511 lines
17 KiB
SQL
511 lines
17 KiB
SQL
--impala CDM DDL Specification for OMOP Common Data Model 5.4
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--HINT DISTRIBUTE ON KEY (person_id)
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CREATE TABLE @cdmDatabaseSchema.person (
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person_id INT,
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gender_concept_id INT,
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year_of_birth INT,
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month_of_birth integer NULL,
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day_of_birth integer NULL,
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birth_datetime TIMESTAMP,
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race_concept_id INT,
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ethnicity_concept_id INT,
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location_id integer NULL,
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provider_id integer NULL,
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care_site_id integer NULL,
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person_source_value VARCHAR(50),
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gender_source_value VARCHAR(50),
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gender_source_concept_id integer NULL,
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race_source_value VARCHAR(50),
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race_source_concept_id integer NULL,
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ethnicity_source_value VARCHAR(50),
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ethnicity_source_concept_id integer NULL );
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--HINT DISTRIBUTE ON KEY (person_id)
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CREATE TABLE @cdmDatabaseSchema.observation_period (
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observation_period_id INT,
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person_id INT,
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observation_period_start_date TIMESTAMP,
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observation_period_end_date TIMESTAMP,
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period_type_concept_id INT );
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--HINT DISTRIBUTE ON KEY (person_id)
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CREATE TABLE @cdmDatabaseSchema.visit_occurrence (
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visit_occurrence_id INT,
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person_id INT,
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visit_concept_id INT,
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visit_start_date TIMESTAMP,
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visit_start_datetime TIMESTAMP,
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visit_end_date TIMESTAMP,
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visit_end_datetime TIMESTAMP,
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visit_type_concept_id INT,
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provider_id integer NULL,
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care_site_id integer NULL,
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visit_source_value VARCHAR(50),
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visit_source_concept_id integer NULL,
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admitted_from_concept_id integer NULL,
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admitted_from_source_value VARCHAR(50),
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discharged_to_concept_id integer NULL,
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discharged_to_source_value VARCHAR(50),
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preceding_visit_occurrence_id integer NULL );
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--HINT DISTRIBUTE ON KEY (person_id)
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CREATE TABLE @cdmDatabaseSchema.visit_detail (
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visit_detail_id INT,
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person_id INT,
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visit_detail_concept_id INT,
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visit_detail_start_date TIMESTAMP,
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visit_detail_start_datetime TIMESTAMP,
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visit_detail_end_date TIMESTAMP,
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visit_detail_end_datetime TIMESTAMP,
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visit_detail_type_concept_id INT,
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provider_id integer NULL,
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care_site_id integer NULL,
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visit_detail_source_value VARCHAR(50),
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visit_detail_source_concept_id Integer NULL,
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admitted_from_concept_id Integer NULL,
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admitted_from_source_value VARCHAR(50),
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discharged_to_source_value VARCHAR(50),
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discharged_to_concept_id integer NULL,
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preceding_visit_detail_id integer NULL,
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parent_visit_detail_id integer NULL,
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visit_occurrence_id INT );
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--HINT DISTRIBUTE ON KEY (person_id)
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CREATE TABLE @cdmDatabaseSchema.condition_occurrence (
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condition_occurrence_id INT,
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person_id INT,
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condition_concept_id INT,
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condition_start_date TIMESTAMP,
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condition_start_datetime TIMESTAMP,
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condition_end_date TIMESTAMP,
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condition_end_datetime TIMESTAMP,
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condition_type_concept_id INT,
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condition_status_concept_id integer NULL,
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stop_reason VARCHAR(20),
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provider_id integer NULL,
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visit_occurrence_id integer NULL,
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visit_detail_id integer NULL,
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condition_source_value VARCHAR(50),
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condition_source_concept_id integer NULL,
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condition_status_source_value VARCHAR(50) );
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--HINT DISTRIBUTE ON KEY (person_id)
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CREATE TABLE @cdmDatabaseSchema.drug_exposure (
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drug_exposure_id INT,
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person_id INT,
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drug_concept_id INT,
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drug_exposure_start_date TIMESTAMP,
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drug_exposure_start_datetime TIMESTAMP,
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drug_exposure_end_date TIMESTAMP,
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drug_exposure_end_datetime TIMESTAMP,
