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OMOP
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OMOP/MySQL/OMOP CDM ddl - MySQL.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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script to create OMOP common data model, version 5.0 for MySQL database
last revised: 03 Mar 2015
original author: Patrick Ryan
modified by Colin Erdman for MySQL;
*************************/
/************************
Standardized vocabulary
************************/
CREATE TABLE concept (
concept_id INT(11) 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 INT(11) NOT NULL
);
CREATE TABLE domain (
domain_id VARCHAR(20) NOT NULL,
domain_name VARCHAR(255) NOT NULL,
domain_concept_id INT(11) NOT NULL
);
CREATE TABLE concept_class (
concept_class_id VARCHAR(20) NOT NULL,
concept_class_name VARCHAR(255) NOT NULL,
concept_class_concept_id INT(11) NOT NULL
);
CREATE TABLE concept_relationship (
concept_id_1 INT(11) NOT NULL,
concept_id_2 INT(11) 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 INT(11) NOT NULL
);
CREATE TABLE concept_synonym (
concept_id INT(11) NOT NULL,
concept_synonym_name VARCHAR(1000) NOT NULL,
language_concept_id INT(11) NOT NULL
);
CREATE TABLE concept_ancestor (
ancestor_concept_id INT(11) NOT NULL,
descendant_concept_id INT(11) NOT NULL,
min_levels_of_separation INT(11) NOT NULL,
max_levels_of_separation INT(11) NOT NULL
);
CREATE TABLE source_to_concept_map (
source_code VARCHAR(50) NOT NULL,
source_concept_id INT(11) NOT NULL,
source_vocabulary_id VARCHAR(20) NOT NULL,
source_code_description VARCHAR(255) NULL,
target_concept_id INT(11) 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 INT(11) NOT NULL,
ingredient_concept_id INT(11) NOT NULL,
amount_value NUMERIC NULL,
amount_unit_concept_id INT(11) NULL,
numerator_value NUMERIC NULL,
numerator_unit_concept_id INT(11) NULL,
denominator_unit_concept_id INT(11) 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 INT(11) NOT NULL,
cohort_definition_name VARCHAR(255) NOT NULL,
cohort_definition_description TEXT NULL,
definition_type_concept_id INT(11) NOT NULL,
cohort_definition_syntax TEXT NULL,
subject_concept_id INT(11) NOT NULL,
cohort_initiation_date DATE NULL
)
;
CREATE TABLE attribute_definition (
attribute_definition_id INT(11) NOT NULL,
attribute_name VARCHAR(255) NOT NULL,
attribute_description TEXT NULL,
attribute_type_concept_id INT(11) 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 INT(11) NOT NULL ,
gender_concept_id INT(11) NOT NULL ,
year_of_birth INT(11) NOT NULL ,
month_of_birth INT(11) NULL,
day_of_birth INT(11) NULL,
time_of_birth VARCHAR(10) NULL,
race_concept_id INT(11) NOT NULL,
ethnicity_concept_id INT(11) NOT NULL,
location_id INT(11) NULL,
provider_id INT(11) NULL,
care_site_id INT(11) NULL,
person_source_value VARCHAR(50) NULL,
gender_source_value VARCHAR(50) NULL,
gender_source_concept_id INT(11) NULL,
race_source_value VARCHAR(50) NULL,
race_source_concept_id INT(11) NULL,
ethnicity_source_value VARCHAR(50) NULL,
ethnicity_source_concept_id INT(11) NULL
)
;
CREATE TABLE observation_period
(
observation_period_id INT(11) NOT NULL ,
person_id INT(11) NOT NULL ,
observation_period_start_date DATE NOT NULL ,
observation_period_end_date DATE NOT NULL ,
period_type_concept_id INT(11) NOT NULL
)
;
CREATE TABLE specimen
(
specimen_id INT(11) NOT NULL ,
person_id INT(11) NOT NULL ,
specimen_concept_id INT(11) NOT NULL ,
specimen_type_concept_id INT(11) NOT NULL ,
specimen_date DATE NOT NULL ,
specimen_time VARCHAR(10) NULL ,
quantity NUMERIC NULL ,
unit_concept_id INT(11) NULL ,
anatomic_site_concept_id INT(11) NULL ,
disease_status_concept_id INT(11) 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 INT(11) NOT NULL ,
death_date DATE NOT NULL ,
