OMOP/BigQuery/OMOP CDM bigquery ddl.txt

/*OMOP CDM v5.3.1 14June2018*/
#standardsql
create table concept (
  concept_id			    INT64			  not null ,
  concept_name			  STRING     	not null ,
  domain_id				    STRING   		not null ,
  vocabulary_id			  STRING   		not null ,
  concept_class_id		STRING  		not null ,
  standard_concept		STRING  		         ,
  concept_code			  STRING  		not null ,
  valid_start_DATE		DATE			  not null ,
  valid_end_DATE		  DATE			  not null ,
  invalid_reason		  STRING
)
;


create table vocabulary (
  vocabulary_id			    STRING   		not null,
  vocabulary_name		    STRING     	not null,
  vocabulary_reference	STRING     	not null,
  vocabulary_version	  STRING     	        ,
  vocabulary_concept_id	INT64			  not null
)
;


create table domain (
  domain_id			    STRING   		not null,
  domain_name		    STRING    	not null,
  domain_concept_id	INT64			  not null
)
;


create table concept_class (
  concept_class_id			    STRING  		not null,
  concept_class_name		    STRING    	not null,
  concept_class_concept_id	INT64		 	  not null
)
;


create table concept_relationship (
  concept_id_1			INT64			not null,
  concept_id_2			INT64			not null,
  relationship_id		STRING  	not null,
  valid_start_DATE	DATE			not null,
  valid_end_DATE		DATE			not null,
  invalid_reason		STRING
  )
;


create table relationship (
  relationship_id			    STRING   		not null,
  relationship_name			  STRING    	not null,
  is_hierarchical			    STRING  		not null,
  defines_ancestry			  STRING  		not null,
  reverse_relationship_id	STRING  		not null,
  relationship_concept_id	INT64			  not null
)
;


create table concept_synonym (
  concept_id			      INT64			  not null,
  concept_synonym_name	STRING    	not null,
  language_concept_id	  INT64			  not null
)
;


create table concept_ancestor (
  ancestor_concept_id		    INT64		not null,
  descendant_concept_id		  INT64		not null,
  min_levels_of_separation	INT64		not null,
  max_levels_of_separation	INT64		not null
)
;


create table source_to_concept_map (
  source_code				      STRING  		not null,
  source_concept_id			  INT64			  not null,
  source_vocabulary_id		STRING  		not null,
  source_code_description	STRING    	        ,
  target_concept_id			  INT64			  not null,
  target_vocabulary_id		STRING  		not null,
  valid_start_DATE			  DATE		    not null,
  valid_end_DATE			    DATE		    not null,
  invalid_reason			    STRING
)
;




create table drug_strength (
  drug_concept_id				      INT64		  not null,
  ingredient_concept_id			  INT64		  not null,
  amount_value					      FLOAT64		        ,
  amount_unit_concept_id		  INT64		          ,
  numerator_value				      FLOAT64		        ,
  numerator_unit_concept_id		INT64		          ,
  denominator_value				    FLOAT64		        ,
  denominator_unit_concept_id	INT64		          ,
  box_size						        INT64		          ,
  valid_start_DATE				    DATE		   not null,
  valid_end_DATE				      DATE		   not null,
  invalid_reason				      STRING
)
;



create table cohort_definition (
  cohort_definition_id				    INT64			  not null,
  cohort_definition_name			    STRING    	not null,
  cohort_definition_description		STRING    	        ,
  definition_type_concept_id		  INT64			  not null,
  cohort_definition_syntax			  STRING     	        ,
  subject_concept_id				      INT64			  not null,
  cohort_initiation_DATE			    DATE
)
;


create table attribute_definition (
  attribute_definition_id		  INT64			  not null,
  attribute_name				      STRING    	not null,
  attribute_description			  STRING    	        ,
  attribute_type_concept_id		INT64			  not null,
  attribute_syntax				    STRING
)
;


create table cdm_source
(
  cdm_source_name					        STRING      	not null ,
  cdm_source_abbreviation			    STRING    		     ,
  cdm_holder							        STRING      	     ,
  source_description					    STRING      	     ,
  source_documentation_reference	STRING      	     ,
  cdm_etl_reference					      STRING      	     ,
  source_release_DATE				      DATE			         ,
  cdm_release_DATE					      DATE			         ,
  cdm_version						          STRING    		     ,
  vocabulary_version					    STRING
)
;


create table metadata
(
  metadata_concept_id       INT64       not null ,
  metadata_type_concept_id  INT64       not null ,
  name                      STRING      not null ,
  value_as_string           STRING               ,
  value_as_concept_id       INT64                ,
  metadata_DATE             DATE                 ,
  metadata_DATETIME         DATETIME
)
;



