OMOP/Impala/OMOP CDM impala ddl.txt

/*********************************************************************************
# Copyright 2018-08 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.
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impala script to create OMOP common data model version 6.0

last revised: 27-Aug-2018

Authors:  Patrick Ryan, Christian Reich, Clair Blacketer


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


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

Standardized vocabulary

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


CREATE TABLE concept (
  concept_id			  INTEGER ,
  concept_name			  VARCHAR(255) ,
  domain_id				  VARCHAR(20) ,
  vocabulary_id			  VARCHAR(20) ,
  concept_class_id		  VARCHAR(20) ,
  standard_concept		  VARCHAR(1) ,
  concept_code			  VARCHAR(50) ,
  valid_start_date		  TIMESTAMP ,
  valid_end_date		  TIMESTAMP ,
  invalid_reason		  VARCHAR(1)
)
;


CREATE TABLE vocabulary (
  vocabulary_id			VARCHAR(20),
  vocabulary_name		VARCHAR(255),
  vocabulary_reference	VARCHAR(255),
  vocabulary_version	VARCHAR(255),
  vocabulary_concept_id	INTEGER
)
;


CREATE TABLE domain (
  domain_id			    VARCHAR(20),
  domain_name		    VARCHAR(255),
  domain_concept_id		INTEGER
)
;


CREATE TABLE concept_class (
  concept_class_id			    VARCHAR(20),
  concept_class_name		    VARCHAR(255),
  concept_class_concept_id		INTEGER
)
;


CREATE TABLE concept_relationship (
  concept_id_1			INTEGER	,
  concept_id_2			INTEGER	,
  relationship_id		VARCHAR(20),
  valid_start_date		TIMESTAMP,
  valid_end_date		TIMESTAMP,
  invalid_reason		VARCHAR(1)
  )
;


CREATE TABLE relationship (
  relationship_id			VARCHAR(20),
  relationship_name			VARCHAR(255),
  is_hierarchical			VARCHAR(1),
  defines_ancestry			VARCHAR(1),
  reverse_relationship_id	VARCHAR(20),
  relationship_concept_id	INTEGER
)
;


CREATE TABLE concept_synonym (
  concept_id			  INTEGER	,
  concept_synonym_name	  STRING,
  language_concept_id	  INTEGER
)
;


CREATE TABLE concept_ancestor (
  ancestor_concept_id		INTEGER	,
  descendant_concept_id		INTEGER	,
  min_levels_of_separation	INTEGER	,
  max_levels_of_separation	INTEGER
)
;


CREATE TABLE source_to_concept_map (
  source_code				VARCHAR(50),
  source_concept_id			INTEGER	,
  source_vocabulary_id		VARCHAR(20),
  source_code_description	VARCHAR(255),
  target_concept_id			INTEGER	,
  target_vocabulary_id		VARCHAR(20),
  valid_start_date			TIMESTAMP,
  valid_end_date			TIMESTAMP,
  invalid_reason			VARCHAR(1)
)
;


CREATE TABLE drug_strength (
  drug_concept_id				  INTEGER	,
  ingredient_concept_id			  INTEGER	,
  amount_value					  FLOAT,
  amount_unit_concept_id		  INTEGER	,
  numerator_value				  FLOAT,
  numerator_unit_concept_id		  INTEGER	,
  denominator_value				  FLOAT,
  denominator_unit_concept_id	  INTEGER	,
  box_size						  INTEGER	,
  valid_start_date				  TIMESTAMP,
  valid_end_date				  TIMESTAMP,
  invalid_reason				  VARCHAR(1)
)
;


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

Standardized meta-data

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


CREATE TABLE cdm_source
(
  cdm_source_name					    VARCHAR(255) ,
  cdm_source_abbreviation			    VARCHAR(25) ,
  cdm_holder							VARCHAR(255) ,
  source_description					STRING ,
  source_documentation_reference		VARCHAR(255) ,
  cdm_etl_reference					    VARCHAR(255) ,
  source_release_date				    TIMESTAMP ,
  cdm_release_date					    TIMESTAMP ,
  cdm_version						    VARCHAR(10) ,
  vocabulary_version					VARCHAR(20)
)
;


CREATE TABLE `metadata`
(
  metadata_concept_id       INTEGER ,
  metadata_type_concept_id  INTEGER ,
  name                      VARCHAR(250) ,
  value_as_string           STRING ,
  value_as_concept_id       INTEGER ,
  metadata_date             TIMESTAMP ,
  metadata_datetime         TIMESTAMP
)
;