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verbatim_end_date TIMESTAMP,
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drug_type_concept_id INT,
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stop_reason VARCHAR(20),
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refills integer NULL,
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quantity FLOAT,
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days_supply integer NULL,
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sig VARCHAR(MAX),
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route_concept_id integer NULL,
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lot_number VARCHAR(50),
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provider_id integer NULL,
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visit_occurrence_id integer NULL,
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visit_detail_id integer NULL,
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drug_source_value VARCHAR(50),
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drug_source_concept_id integer NULL,
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route_source_value VARCHAR(50),
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dose_unit_source_value VARCHAR(50) );
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--HINT DISTRIBUTE ON KEY (person_id)
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CREATE TABLE @cdmDatabaseSchema.procedure_occurrence (
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procedure_occurrence_id INT,
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person_id INT,
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procedure_concept_id INT,
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procedure_date TIMESTAMP,
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procedure_datetime TIMESTAMP,
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procedure_end_date TIMESTAMP,
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procedure_end_datetime TIMESTAMP,
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procedure_type_concept_id INT,
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modifier_concept_id integer NULL,
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quantity integer NULL,
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provider_id integer NULL,
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visit_occurrence_id integer NULL,
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visit_detail_id integer NULL,
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procedure_source_value VARCHAR(50),
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procedure_source_concept_id integer NULL,
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modifier_source_value VARCHAR(50) );
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--HINT DISTRIBUTE ON KEY (person_id)
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CREATE TABLE @cdmDatabaseSchema.device_exposure (
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device_exposure_id INT,
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person_id INT,
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device_concept_id INT,
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device_exposure_start_date TIMESTAMP,
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device_exposure_start_datetime TIMESTAMP,
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device_exposure_end_date TIMESTAMP,
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device_exposure_end_datetime TIMESTAMP,
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device_type_concept_id INT,
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unique_device_id VARCHAR(255),
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production_id VARCHAR(255),
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quantity integer NULL,
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provider_id integer NULL,
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visit_occurrence_id integer NULL,
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visit_detail_id integer NULL,
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device_source_value VARCHAR(50),
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device_source_concept_id integer NULL,
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unit_concept_id integer NULL,
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unit_source_value VARCHAR(50),
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unit_source_concept_id integer NULL );
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--HINT DISTRIBUTE ON KEY (person_id)
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CREATE TABLE @cdmDatabaseSchema.measurement (
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measurement_id INT,
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person_id INT,
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measurement_concept_id INT,
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measurement_date TIMESTAMP,
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measurement_datetime TIMESTAMP,
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measurement_time VARCHAR(10),
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measurement_type_concept_id INT,
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operator_concept_id integer NULL,
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value_as_number FLOAT,
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value_as_concept_id integer NULL,
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unit_concept_id integer NULL,
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range_low FLOAT,
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range_high FLOAT,
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provider_id integer NULL,
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visit_occurrence_id integer NULL,
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visit_detail_id integer NULL,
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measurement_source_value VARCHAR(50),
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measurement_source_concept_id integer NULL,
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unit_source_value VARCHAR(50),
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unit_source_concept_id integer NULL,
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value_source_value VARCHAR(50),
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measurement_event_id integer NULL,
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meas_event_field_concept_id integer NULL );
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--HINT DISTRIBUTE ON KEY (person_id)
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CREATE TABLE @cdmDatabaseSchema.observation (
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observation_id INT,
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person_id INT,
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observation_concept_id INT,
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observation_date TIMESTAMP,
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observation_datetime TIMESTAMP,
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observation_type_concept_id INT,
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value_as_number FLOAT,
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value_as_string VARCHAR(60),
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value_as_concept_id Integer NULL,
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qualifier_concept_id integer NULL,
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unit_concept_id integer NULL,
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provider_id integer NULL,
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visit_occurrence_id integer NULL,
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visit_detail_id integer NULL,
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observation_source_value VARCHAR(50),
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observation_source_concept_id integer NULL,