--HINT DISTRIBUTE_ON_KEY(person_id)
create table person
(
  person_id						        INT64	  	not null ,
  gender_concept_id				    INT64	  	not null ,
  year_of_birth					      INT64	  	not null ,
  month_of_birth				      INT64	  	         ,
  day_of_birth					      INT64	  	         ,
  birth_DATETIME				      DATETIME	         ,
  race_concept_id				      INT64		  not null,
  ethnicity_concept_id			  INT64	  	not null,
  location_id					        INT64		           ,
  provider_id					        INT64		           ,
  care_site_id					      INT64		           ,
  person_source_value			    STRING             ,
  gender_source_value			    STRING             ,
  gender_source_concept_id	  INT64		           ,
  race_source_value				    STRING             ,
  race_source_concept_id		  INT64		           ,
  ethnicity_source_value		  STRING             ,
  ethnicity_source_concept_id	INT64
)
;


--HINT DISTRIBUTE_ON_KEY(person_id)
create table observation_period
(
  observation_period_id				      INT64		not null ,
  person_id							            INT64		not null ,
  observation_period_start_DATE		  DATE		not null ,
  observation_period_end_DATE		    DATE		not null ,
  period_type_concept_id			      INT64		not null
)
;


--HINT DISTRIBUTE_ON_KEY(person_id)
create table specimen
(
  specimen_id						      INT64			not null ,
  person_id							      INT64			not null ,
  specimen_concept_id				  INT64			not null ,
  specimen_type_concept_id		INT64			not null ,
  specimen_DATE						    DATE			not null ,
  specimen_DATETIME					  DATETIME	      	 ,
  quantity							      FLOAT64			       ,
  unit_concept_id					    INT64			         ,
  anatomic_site_concept_id		INT64			         ,
  disease_status_concept_id		INT64			         ,
  specimen_source_id				  STRING  	         ,
  specimen_source_value				STRING  	         ,
  unit_source_value					  STRING  	         ,
  anatomic_site_source_value	STRING  	         ,
  disease_status_source_value STRING
)
;


--HINT DISTRIBUTE_ON_KEY(person_id)
create table death
(
  person_id							  INT64			not null ,
  death_DATE							DATE			not null ,
  death_DATETIME					DATETIME	      	 ,
  death_type_concept_id   INT64			not null ,
  cause_concept_id			  INT64			         ,
  cause_source_value			STRING  	         ,
  cause_source_concept_id INT64
)
;


--HINT DISTRIBUTE_ON_KEY(person_id)
create table visit_occurrence
(
  visit_occurrence_id			      INT64			not null ,
  person_id						          INT64			not null ,
  visit_concept_id				      INT64			not null ,
  visit_start_DATE				      DATE			not null ,
  visit_start_DATETIME				  DATETIME	         ,
  visit_end_DATE					      DATE			not null ,
  visit_end_DATETIME					  DATETIME		       ,
  visit_type_concept_id			    INT64			not null ,
  provider_id					          INT64			         ,
  care_site_id					        INT64			         ,
  visit_source_value				    STRING  	         ,
  visit_source_concept_id		    INT64			         ,
  admitting_source_concept_id	  INT64			         ,
  admitting_source_value		    STRING  	         ,
  discharge_to_concept_id		    INT64   	         ,
  discharge_to_source_value		  STRING  	         ,
  preceding_visit_occurrence_id	INT64
)
;