INSERT INTO `metadata` (metadata_concept_id, metadata_type_concept_id, name, value_as_string, value_as_concept_id, metadata_date, metadata_datetime) --Added cdm version record
VALUES (0,0,'CDM Version', '6.0',0,NULL,NULL)
;


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

Standardized clinical data

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


--HINT DISTRIBUTE_ON_KEY(person_id)
CREATE TABLE person
(
  person_id						    BIGINT , 
  gender_concept_id				    INTEGER ,
  year_of_birth					    INTEGER	,
  month_of_birth				    INTEGER	,
  day_of_birth					    INTEGER	,
  birth_datetime				    TIMESTAMP	,
  death_datetime					TIMESTAMP	,
  race_concept_id				    INTEGER	,
  ethnicity_concept_id			  	INTEGER	,
  location_id					    BIGINT	,
  provider_id					    BIGINT	,
  care_site_id					    BIGINT	,
  person_source_value			    VARCHAR(50),
  gender_source_value			    VARCHAR(50),
  gender_source_concept_id	  		INTEGER	,
  race_source_value				    VARCHAR(50),
  race_source_concept_id		  	INTEGER	,
  ethnicity_source_value		  	VARCHAR(50),
  ethnicity_source_concept_id		INTEGER
)
;


--HINT DISTRIBUTE_ON_KEY(person_id)
CREATE TABLE observation_period
(
  observation_period_id				  BIGINT ,
  person_id							  BIGINT ,
  observation_period_start_date		  TIMESTAMP ,
  observation_period_end_date		  TIMESTAMP ,
  period_type_concept_id			  INTEGER
)
;


--HINT DISTRIBUTE_ON_KEY(person_id)
CREATE TABLE specimen
(
  specimen_id					BIGINT ,
  person_id						BIGINT ,
  specimen_concept_id			INTEGER	,
  specimen_type_concept_id		INTEGER	,
  specimen_date					TIMESTAMP ,
  specimen_datetime				TIMESTAMP	,
  quantity						FLOAT ,
  unit_concept_id				INTEGER	,
  anatomic_site_concept_id		INTEGER	,
  disease_status_concept_id		INTEGER	,
  specimen_source_id			VARCHAR(50) ,
  specimen_source_value			VARCHAR(50) ,
  unit_source_value				VARCHAR(50) ,
  anatomic_site_source_value	VARCHAR(50) ,
  disease_status_source_value 	VARCHAR(50)
)
;


--HINT DISTRIBUTE_ON_KEY(person_id)
CREATE TABLE visit_occurrence
(
  visit_occurrence_id			BIGINT ,
  person_id						BIGINT ,
  visit_concept_id				INTEGER	,
  visit_start_date				TIMESTAMP ,
  visit_start_datetime			TIMESTAMP	,
  visit_end_date				TIMESTAMP ,
  visit_end_datetime			TIMESTAMP	,
  visit_type_concept_id			INTEGER	,
  provider_id					BIGINT	,
  care_site_id					BIGINT	,
  visit_source_value			VARCHAR(50),
  visit_source_concept_id		INTEGER	,
  admitted_from_concept_id      INTEGER ,   
  admitted_from_source_value    VARCHAR(50),
  discharge_to_source_value		VARCHAR(50) ,
  discharge_to_concept_id		INTEGER ,
  preceding_visit_occurrence_id	BIGINT
)
;


--HINT DISTRIBUTE_ON_KEY(person_id)
CREATE TABLE visit_detail
(
  visit_detail_id                    BIGINT ,
  person_id                          BIGINT ,
  visit_detail_concept_id            INTEGER ,
  visit_detail_start_date            TIMESTAMP ,
  visit_detail_start_datetime        TIMESTAMP ,
  visit_detail_end_date              TIMESTAMP ,
  visit_detail_end_datetime          TIMESTAMP ,
  visit_detail_type_concept_id       INTEGER   ,
  provider_id                        BIGINT   ,
  care_site_id                       BIGINT   ,
  discharge_to_concept_id            INTEGER   ,
  admitted_from_concept_id           INTEGER   , 
  admitted_from_source_value         VARCHAR(50) ,
  visit_detail_source_value          VARCHAR(50) ,
  visit_detail_source_concept_id     INTEGER ,
  discharge_to_source_value          VARCHAR(50) ,
  preceding_visit_detail_id          BIGINT ,
  visit_detail_parent_id             BIGINT ,
  visit_occurrence_id                BIGINT
)
;