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unit_source_value VARCHAR(50),
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qualifier_source_value VARCHAR(50),
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value_source_value VARCHAR(50),
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observation_event_id integer NULL,
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obs_event_field_concept_id integer NULL );
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--HINT DISTRIBUTE ON KEY (person_id)
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CREATE TABLE @cdmDatabaseSchema.death (
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person_id INT,
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death_date TIMESTAMP,
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death_datetime TIMESTAMP,
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death_type_concept_id integer NULL,
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cause_concept_id integer NULL,
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cause_source_value VARCHAR(50),
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cause_source_concept_id integer NULL );
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--HINT DISTRIBUTE ON KEY (person_id)
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CREATE TABLE @cdmDatabaseSchema.note (
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note_id INT,
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person_id INT,
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note_date TIMESTAMP,
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note_datetime TIMESTAMP,
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note_type_concept_id INT,
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note_class_concept_id INT,
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note_title VARCHAR(250),
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note_text VARCHAR(MAX),
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encoding_concept_id INT,
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language_concept_id INT,
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provider_id integer NULL,
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visit_occurrence_id integer NULL,
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visit_detail_id integer NULL,
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note_source_value VARCHAR(50),
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note_event_id integer NULL,
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note_event_field_concept_id integer NULL );
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--HINT DISTRIBUTE ON RANDOM
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CREATE TABLE @cdmDatabaseSchema.note_nlp (
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note_nlp_id INT,
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note_id INT,
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section_concept_id integer NULL,
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snippet VARCHAR(250),
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"offset" VARCHAR(50),
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lexical_variant VARCHAR(250),
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note_nlp_concept_id integer NULL,
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note_nlp_source_concept_id integer NULL,
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nlp_system VARCHAR(250),
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nlp_date TIMESTAMP,
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nlp_datetime TIMESTAMP,
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term_exists VARCHAR(1),
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term_temporal VARCHAR(50),
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term_modifiers VARCHAR(2000) );
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--HINT DISTRIBUTE ON KEY (person_id)
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CREATE TABLE @cdmDatabaseSchema.specimen (
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specimen_id INT,
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person_id INT,
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specimen_concept_id INT,
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specimen_type_concept_id INT,
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specimen_date TIMESTAMP,
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specimen_datetime TIMESTAMP,
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quantity FLOAT,
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unit_concept_id integer NULL,
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anatomic_site_concept_id integer NULL,
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disease_status_concept_id integer NULL,
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specimen_source_id VARCHAR(50),
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specimen_source_value VARCHAR(50),
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unit_source_value VARCHAR(50),
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anatomic_site_source_value VARCHAR(50),
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disease_status_source_value VARCHAR(50) );
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--HINT DISTRIBUTE ON RANDOM
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CREATE TABLE @cdmDatabaseSchema.fact_relationship (
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domain_concept_id_1 INT,
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fact_id_1 INT,
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domain_concept_id_2 INT,
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fact_id_2 INT,
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relationship_concept_id INT );
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--HINT DISTRIBUTE ON RANDOM
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CREATE TABLE @cdmDatabaseSchema.`location` (
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location_id INT,
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address_1 VARCHAR(50),
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address_2 VARCHAR(50),
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city VARCHAR(50),
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state VARCHAR(2),
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zip VARCHAR(9),
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county VARCHAR(20),
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location_source_value VARCHAR(50),
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country_concept_id integer NULL,
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country_source_value VARCHAR(80),
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latitude FLOAT,
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longitude FLOAT );
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--HINT DISTRIBUTE ON RANDOM
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CREATE TABLE @cdmDatabaseSchema.care_site (
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care_site_id INT,
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care_site_name VARCHAR(255),
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place_of_service_concept_id integer NULL,
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location_id integer NULL,
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care_site_source_value VARCHAR(50),
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place_of_service_source_value VARCHAR(50) );
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--HINT DISTRIBUTE ON RANDOM
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CREATE TABLE @cdmDatabaseSchema.provider (
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provider_id INT,
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provider_name VARCHAR(255),
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npi VARCHAR(20),
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dea VARCHAR(20),