death_type_concept_id INT(11) NOT NULL ,
cause_concept_id INT(11) NULL ,
cause_source_value VARCHAR(50) NULL,
cause_source_concept_id INT(11) NULL
)
;
CREATE TABLE visit_occurrence
(
visit_occurrence_id INT(11) NOT NULL ,
person_id INT(11) NOT NULL ,
visit_concept_id INT(11) 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 INT(11) NOT NULL ,
provider_id INT(11) NULL,
care_site_id INT(11) NULL,
visit_source_value VARCHAR(50) NULL,
visit_source_concept_id INT(11) NULL
)
;
CREATE TABLE procedure_occurrence
(
procedure_occurrence_id INT(11) NOT NULL ,
person_id INT(11) NOT NULL ,
procedure_concept_id INT(11) NOT NULL ,
procedure_date DATE NOT NULL ,
procedure_type_concept_id INT(11) NOT NULL ,
modifier_concept_id INT(11) NULL ,
quantity INT(11) NULL ,
provider_id INT(11) NULL ,
visit_occurrence_id INT(11) NULL ,
procedure_source_value VARCHAR(50) NULL ,
procedure_source_concept_id INT(11) NULL ,
qualifier_source_value VARCHAR(50) NULL
)
;
CREATE TABLE drug_exposure
(
drug_exposure_id INT(11) NOT NULL ,
person_id INT(11) NOT NULL ,
drug_concept_id INT(11) NOT NULL ,
drug_exposure_start_date DATE NOT NULL ,
drug_exposure_end_date DATE NULL ,
drug_type_concept_id INT(11) NOT NULL ,
stop_reason VARCHAR(20) NULL ,
refills INT(11) NULL ,
quantity NUMERIC NULL ,
days_supply INT(11) NULL ,
sig TEXT NULL ,
route_concept_id INT(11) NULL ,
effective_drug_dose NUMERIC NULL ,
dose_unit_concept_id INT(11) NULL ,
lot_number VARCHAR(50) NULL ,
provider_id INT(11) NULL ,
visit_occurrence_id INT(11) NULL ,
drug_source_value VARCHAR(50) NULL ,
drug_source_concept_id INT(11) NULL ,
route_source_value VARCHAR(50) NULL ,
dose_unit_source_value VARCHAR(50) NULL
)
;
CREATE TABLE device_exposure
(
device_exposure_id INT(11) NOT NULL ,
person_id INT(11) NOT NULL ,
device_concept_id INT(11) NOT NULL ,
device_exposure_start_date DATE NOT NULL ,
device_exposure_end_date DATE NULL ,
device_type_concept_id INT(11) NOT NULL ,
unique_device_id VARCHAR(50) NULL ,
quantity INT(11) NULL ,
provider_id INT(11) NULL ,
visit_occurrence_id INT(11) NULL ,
device_source_value VARCHAR(100) NULL ,
device_source_concept_id INT(11) NULL
)
;
CREATE TABLE condition_occurrence
(
condition_occurrence_id INT(11) NOT NULL ,
person_id INT(11) NOT NULL ,
condition_concept_id INT(11) NOT NULL ,
condition_start_date DATE NOT NULL ,
condition_end_date DATE NULL ,
condition_type_concept_id INT(11) NOT NULL ,
stop_reason VARCHAR(20) NULL ,
provider_id INT(11) NULL ,
visit_occurrence_id INT(11) NULL ,
condition_source_value VARCHAR(50) NULL ,
condition_source_concept_id INT(11) NULL
)
;
CREATE TABLE measurement
(
measurement_id INT(11) NOT NULL ,
person_id INT(11) NOT NULL ,
measurement_concept_id INT(11) NOT NULL ,
measurement_date DATE NOT NULL ,
measurement_time VARCHAR(10) NULL ,
measurement_type_concept_id INT(11) NOT NULL ,
operator_concept_id INT(11) NULL ,
value_as_number NUMERIC NULL ,
value_as_concept_id INT(11) NULL ,
unit_concept_id INT(11) NULL ,
range_low NUMERIC NULL ,
range_high NUMERIC NULL ,
provider_id INT(11) NULL ,
visit_occurrence_id INT(11) NULL ,
measurement_source_value VARCHAR(50) NULL ,
measurement_source_concept_id INT(11) NULL ,
unit_source_value VARCHAR(50) NULL ,
value_source_value VARCHAR(50) NULL
)
;
CREATE TABLE note
(
note_id INT(11) NOT NULL ,
person_id INT(11) NOT NULL ,
note_date DATE NOT NULL ,
note_time VARCHAR(10) NULL ,
note_type_concept_id INT(11) NOT NULL ,
note_text TEXT NOT NULL ,
provider_id INT(11) NULL ,
visit_occurrence_id INT(11) NULL ,
note_source_value VARCHAR(50) NULL
)
;
CREATE TABLE observation
(
observation_id INT(11) NOT NULL ,
person_id INT(11) NOT NULL ,
observation_concept_id INT(11) NOT NULL ,
observation_date DATE NOT NULL ,
observation_time VARCHAR(10) NULL ,
observation_type_concept_id INT(11) NOT NULL ,
value_as_number NUMERIC NULL ,