--HINT DISTRIBUTE_ON_KEY(person_id)
CREATE TABLE procedure_occurrence
(
  procedure_occurrence_id		BIGINT ,
  person_id						BIGINT ,
  procedure_concept_id			INTEGER	,
  procedure_date				TIMESTAMP ,
  procedure_datetime			TIMESTAMP	,
  procedure_type_concept_id		INTEGER	,
  modifier_concept_id			INTEGER	,
  quantity						INTEGER	,
  provider_id					BIGINT	,
  visit_occurrence_id			BIGINT	,
  visit_detail_id             	BIGINT ,
  procedure_source_value		VARCHAR(50) ,
  procedure_source_concept_id	INTEGER	,
  modifier_source_value		    VARCHAR(50)
)
;


--HINT DISTRIBUTE_ON_KEY(person_id)
CREATE TABLE drug_exposure
(
  drug_exposure_id				BIGINT ,
  person_id						BIGINT ,
  drug_concept_id				INTEGER	,
  drug_exposure_start_date		TIMESTAMP ,
  drug_exposure_start_datetime  TIMESTAMP	,
  drug_exposure_end_date		TIMESTAMP ,
  drug_exposure_end_datetime	TIMESTAMP	,
  verbatim_end_date				TIMESTAMP ,
  drug_type_concept_id			INTEGER		,
  stop_reason					VARCHAR(20) ,
  refills						INTEGER	,
  quantity						FLOAT ,
  days_supply					INTEGER	,
  sig							STRING ,
  route_concept_id				INTEGER	,
  lot_number					VARCHAR(50) ,
  provider_id					BIGINT	,
  visit_occurrence_id			BIGINT	,
  visit_detail_id               BIGINT ,
  drug_source_value				VARCHAR(50) ,
  drug_source_concept_id		INTEGER	,
  route_source_value			VARCHAR(50) ,
  dose_unit_source_value		VARCHAR(50)
)
;


--HINT DISTRIBUTE_ON_KEY(person_id)
CREATE TABLE device_exposure
(
  device_exposure_id			  BIGINT ,
  person_id						  BIGINT ,
  device_concept_id			      INTEGER	,
  device_exposure_start_date	  TIMESTAMP ,
  device_exposure_start_datetime  TIMESTAMP	,
  device_exposure_end_date		  TIMESTAMP ,
  device_exposure_end_datetime    TIMESTAMP	,
  device_type_concept_id		  INTEGER		,
  unique_device_id			      VARCHAR(50) ,
  quantity						  INTEGER		,
  provider_id					  BIGINT		,
  visit_occurrence_id			  BIGINT		,
  visit_detail_id                 BIGINT   ,
  device_source_value			  VARCHAR(100) ,
  device_source_concept_id		  INTEGER
)
;


--HINT DISTRIBUTE_ON_KEY(person_id)
CREATE TABLE condition_occurrence
(
  condition_occurrence_id		    BIGINT ,
  person_id						    BIGINT ,
  condition_concept_id			    INTEGER	,
  condition_start_date			    TIMESTAMP ,
  condition_start_datetime		  	TIMESTAMP	,
  condition_end_date			    TIMESTAMP ,
  condition_end_datetime		    TIMESTAMP	,
  condition_type_concept_id		  	INTEGER	,
  condition_status_concept_id	  	INTEGER	,
  stop_reason					    VARCHAR(20) ,
  provider_id					    BIGINT	,
  visit_occurrence_id			    BIGINT	,
  visit_detail_id               	BIGINT ,
  condition_source_value		    VARCHAR(50) ,
  condition_source_concept_id	  	INTEGER	,
  condition_status_source_value		VARCHAR(50)
)
;


--HINT DISTRIBUTE_ON_KEY(person_id)
CREATE TABLE measurement
(
  measurement_id				    BIGINT ,
  person_id						    BIGINT ,
  measurement_concept_id		    INTEGER	,
  measurement_date				    TIMESTAMP ,
  measurement_datetime			    TIMESTAMP	,
  measurement_time              	VARCHAR(10),
  measurement_type_concept_id	  	INTEGER		,
  operator_concept_id			    INTEGER		,
  value_as_number				    FLOAT ,
  value_as_concept_id			    INTEGER		,
  unit_concept_id				    INTEGER		,
  range_low					        FLOAT ,
  range_high					    FLOAT ,
  provider_id					    BIGINT		,
  visit_occurrence_id			    BIGINT		,
  visit_detail_id               	BIGINT   ,
  measurement_source_value		  	VARCHAR(50) ,
  measurement_source_concept_id		INTEGER		,
  unit_source_value				    VARCHAR(50) ,
  value_source_value			    VARCHAR(50)
)
;


