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Merge pull request #87 from alondhe/master 

Added Amazon Redshift DDL
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clairblacketer 2017-07-27 14:06:58 -04:00 committed by GitHub
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5
README.md
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This version is **backwards compatibile with v5.0.1**.
---------
This repo contains the definition of the OMOP Common Data Model. It supports the 4 SQL technologies: Impala, Oracle, Postgres, SQL Server and Redshift. For each, the DDL, constraints and indexes (if appropriate) are defined.
This repo contains the definition of the OMOP Common Data Model. It supports the 5 SQL technologies: Impala, Oracle, Postgres, Redshift, and SQL Server. For each, the DDL, constraints and indexes (if appropriate) are defined.
Versions are defined using tagging and versioning. Full versions (V6, 7 etc.) are released each year (1-Jan) and are not backwards compatible. Minor versions (V5.1, 5.2 etc.) are released each quarter (1-Apr, 1-Jul and 1-Sep) and are not guaranteed to be backwards compatible though an effort is made to make sure that current queries will not break. Micro versions (V5.1.1, V5.1.2 etc.) are released irregularly and often, and contain small hot fixes or backward compatible changes to the last minor version.

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Redshift/OMOP CDM ddl - Redshift.sql Normal file
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/*********************************************************************************
# Copyright 2017 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 5.1.0 for Amazon Redshift database
last revised: 20-July-2017
Authors: Patrick Ryan, Christian Reich
Editors: Komathi Sunilkumar, Ajit Londhe
*************************/
/************************
Standardized vocabulary
************************/
create table concept
(
concept_id integer not null,
concept_name varchar(255) null,
domain_id varchar(20) not null,
vocabulary_id varchar(20) not null,
concept_class_id varchar(20) not null,
standard_concept char(1) null,
concept_code varchar(50) null,
valid_start_date date not null,
valid_end_date date not null,
invalid_reason varchar(1) null
)
diststyle all;
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
)
diststyle all;
create table domain
(
domain_id varchar(20) not null,
domain_name varchar(255) not null,
domain_concept_id integer not null
)
diststyle all;
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
)
diststyle all;
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
)
diststyle all;
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
)
diststyle all;
create table concept_synonym
(
concept_id integer not null,
concept_synonym_name varchar(1000) not null,
language_concept_id integer not null
)
diststyle all;
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
)
diststyle all;
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
)
diststyle all;
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
)
diststyle all;
create table cohort_definition
(
cohort_definition_id integer not null,
cohort_definition_name varchar(255) not null,
cohort_definition_description varchar(8000) null,
definition_type_concept_id integer not null,
cohort_definition_syntax varchar(8000) null,
subject_concept_id integer not null,
cohort_initiation_date date null
)
diststyle all;
create table attribute_definition
(
attribute_definition_id integer not null,
attribute_name varchar(255) not null,
attribute_description varchar(8000) null,
attribute_type_concept_id integer not null,
attribute_syntax varchar(8000) null
)
diststyle all;
/**************************
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(8000) 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
)
diststyle all;
/************************
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,
birth_datetime timestamp 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
)
distkey(person_id)
sortkey(person_id);
create table observation_period
(
observation_period_id integer not null ,
person_id integer not null ,
observation_period_start_date date not null ,
observation_period_start_datetime timestamp not null ,
observation_period_end_date date not null ,
observation_period_end_datetime timestamp not null ,
period_type_concept_id integer not null
)
distkey(person_id)
interleaved sortkey(person_id, observation_period_start_date, observation_period_end_date);
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_datetime timestamp 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
)
distkey(person_id)
sortkey(person_id);
create table death
(
person_id integer not null ,
death_date date not null ,
death_datetime timestamp 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
)
distkey(person_id)
sortkey(person_id);
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_datetime timestamp null ,
visit_end_date date not null ,
visit_end_datetime timestamp 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
)
distkey(payer_plan_period_id)
sortkey(payer_plan_period_id);
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_datetime timestamp 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
)
distkey(person_id)
interleaved sortkey(person_id, procedure_date);
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_start_datetime timestamp not null ,
drug_exposure_end_date date null ,
drug_exposure_end_datetime timestamp 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(8000) 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
)
distkey(person_id)
INTERLEAVED SORTKEY(person_id, drug_concept_id, drug_exposure_start_date, drug_exposure_end_date);
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_start_datetime timestamp not null ,
device_exposure_end_date date null ,
device_exposure_end_datetime timestamp 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
)
distkey(person_id)
interleaved sortkey(person_id, device_concept_id, device_exposure_start_date, device_exposure_end_date);
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_start_datetime timestamp not null ,
condition_end_date date null ,
condition_end_datetime timestamp 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
)
distkey(person_id)
interleaved sortkey(person_id, condition_concept_id, condition_start_date, condition_end_date);
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_datetime timestamp 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
)
distkey(person_id)
interleaved sortkey(person_id, measurement_concept_id, measurement_date);
create table note
(
note_id integer not null ,
person_id integer not null ,
note_date date not null ,
note_datetime timestamp 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
)
distkey(person_id)
sortkey(person_id);
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_datetime timestamp 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
)
distkey(person_id)
interleaved sortkey(person_id, observation_concept_id, observation_date);
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
)
diststyle all;
/************************
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
)
diststyle all;
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
)
diststyle all;
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
)
distkey(provider_id);
/************************
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
)
distkey(person_id)
interleaved sortkey(person_id, payer_plan_period_start_date, payer_plan_period_end_date);
/* 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
)
distkey(payer_plan_period_id)
sortkey(payer_plan_period_id);
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
)
distkey(procedure_occurrence_id)
sortkey(procedure_occurrence_id);
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
)
distkey(payer_plan_period_id)
sortkey(payer_plan_period_id);
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
)
distkey(payer_plan_period_id)
sortkey(payer_plan_period_id);
*/
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
)
distkey(payer_plan_period_id)
sortkey(payer_plan_period_id);
/************************
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
)
distkey(subject_id)
sortkey(subject_id);
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
)
distkey(subject_id)
sortkey(subject_id);
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
)
distkey(person_id)
interleaved sortkey(person_id, drug_concept_id, drug_era_start_date, drug_era_end_date);
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
)
distkey(person_id)
sortkey(person_id);
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
)
distkey(person_id)
interleaved sortkey(person_id, condition_concept_id, condition_era_start_date, condition_era_end_date);

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Common-Data-Model / Redshift
=================
This folder contains the SQL scripts for Amazon Redshift.
In order to create your instantiation of the Common Data Model, we recommend following these steps:
1. Create an empty schema.
2. Set the search_path to that schema.
3. Execute the script `OMOP CDM ddl - Redshift.sql` to create the tables and fields.
4. Load your data into the schema using COPY commands from Amazon S3.