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specialty_concept_id integer NULL,
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care_site_id integer NULL,
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year_of_birth integer NULL,
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gender_concept_id integer NULL,
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provider_source_value VARCHAR(50),
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specialty_source_value VARCHAR(50),
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specialty_source_concept_id integer NULL,
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gender_source_value VARCHAR(50),
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gender_source_concept_id integer NULL );
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--HINT DISTRIBUTE ON KEY (person_id)
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CREATE TABLE @cdmDatabaseSchema.payer_plan_period (
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payer_plan_period_id INT,
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person_id INT,
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payer_plan_period_start_date TIMESTAMP,
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payer_plan_period_end_date TIMESTAMP,
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payer_concept_id integer NULL,
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payer_source_value VARCHAR(50),
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payer_source_concept_id integer NULL,
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plan_concept_id integer NULL,
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plan_source_value VARCHAR(50),
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plan_source_concept_id integer NULL,
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sponsor_concept_id integer NULL,
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sponsor_source_value VARCHAR(50),
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sponsor_source_concept_id integer NULL,
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family_source_value VARCHAR(50),
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stop_reason_concept_id integer NULL,
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stop_reason_source_value VARCHAR(50),
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stop_reason_source_concept_id integer NULL );
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--HINT DISTRIBUTE ON RANDOM
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CREATE TABLE @cdmDatabaseSchema.cost (
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cost_id INT,
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cost_event_id INT,
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cost_domain_id VARCHAR(20),
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cost_type_concept_id INT,
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currency_concept_id integer NULL,
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total_charge FLOAT,
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total_cost FLOAT,
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total_paid FLOAT,
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paid_by_payer FLOAT,
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paid_by_patient FLOAT,
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paid_patient_copay FLOAT,
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paid_patient_coinsurance FLOAT,
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paid_patient_deductible FLOAT,
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paid_by_primary FLOAT,
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paid_ingredient_cost FLOAT,
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paid_dispensing_fee FLOAT,
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payer_plan_period_id integer NULL,
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amount_allowed FLOAT,
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revenue_code_concept_id integer NULL,
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revenue_code_source_value VARCHAR(50),
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drg_concept_id integer NULL,
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drg_source_value VARCHAR(3) );
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--HINT DISTRIBUTE ON KEY (person_id)
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CREATE TABLE @cdmDatabaseSchema.drug_era (
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drug_era_id INT,
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person_id INT,
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drug_concept_id INT,
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drug_era_start_date TIMESTAMP,
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drug_era_end_date TIMESTAMP,
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drug_exposure_count integer NULL,
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gap_days integer NULL );
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--HINT DISTRIBUTE ON KEY (person_id)
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CREATE TABLE @cdmDatabaseSchema.dose_era (
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dose_era_id INT,
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person_id INT,
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drug_concept_id INT,
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unit_concept_id INT,
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dose_value FLOAT,
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dose_era_start_date TIMESTAMP,
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dose_era_end_date TIMESTAMP );
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--HINT DISTRIBUTE ON KEY (person_id)
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CREATE TABLE @cdmDatabaseSchema.condition_era (
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condition_era_id INT,
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person_id INT,
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condition_concept_id INT,
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condition_era_start_date TIMESTAMP,
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condition_era_end_date TIMESTAMP,
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condition_occurrence_count integer NULL );
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--HINT DISTRIBUTE ON KEY (person_id)
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CREATE TABLE @cdmDatabaseSchema.episode (
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episode_id INT,
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person_id INT,
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episode_concept_id INT,
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episode_start_date TIMESTAMP,
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episode_start_datetime TIMESTAMP,
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episode_end_date TIMESTAMP,
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episode_end_datetime TIMESTAMP,
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episode_parent_id integer NULL,
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episode_number integer NULL,
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episode_object_concept_id INT,
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episode_type_concept_id INT,
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episode_source_value VARCHAR(50),
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episode_source_concept_id integer NULL );
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--HINT DISTRIBUTE ON RANDOM
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CREATE TABLE @cdmDatabaseSchema.episode_event (
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episode_id INT,
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event_id INT,
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episode_event_field_concept_id INT );