--HINT DISTRIBUTE_ON_KEY(person_id)
CREATE TABLE note
(
  note_id						BIGINT ,
  person_id						BIGINT ,
  note_event_id         		BIGINT , 
  note_event_field_concept_id	INTEGER , 
  note_date			 	  		TIMESTAMP ,
  note_datetime					TIMESTAMP	,
  note_type_concept_id			INTEGER	,
  note_class_concept_id 		INTEGER	,
  note_title					VARCHAR(250) ,
  note_text						STRING ,
  encoding_concept_id			INTEGER	,
  language_concept_id			INTEGER	,
  provider_id					BIGINT	,
  visit_occurrence_id			BIGINT	,
  visit_detail_id       		BIGINT ,
  note_source_value				VARCHAR(50)
)
;


CREATE TABLE note_nlp
(
  note_nlp_id					BIGINT ,
  note_id						BIGINT ,
  section_concept_id			INTEGER	,
  snippet						VARCHAR(250) ,
  `offset`					    VARCHAR(250) ,
  lexical_variant				VARCHAR(250) ,
  note_nlp_concept_id			INTEGER	,
  nlp_system					VARCHAR(250) ,
  nlp_date						TIMESTAMP ,
  nlp_datetime					TIMESTAMP	,
  term_exists					VARCHAR(1) ,
  term_temporal					VARCHAR(50) ,
  term_modifiers				VARCHAR(2000) ,
  note_nlp_source_concept_id	INTEGER
)
;


--HINT DISTRIBUTE_ON_KEY(person_id)
CREATE TABLE observation
(
  observation_id					BIGINT ,
  person_id						    BIGINT ,
  observation_concept_id			INTEGER	,
  observation_date				    TIMESTAMP ,
  observation_datetime				TIMESTAMP	,
  observation_type_concept_id	    INTEGER	,
  value_as_number				    FLOAT ,
  value_as_string				    VARCHAR(60) ,
  value_as_concept_id			    INTEGER	,
  qualifier_concept_id			    INTEGER	,
  unit_concept_id				    INTEGER	,
  provider_id					    BIGINT	,
  visit_occurrence_id			    BIGINT ,
  visit_detail_id               	BIGINT ,
  observation_source_value		  	VARCHAR(50) ,
  observation_source_concept_id		INTEGER	,
  unit_source_value				    VARCHAR(50) ,
  qualifier_source_value		    VARCHAR(50) ,
  observation_event_id			    BIGINT , 
  obs_event_field_concept_id		INTEGER	, 
  value_as_datetime					TIMESTAMP
)
;


CREATE TABLE survey_conduct
(
  survey_conduct_id					BIGINT ,
  person_id						    BIGINT ,
  survey_concept_id			  		INTEGER	,
  survey_start_date				    TIMESTAMP ,
  survey_start_datetime				TIMESTAMP	,
  survey_end_date					TIMESTAMP ,
  survey_end_datetime				TIMESTAMP	,
  provider_id						BIGINT ,
  assisted_concept_id	  			INTEGER	,
  respondent_type_concept_id		INTEGER	,
  timing_concept_id					INTEGER	,
  collection_method_concept_id		INTEGER	,
  assisted_source_value		  		VARCHAR(50) ,
  respondent_type_source_value		VARCHAR(100) ,
  timing_source_value				VARCHAR(100) ,
  collection_method_source_value	VARCHAR(100) ,
  survey_source_value				VARCHAR(100) ,
  survey_source_concept_id			INTEGER	,
  survey_source_identifier			VARCHAR(100) ,
  validated_survey_concept_id		INTEGER	,
  validated_survey_source_value		VARCHAR(100) ,
  survey_version_number			    VARCHAR(20) ,
  visit_occurrence_id				BIGINT ,
  visit_detail_id					BIGINT ,
  response_visit_occurrence_id	BIGINT
)
;


CREATE TABLE fact_relationship
(
  domain_concept_id_1			INTEGER	,
  fact_id_1						BIGINT ,
  domain_concept_id_2			INTEGER	,
  fact_id_2						BIGINT ,
  relationship_concept_id		INTEGER
)
;


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

Standardized health system data

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


CREATE TABLE `location`
(
  location_id					  BIGINT ,
  address_1						  VARCHAR(50) ,
  address_2						  VARCHAR(50) ,
  city							  VARCHAR(50) ,
  state							  VARCHAR(2) ,
  zip							  VARCHAR(9) ,
  county						  VARCHAR(20) ,
  country						  VARCHAR(100) ,
  location_source_value 		  VARCHAR(50) ,
  latitude						  FLOAT ,
  longitude						  FLOAT
)
;

