OMOP/DDLGeneratr/output/bigquery/OMOP CDM bigquery ddl.txt

/*********************************************************************************
# Copyright 2017-11 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
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#     http://www.apache.org/licenses/LICENSE-2.0
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# 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
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********************************************************************************/

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

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bigquery script to create OMOP common data model version 5.3

last revised: 6-Nov-2017

Authors:  Patrick Ryan, Christian Reich, Clair Blacketer


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


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

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)	not null,
  vocabulary_version	  varchar(255)	not 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
)
;


create table metadata
(
  metadata_concept_id       integer       not null ,
  metadata_type_concept_id  integer       not null ,
  name                      varchar(250)  not null ,
  value_as_string           varchar(max)  null ,
  value_as_concept_id       integer       null ,
  metadata_date             date          null ,
  metadata_datetime         datetime      null
)
;


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

Standardized clinical data

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

--HINT DISTRIBUTE_ON_KEY(person_id)
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				      datetime	  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
)
;


--HINT DISTRIBUTE_ON_KEY(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_end_date		    date		  not null ,
  period_type_concept_id			      integer		not null
)
;


--HINT DISTRIBUTE_ON_KEY(person_id)
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					  datetime		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
)
;


--HINT DISTRIBUTE_ON_KEY(person_id)
create table death
(
  person_id							  integer			not null ,
  death_date							date			  not null ,
  death_datetime					datetime		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
)
;


--HINT DISTRIBUTE_ON_KEY(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				  datetime		null ,
  visit_end_date					      date			  not null ,
  visit_end_datetime					  datetime		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
)
;


--HINT DISTRIBUTE_ON_KEY(person_id)
create table visit_detail
(
  visit_detail_id             integer     not null ,
  person_id                   integer     not null ,
  visit_detail_concept_id     integer     not null ,
  visit_start_date            date        not null ,
  visit_start_datetime        datetime   null ,
  visit_end_date              date        not null ,
  visit_end_datetime          datetime   null ,
  visit_type_concept_id       integer     not null ,
  provider_id                 integer     null ,
  care_site_id                integer     null ,
  admitting_source_concept_id integer     null ,
  discharge_to_concept_id     integer     null ,
  preceding_visit_detail_id   integer     null ,
  visit_source_value          varchar(50) null ,
  visit_source_concept_id     integer     null ,
  admitting_source_value      varchar(50) null ,
  discharge_to_source_value   varchar(50) null ,
  visit_detail_parent_id      integer     null ,
  visit_occurrence_id         integer     not null
)
;


--HINT DISTRIBUTE_ON_KEY(person_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			    datetime		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 ,
  visit_detail_id             integer     null ,
  procedure_source_value		  varchar(50)	null ,
  procedure_source_concept_id	integer			null ,
  modifier_source_value		   varchar(50)	null
)
;


--HINT DISTRIBUTE_ON_KEY(person_id)
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  datetime		  null ,
  drug_exposure_end_date		    date			    not null ,
  drug_exposure_end_datetime	  datetime		  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 ,
  visit_detail_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
)
;


--HINT DISTRIBUTE_ON_KEY(person_id)
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  datetime		  null ,
  device_exposure_end_date		    date			    null ,
  device_exposure_end_datetime    datetime		  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 ,
  visit_detail_id                 integer       null ,
  device_source_value			        varchar(100)	null ,
  device_source_concept_id		    integer			  null
)
;


--HINT DISTRIBUTE_ON_KEY(person_id)
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		  datetime		null ,
  condition_end_date			      date			  null ,
  condition_end_datetime		    datetime		null ,
  condition_type_concept_id		  integer			not null ,
  stop_reason					          varchar(20)	null ,
  provider_id					          integer			null ,
  visit_occurrence_id			      integer			null ,
  visit_detail_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
)
;


--HINT DISTRIBUTE_ON_KEY(person_id)
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_datetime			    datetime		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 ,
  visit_detail_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
)
;


--HINT DISTRIBUTE_ON_KEY(person_id)
create table note
(
  note_id						    integer			  not null ,
  person_id						  integer			  not null ,
  note_date						  date			    not null ,
  note_datetime					datetime		  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 ,
  visit_detail_id       integer       null ,
  note_source_value			varchar(50)		null
)
;



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					      datetime		  null ,
  term_exists					        varchar(1)		null ,
  term_temporal					      varchar(50)		null ,
  term_modifiers				      varchar(2000)	null
)
;


--HINT DISTRIBUTE_ON_KEY(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				  datetime		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 ,
  visit_detail_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

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


--HINT DISTRIBUTE_ON_KEY(person_id)
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_concept_id              integer       null ,
  payer_source_value				    varchar(50)	  null ,
  payer_source_concept_id       integer       null ,
  plan_concept_id               integer       null ,
  plan_source_value				      varchar(50)	  null ,
  plan_source_concept_id        integer       null ,
  sponsor_concept_id            integer       null ,
  sponsor_source_value          varchar(50)   null ,
  sponsor_source_concept_id     integer       null ,
  family_source_value			      varchar(50)	  null ,
  stop_reason_concept_id        integer       null ,
  stop_reason_source_value      integer       null ,
  stop_reason_source_concept_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,
  drg_concept_id			      integer		  null,
  drg_source_value			    varchar(3)	null
)
;


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

Standardized derived elements

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


--HINT DISTRIBUTE_ON_KEY(subject_id)
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
)
;


--HINT DISTRIBUTE_ON_KEY(subject_id)
create table cohort_attribute
(
  cohort_definition_id		integer		not null ,
  subject_id						  integer		not null ,
  cohort_start_date				date			not null ,
  cohort_end_date				  date			not null ,
  attribute_definition_id integer		not null ,
  value_as_number				  float			null ,
  value_as_concept_id			integer		null
)
;


--HINT DISTRIBUTE_ON_KEY(person_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
)
;


--HINT DISTRIBUTE_ON_KEY(person_id)
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
)
;


--HINT DISTRIBUTE_ON_KEY(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
)
;