--HINT DISTRIBUTE_ON_KEY(person_id)
create table visit_detail
(
  visit_detail_id                    INT64     not null ,
  person_id                          INT64     not null ,
  visit_detail_concept_id            INT64     not null ,
  visit_detail_start_DATE            DATE      not null ,
  visit_detail_start_DATETIME        DATETIME           ,
  visit_detail_end_DATE              DATE      not null ,
  visit_detail_end_DATETIME          DATETIME           ,
  visit_deatil_type_concept_id       INT64     not null ,
  provider_id                        INT64              ,
  care_site_id                       INT64              ,
  admitting_source_concept_id        INT64              ,
  discharge_to_concept_id            INT64              ,
  preceding_visit_detail_id          INT64              ,
  visit_detail_source_value          STRING             ,
  visit_deatil_source_concept_id     INT64              ,
  admitting_source_value             STRING             ,
  discharge_to_source_value          STRING             ,
  visit_detail_parent_id             INT64              ,
  visit_occurrence_id                INT64     not null
)
;


--HINT DISTRIBUTE_ON_KEY(person_id)
create table procedure_occurrence
(
  procedure_occurrence_id		  INT64			not null ,
  person_id						        INT64			not null ,
  procedure_concept_id			  INT64			not null ,
  procedure_DATE				      DATE			not null ,
  procedure_DATETIME			    DATETIME	  	     ,
  procedure_type_concept_id		INT64			not null ,
  modifier_concept_id			    INT64			         ,
  quantity						        INT64			         ,
  provider_id					        INT64			         ,
  visit_occurrence_id			    INT64			         ,
  visit_detail_id             INT64              ,
  procedure_source_value		  STRING  	         ,
  procedure_source_concept_id	INT64			         ,
  modifier_source_value		   STRING
)
;


--HINT DISTRIBUTE_ON_KEY(person_id)
create table drug_exposure
(
  drug_exposure_id				      INT64			  not null ,
  person_id						          INT64			  not null ,
  drug_concept_id				        INT64			  not null ,
  drug_exposure_start_DATE		  DATE			  not null ,
  drug_exposure_start_DATETIME  DATETIME		         ,
  drug_exposure_end_DATE		    DATE			  not null ,
  drug_exposure_end_DATETIME	  DATETIME		         ,
  verbatim_end_DATE				      DATE			           ,
  drug_type_concept_id			    INT64			  not null ,
  stop_reason					          STRING  		         ,
  refills						            INT64		  	         ,
  quantity						          FLOAT64			         ,
  days_supply					          INT64		  	         ,
  sig							              STRING               ,
  route_concept_id				      INT64			           ,
  lot_number					          STRING  	           ,
  provider_id					          INT64			           ,
  visit_occurrence_id			      INT64			           ,
  visit_detail_id               INT64                ,
  drug_source_value				      STRING  	           ,
  drug_source_concept_id		    INT64			           ,
  route_source_value			      STRING  	           ,
  dose_unit_source_value		    STRING
)
;


--HINT DISTRIBUTE_ON_KEY(person_id)
create table device_exposure
(
  device_exposure_id			        INT64		  	not null ,
  person_id						            INT64			  not null ,
  device_concept_id			        	INT64			  not null ,
  device_exposure_start_DATE	    DATE			  not null ,
  device_exposure_start_DATETIME  DATETIME		         ,
  device_exposure_end_DATE		    DATE			           ,
  device_exposure_end_DATETIME    DATETIME		         ,
  device_type_concept_id		      INT64			  not null ,
  unique_device_id			        	STRING  		         ,
  quantity						            INT64			           ,
  provider_id					            INT64			           ,
  visit_occurrence_id			        INT64			           ,
  visit_detail_id                 INT64                ,
  device_source_value			        STRING    	         ,
  device_source_concept_id		    INT64
)
;


--HINT DISTRIBUTE_ON_KEY(person_id)
create table condition_occurrence
(
  condition_occurrence_id		    INT64			not null ,
  person_id						          INT64			not null ,
  condition_concept_id			    INT64			not null ,
  condition_start_DATE			    DATE			not null ,
  condition_start_DATETIME		  DATETIME		       ,
  condition_end_DATE			      DATE			         ,
  condition_end_DATETIME		    DATETIME		       ,
  condition_type_concept_id		  INT64			not null ,
  stop_reason					          STRING   	         ,
  provider_id					          INT64			         ,
  visit_occurrence_id			      INT64			         ,
  visit_detail_id               INT64              ,
  condition_source_value		    STRING  	         ,
  condition_source_concept_id	  INT64			         ,
  condition_status_source_value	STRING             ,
  condition_status_concept_id	  INT64
)
;