CREATE TABLE location_history
(
  location_history_id           BIGINT ,
  location_id			        BIGINT ,
  relationship_type_concept_id	INTEGER	,  
  domain_id				        VARCHAR(50) ,
  entity_id				        BIGINT ,
  start_date			        TIMESTAMP ,
  end_date				        TIMESTAMP
)
;


CREATE TABLE care_site
(
  care_site_id					BIGINT ,
  care_site_name				VARCHAR(255) ,
  place_of_service_concept_id	INTEGER	,
  location_id					BIGINT ,
  care_site_source_value		VARCHAR(50) ,
  place_of_service_source_value	VARCHAR(50)
)
;


CREATE TABLE provider
(
  provider_id					BIGINT ,
  provider_name					VARCHAR(255) ,
  NPI							VARCHAR(20) ,
  DEA							VARCHAR(20) ,
  specialty_concept_id			INTEGER	,
  care_site_id					BIGINT ,
  year_of_birth					INTEGER	,
  gender_concept_id				INTEGER	,
  provider_source_value			VARCHAR(50) ,
  specialty_source_value		VARCHAR(50) ,
  specialty_source_concept_id	INTEGER	,
  gender_source_value			VARCHAR(50) ,
  gender_source_concept_id		INTEGER
)
;


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

Standardized health economics

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


--HINT DISTRIBUTE_ON_KEY(person_id)
CREATE TABLE payer_plan_period
(
  payer_plan_period_id			BIGINT ,
  person_id						BIGINT ,
  contract_person_id            BIGINT ,
  payer_plan_period_start_date  TIMESTAMP ,
  payer_plan_period_end_date	TIMESTAMP ,
  payer_concept_id              INTEGER ,
  plan_concept_id               INTEGER ,
  contract_concept_id           INTEGER ,
  sponsor_concept_id            INTEGER ,
  stop_reason_concept_id        INTEGER ,
  payer_source_value			VARCHAR(50) ,
  payer_source_concept_id       INTEGER ,
  plan_source_value				VARCHAR(50) ,
  plan_source_concept_id        INTEGER ,
  contract_source_value         VARCHAR(50) ,
  contract_source_concept_id    INTEGER ,
  sponsor_source_value          VARCHAR(50) ,
  sponsor_source_concept_id     INTEGER ,
  family_source_value			VARCHAR(50) ,
  stop_reason_source_value      VARCHAR(50) ,
  stop_reason_source_concept_id INTEGER
)
;


CREATE TABLE cost
(
  cost_id						BIGINT ,
  person_id						BIGINT,
  cost_event_id					BIGINT ,
  cost_event_field_concept_id	INTEGER	, 
  cost_concept_id				INTEGER	,
  cost_type_concept_id		  	INTEGER ,
  currency_concept_id			INTEGER	,
  cost							FLOAT ,
  incurred_date					TIMESTAMP ,
  billed_date					TIMESTAMP ,
  paid_date						TIMESTAMP ,
  revenue_code_concept_id		INTEGER	,
  drg_concept_id				INTEGER	,
  cost_source_value				VARCHAR(50) ,
  cost_source_concept_id		INTEGER	,
  revenue_code_source_value		VARCHAR(50) ,
  drg_source_value			    VARCHAR(3) ,
  payer_plan_period_id			BIGINT
)
;


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

Standardized derived elements

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


--HINT DISTRIBUTE_ON_KEY(person_id)
CREATE TABLE drug_era
(
  drug_era_id				BIGINT ,
  person_id					BIGINT ,
  drug_concept_id			INTEGER	,
  drug_era_start_datetime	TIMESTAMP ,
  drug_era_end_datetime		TIMESTAMP ,
  drug_exposure_count		INTEGER	,
  gap_days					INTEGER
)
;


--HINT DISTRIBUTE_ON_KEY(person_id)
CREATE TABLE dose_era
(
  dose_era_id				BIGINT ,
  person_id					BIGINT ,
  drug_concept_id			INTEGER	,
  unit_concept_id			INTEGER	,
  dose_value				FLOAT ,
  dose_era_start_datetime	TIMESTAMP ,
  dose_era_end_datetime		TIMESTAMP
)
;


--HINT DISTRIBUTE_ON_KEY(person_id)
CREATE TABLE condition_era
(
  condition_era_id					BIGINT ,
  person_id							BIGINT ,
  condition_concept_id				INTEGER	,
  condition_era_start_datetime		TIMESTAMP ,
  condition_era_end_datetime		TIMESTAMP ,
  condition_occurrence_count		INTEGER
)
;