value_as_string VARCHAR(60) NULL ,
value_as_concept_id INT(11) NULL ,
qualifier_concept_id INT(11) NULL ,
unit_concept_id INT(11) NULL ,
provider_id INT(11) NULL ,
visit_occurrence_id INT(11) NULL ,
observation_source_value VARCHAR(50) NULL ,
observation_source_concept_id INT(11) NULL ,
unit_source_value VARCHAR(50) NULL ,
qualifier_source_value VARCHAR(50) NULL
)
;
CREATE TABLE fact_relationship
(
domain_concept_id_1 INT(11) NOT NULL ,
fact_id_1 INT(11) NOT NULL ,
domain_concept_id_2 INT(11) NOT NULL ,
fact_id_2 INT(11) NOT NULL ,
relationship_concept_id INT(11) NOT NULL
)
;
/************************
Standardized health system data
************************/
CREATE TABLE location
(
location_id INT(11) 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 INT(11) NOT NULL ,
care_site_name VARCHAR(255) NULL ,
place_of_service_concept_id INT(11) NULL ,
location_id INT(11) NULL ,
care_site_source_value VARCHAR(50) NULL ,
place_of_service_source_value VARCHAR(50) NULL
)
;
CREATE TABLE provider
(
provider_id INT(11) NOT NULL ,
provider_name VARCHAR(255) NULL ,
NPI VARCHAR(20) NULL ,
DEA VARCHAR(20) NULL ,
specialty_concept_id INT(11) NULL ,
care_site_id INT(11) NULL ,
year_of_birth INT(11) NULL ,
gender_concept_id INT(11) NULL ,
provider_source_value VARCHAR(50) NULL ,
specialty_source_value VARCHAR(50) NULL ,
specialty_source_concept_id INT(11) NULL ,
gender_source_value VARCHAR(50) NULL ,
gender_source_concept_id INT(11) NULL
)
;
/************************
Standardized health economics
************************/
CREATE TABLE payer_plan_period
(
payer_plan_period_id INT(11) NOT NULL ,
person_id INT(11) 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
)
;
CREATE TABLE visit_cost
(
visit_cost_id INT(11) NOT NULL ,
visit_occurrence_id INT(11) NOT NULL ,
currency_concept_id INT(11) 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 INT(11) NULL
)
;
CREATE TABLE procedure_cost
(
procedure_cost_id INT(11) NOT NULL ,
procedure_occurrence_id INT(11) NOT NULL ,
currency_concept_id INT(11) 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 INT(11) NULL ,
payer_plan_period_id INT(11) NULL ,
revenue_code_source_value VARCHAR(50) NULL
)
;
CREATE TABLE drug_cost
(
drug_cost_id INT(11) NOT NULL ,
drug_exposure_id INT(11) NOT NULL ,
currency_concept_id INT(11) 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 INT(11) NULL
)
;
CREATE TABLE device_cost
(
device_cost_id INT(11) NOT NULL ,
device_exposure_id INT(11) NOT NULL ,
currency_concept_id INT(11) 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 INT(11) NULL
)
;
/************************
Standardized derived elements
************************/
CREATE TABLE cohort
(
cohort_definition_id INT(11) NOT NULL ,
subject_id INT(11) NOT NULL ,
cohort_start_date DATE NOT NULL ,
cohort_end_date DATE NOT NULL
)
;
CREATE TABLE cohort_attribute
(
cohort_definition_id INT(11) NOT NULL ,
cohort_start_date DATE NOT NULL ,
cohort_end_date DATE NOT NULL ,
subject_id INT(11) NOT NULL ,
attribute_definition_id INT(11) NOT NULL ,
value_as_number NUMERIC NULL ,
value_as_concept_id INT(11) NULL
)
;
CREATE TABLE drug_era
(
drug_era_id INT(11) NOT NULL ,
person_id INT(11) NOT NULL ,
drug_concept_id INT(11) NOT NULL ,
drug_era_start_date DATE NOT NULL ,
drug_era_end_date DATE NOT NULL ,
drug_exposure_count INT(11) NULL ,
gap_days INT(11) NULL
)
;
CREATE TABLE dose_era
(
dose_era_id INT(11) NOT NULL ,
person_id INT(11) NOT NULL ,
drug_concept_id INT(11) NOT NULL ,
unit_concept_id INT(11) 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 INT(11) NOT NULL ,
person_id INT(11) NOT NULL ,
condition_concept_id INT(11) NOT NULL ,
condition_era_start_date DATE NOT NULL ,
condition_era_end_date DATE NOT NULL ,
condition_occurrence_count INT(11) NULL
)
;
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