
)

19
Version4/Oracle/VocabImport/drug_strength.ctl
View File

@ -1,19 +0,0 @@
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
)

14
Version4/Oracle/VocabImport/relationship.ctl
View File

@ -1,14 +0,0 @@
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
)

19
Version4/Oracle/VocabImport/source_to_concept_map.ctl
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@ -1,19 +0,0 @@
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
)

11
Version4/Oracle/VocabImport/vocabulary.ctl
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@ -1,11 +0,0 @@
options (skip=1)
load data
infile vocabulary.csv
into table vocabulary
replace
fields terminated by '\t'
trailing nullcols
(
vocabulary_id,
vocabulary_name
)

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@ -1,131 +0,0 @@
/*********************************************************************************
# 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
)
;

13
Version4/PostgreSQL/README.md
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@ -1,13 +0,0 @@
Common-Data-Model / PostgreSQL
=================
This folder contains the SQL scripts for PostgreSQL.
In order to create your instantiation of the Common Data Model, we recommend following these steps:
1. Create an empty schema.
2. Execute the script `CDM V4 ddl.sql` to create the tables and fields.
3. Load your data into the schema.

54
Version4/PostgreSQL/VocabImport/OMOP CDM vocabulary load - PostgreSQL.sql
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@ -1,54 +0,0 @@
/*********************************************************************************
# 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
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@ -1,117 +0,0 @@
/*********************************************************************************
# 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
);

14
Version4/SQL Server/README.md
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@ -1,14 +0,0 @@
Common-Data-Model / SQL Server
=================
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:
1. Create an empty schema.
2. Execute the script `CDM V4 ddl.sql` to create the tables and fields.
3. Load your data into the schema using the loading scripts in VocabImport
Note: you could also apply the constraints and the indexes after loading the data, this will speed up the insertion of the data considerably.

130
Version4/SQL Server/VocabImport/OMOP CDM vocabulary load - SQL Server.sql
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@ -1,130 +0,0 @@
/*********************************************************************************
# 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
);