--HINT DISTRIBUTE_ON_KEY(person_id)
create table measurement
(
  measurement_id				        INT64			not null ,
  person_id						          INT64			not null ,
  measurement_concept_id		    INT64			not null ,
  measurement_DATE				      DATE			not null ,
  measurement_DATETIME          DATETIME           ,
  measurement_time              STRING             ,
  measurement_type_concept_id	  INT64			not null ,
  operator_concept_id			      INT64			         ,
  value_as_number				        FLOAT64			       ,
  value_as_concept_id			      INT64			         ,
  unit_concept_id				        INT64			         ,
  range_low					          	FLOAT64			       ,
  range_high					          FLOAT64			       ,
  provider_id					          INT64			         ,
  visit_occurrence_id			      INT64			         ,
  visit_detail_id               INT64              ,
  measurement_source_value		  STRING             ,
  measurement_source_concept_id	INT64			         ,
  unit_source_value				      STRING  	         ,
  value_source_value			      STRING
)
;


--HINT DISTRIBUTE_ON_KEY(person_id)
create table note
(
  note_id						    INT64			  not null ,
  person_id						  INT64			  not null ,
  note_DATE						  DATE			  not null ,
  note_DATETIME					DATETIME	           ,
  note_type_concept_id	INT64			  not null ,
  note_class_concept_id INT64			  not null ,
  note_title					  STRING    	         ,
  note_text						  STRING               ,
  encoding_concept_id		INT64			  not null ,
  language_concept_id		INT64			  not null ,
  provider_id					  INT64			           ,
  visit_occurrence_id		INT64			           ,
  visit_detail_id       INT64                ,
  note_source_value			STRING
)
;



create table note_nlp
(
  note_nlp_id					        INT64			           ,
  note_id						          INT64			           ,
  section_concept_id			    INT64			           ,
  snippet						          STRING    	         ,
  "offset"					          STRING    	         ,
  lexical_variant				      STRING    	not null ,
  note_nlp_concept_id			    INT64			           ,
  note_nlp_source_concept_id  INT64			           ,
  nlp_system					        STRING	             ,
  nlp_DATE						        DATE			  not null ,
  nlp_DATETIME					      DATETIME		         ,
  term_exists					        STRING   		         ,
  term_temporal					      STRING   		         ,
  term_modifiers				      STRING
)
;


--HINT DISTRIBUTE_ON_KEY(person_id)
create table observation
(
  observation_id					      INT64			not null ,
  person_id						          INT64			not null ,
  observation_concept_id			  INT64			not null ,
  observation_DATE				      DATE			not null ,
  observation_DATETIME				  DATETIME		       ,
  observation_type_concept_id	  INT64			not null ,
  value_as_number				        FLOAT64			   ,
  value_as_string				        STRING   	     ,
  value_as_concept_id			      INT64			     ,
  qualifier_concept_id			    INT64			     ,
  unit_concept_id				        INT64			     ,
  provider_id					          INT64			     ,
  visit_occurrence_id			      INT64			     ,
  visit_detail_id               INT64          ,
  observation_source_value		  STRING  	     ,
  observation_source_concept_id	INT64			     ,
  unit_source_value				      STRING  	     ,
  qualifier_source_value			  STRING
)
;


create table fact_relationship
(
  domain_concept_id_1			INT64			not null ,
  fact_id_1						    INT64			not null ,
  domain_concept_id_2			INT64			not null ,
  fact_id_2						    INT64			not null ,
  relationship_concept_id	INT64			not null
)
;


create table location
(
  location_id					  INT64			not null ,
  address_1						  STRING	           ,
  address_2						  STRING    		     ,
  city							    STRING    		     ,
  state							    STRING   		       ,
  zip							      STRING   	         ,
  county							  STRING    		     ,
  location_source_value STRING
)
;


