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

/*********************************************************************************
# 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.
********************************************************************************/

/************************

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script to create OMOP common data model, version 5.2 for SQL Server database

last revised: 14-July-2017

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,
  birth_datetime				DATETIME2	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_start_datetime	DATETIME2		NOT NULL ,
  observation_period_end_date		DATE		NOT NULL ,
  observation_period_end_datetime	DATETIME2		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_datetime					DATETIME2		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_datetime							DATETIME2			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_datetime				DATETIME2		NULL ,
  visit_end_date					DATE			NOT NULL ,
  visit_end_datetime					DATETIME2		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 ,
  admitting_source_concept_id	INTEGER			NULL ,
  admitting_source_value		VARCHAR(50)		NULL ,
  discharge_to_concept_id		INTEGER			NULL ,
  discharge_to_source_value		VARCHAR(50)		NULL ,
  preceding_visit_occurrence_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_datetime			DATETIME2			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_start_datetime	DATETIME2		NOT NULL ,
  drug_exposure_end_date		DATE			NOT NULL ,
  drug_exposure_end_datetime	DATETIME2		NULL ,
  verbatim_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 ,
  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_start_datetime DATETIME2		NOT NULL ,
  device_exposure_end_date		DATE			NULL ,
  device_exposure_end_datetime	DATETIME2		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_start_datetime		DATETIME2			NOT NULL ,
  condition_end_date			DATE			NULL ,
  condition_end_datetime		DATETIME2			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 ,
  condition_status_source_value	VARCHAR(50)		NULL ,
  condition_status_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_datetime			DATETIME2		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_datetime					DATETIME2		NULL ,
  note_type_concept_id			INTEGER			NOT NULL ,
  note_class_concept_id			INTEGER			NOT NULL ,
  note_title					VARCHAR(250)	NULL ,
  note_text						VARCHAR(MAX)	NULL ,
  encoding_concept_id			INTEGER			NOT NULL ,
  language_concept_id			INTEGER			NOT NULL ,
  provider_id					INTEGER			NULL ,
  visit_occurrence_id			INTEGER			NULL ,
  note_source_value				VARCHAR(50)		NULL
)
;


/*This table is new in CDM v5.2*/
CREATE TABLE note_nlp
(
  note_nlp_id					BIGINT			NOT NULL ,
  note_id						INTEGER			NOT NULL ,
  section_concept_id			INTEGER			NULL ,
  snippet						VARCHAR(250)	NULL ,
  offset						VARCHAR(250)	NULL ,
  lexical_variant				VARCHAR(250)	NOT NULL ,
  note_nlp_concept_id			INTEGER			NULL ,
  note_nlp_source_concept_id	INTEGER			NULL ,
  nlp_system					VARCHAR(250)	NULL ,
  nlp_date						DATE			NOT NULL ,
  nlp_datetime					DATETIME2		NULL ,
  term_exists					VARCHAR(1)		NULL ,
  term_temporal					VARCHAR(50)		NULL ,
  term_modifiers				VARCHAR(2000)	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_datetime				DATETIME2		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
)
;


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,
  drg_concept_id			INTEGER		NULL,
  drg_source_value			VARCHAR(3)		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
)
;