create table care_site
(
  care_site_id						      INT64			  not null ,
  care_site_name						    STRING               ,
  place_of_service_concept_id	  INT64			           ,
  location_id						        INT64			           ,
  care_site_source_value			  STRING    		       ,
  place_of_service_source_value STRING
)
;


create table provider
(
  provider_id					        INT64			  not null ,
  provider_name					      STRING     	         ,
  npi							            STRING    	         ,
  dea							            STRING    		       ,
  specialty_concept_id			  INT64			           ,
  care_site_id					      INT64			           ,
  year_of_birth					      INT64			           ,
  gender_concept_id				    INT64			           ,
  provider_source_value			  STRING    		       ,
  specialty_source_value			STRING    		       ,
  specialty_source_concept_id	INT64			           ,
  gender_source_value			    STRING    		       ,
  gender_source_concept_id		INT64
)
;


--HINT DISTRIBUTE_ON_KEY(person_id)
create table payer_plan_period
(
  payer_plan_period_id			    INT64			not null ,
  person_id						          INT64			not null ,
  payer_plan_period_start_DATE  DATE			not null ,
  payer_plan_period_end_DATE		DATE			not null ,
  payer_concept_id              INT64              ,
  payer_source_value				    STRING    	       ,
  payer_source_concept_id       INT64              ,
  plan_concept_id               INT64              ,
  plan_source_value				      STRING    	       ,
  plan_source_concept_id        INT64              ,
  sponsor_concept_id            INT64              ,
  sponsor_source_value          STRING             ,
  sponsor_source_concept_id     INT64              ,
  family_source_value			      STRING    	       ,
  stop_reason_concept_id        INT64              ,
  stop_reason_source_value      STRING             ,
  stop_reason_source_concept_id INT64
)
;


create table cost
(
  cost_id					          INT64	    not null ,
  cost_event_id             INT64     not null ,
  cost_domain_id            STRING    not null ,
  cost_type_concept_id      INT64     not null ,
  currency_concept_id			  INT64			         ,
  total_charge						  FLOAT64			       ,
  total_cost						    FLOAT64			       ,
  total_paid						    FLOAT64			       ,
  paid_by_payer					    FLOAT64			       ,
  paid_by_patient						FLOAT64			       ,
  paid_patient_copay				FLOAT64			       ,
  paid_patient_coinsurance  FLOAT64			       ,
  paid_patient_deductible		FLOAT64			       ,
  paid_by_primary						FLOAT64			       ,
  paid_ingredient_cost			FLOAT64			       ,
  paid_dispensing_fee				FLOAT64			       ,
  payer_plan_period_id			INT64			         ,
  amount_allowed		        FLOAT64			       ,
  revenue_code_concept_id		INT64			         ,
  revenue_code_source_value  STRING            ,
  drg_concept_id			      INT64		           ,
  drg_source_value			    STRING
)
;


--HINT DISTRIBUTE_ON_KEY(subject_id)
create table cohort
(
  cohort_definition_id	INT64		not null ,
  subject_id						INT64		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		INT64		  not null ,
  subject_id						  INT64		  not null ,
  cohort_start_DATE				DATE			not null ,
  cohort_end_DATE				  DATE			not null ,
  attribute_definition_id INT64		  not null ,
  value_as_number				  FLOAT64			       ,
  value_as_concept_id			INT64
)
;


--HINT DISTRIBUTE_ON_KEY(person_id)
create table drug_era
(
  drug_era_id					INT64			not null ,
  person_id						INT64			not null ,
  drug_concept_id			INT64			not null ,
  drug_era_start_DATE	DATE			not null ,
  drug_era_end_DATE		DATE		  not null ,
  drug_exposure_count	INT64	             ,
  gap_days						INT64
)
;


--HINT DISTRIBUTE_ON_KEY(person_id)
create table dose_era
(
  dose_era_id					  INT64			not null ,
  person_id						  INT64			not null ,
  drug_concept_id				INT64			not null ,
  unit_concept_id				INT64			not null ,
  dose_value						FLOAT64		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				    INT64			not null ,
  person_id						        INT64			not null ,
  condition_concept_id			  INT64			not null ,
  condition_era_start_DATE		DATE			not null ,
  condition_era_end_DATE			DATE			not null ,
  condition_occurrence_count	INT64
)
;