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--HINT DISTRIBUTE ON RANDOM
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CREATE TABLE @cdmDatabaseSchema.metadata (
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metadata_id INT,
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metadata_concept_id INT,
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metadata_type_concept_id INT,
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name VARCHAR(250),
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value_as_string VARCHAR(250),
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value_as_concept_id integer NULL,
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value_as_number FLOAT,
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metadata_date TIMESTAMP,
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metadata_datetime TIMESTAMP );
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--HINT DISTRIBUTE ON RANDOM
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CREATE TABLE @cdmDatabaseSchema.cdm_source (
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cdm_source_name VARCHAR(255),
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cdm_source_abbreviation VARCHAR(25),
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cdm_holder VARCHAR(255),
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source_description VARCHAR(MAX),
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source_documentation_reference VARCHAR(255),
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cdm_etl_reference VARCHAR(255),
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source_release_date TIMESTAMP,
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cdm_release_date TIMESTAMP,
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cdm_version VARCHAR(10),
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cdm_version_concept_id INT,
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vocabulary_version VARCHAR(20) );
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--HINT DISTRIBUTE ON RANDOM
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CREATE TABLE @cdmDatabaseSchema.concept (
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concept_id INT,
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concept_name VARCHAR(255),
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domain_id VARCHAR(20),
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vocabulary_id VARCHAR(20),
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concept_class_id VARCHAR(20),
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standard_concept VARCHAR(1),
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concept_code VARCHAR(50),
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valid_start_date TIMESTAMP,
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valid_end_date TIMESTAMP,
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invalid_reason VARCHAR(1) );
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--HINT DISTRIBUTE ON RANDOM
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CREATE TABLE @cdmDatabaseSchema.vocabulary (
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vocabulary_id VARCHAR(20),
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vocabulary_name VARCHAR(255),
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vocabulary_reference VARCHAR(255),
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vocabulary_version VARCHAR(255),
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vocabulary_concept_id INT );
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--HINT DISTRIBUTE ON RANDOM
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CREATE TABLE @cdmDatabaseSchema.domain (
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domain_id VARCHAR(20),
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domain_name VARCHAR(255),
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domain_concept_id INT );
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--HINT DISTRIBUTE ON RANDOM
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CREATE TABLE @cdmDatabaseSchema.concept_class (
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concept_class_id VARCHAR(20),
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concept_class_name VARCHAR(255),
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concept_class_concept_id INT );
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--HINT DISTRIBUTE ON RANDOM
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CREATE TABLE @cdmDatabaseSchema.concept_relationship (
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concept_id_1 INT,
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concept_id_2 INT,
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relationship_id VARCHAR(20),
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valid_start_date TIMESTAMP,
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valid_end_date TIMESTAMP,
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invalid_reason VARCHAR(1) );
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--HINT DISTRIBUTE ON RANDOM
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CREATE TABLE @cdmDatabaseSchema.relationship (
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relationship_id VARCHAR(20),
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relationship_name VARCHAR(255),
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is_hierarchical VARCHAR(1),
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defines_ancestry VARCHAR(1),
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reverse_relationship_id VARCHAR(20),
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relationship_concept_id INT );
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--HINT DISTRIBUTE ON RANDOM
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CREATE TABLE @cdmDatabaseSchema.concept_synonym (
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concept_id INT,
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concept_synonym_name VARCHAR(1000),
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language_concept_id INT );
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--HINT DISTRIBUTE ON RANDOM
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CREATE TABLE @cdmDatabaseSchema.concept_ancestor (
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ancestor_concept_id INT,
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descendant_concept_id INT,
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min_levels_of_separation INT,
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max_levels_of_separation INT );
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--HINT DISTRIBUTE ON RANDOM
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CREATE TABLE @cdmDatabaseSchema.source_to_concept_map (
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source_code VARCHAR(50),
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source_concept_id INT,
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source_vocabulary_id VARCHAR(20),
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source_code_description VARCHAR(255),
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target_concept_id INT,
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target_vocabulary_id VARCHAR(20),
|
|
valid_start_date TIMESTAMP,
|
|
valid_end_date TIMESTAMP,
|
|
invalid_reason VARCHAR(1) );
|
|
--HINT DISTRIBUTE ON RANDOM
|
|
CREATE TABLE @cdmDatabaseSchema.drug_strength (
|
|
drug_concept_id INT,
|
|
ingredient_concept_id INT,
|
|
amount_value FLOAT,
|
|
amount_unit_concept_id integer NULL,
|
|
numerator_value FLOAT,
|
|
numerator_unit_concept_id integer NULL,
|
|
denominator_value FLOAT,
|
|
denominator_unit_concept_id integer NULL,
|
|
box_size integer NULL,
|
|
valid_start_date TIMESTAMP,
|
|
valid_end_date TIMESTAMP,
|
|
invalid_reason VARCHAR(1) );
|
|
--HINT DISTRIBUTE ON RANDOM
|
|
CREATE TABLE @cdmDatabaseSchema.cohort (
|
|
cohort_definition_id INT,
|
|
subject_id INT,
|
|
cohort_start_date TIMESTAMP,
|
|
cohort_end_date TIMESTAMP );
|
|
--HINT DISTRIBUTE ON RANDOM
|
|
CREATE TABLE @cdmDatabaseSchema.cohort_definition (
|
|
cohort_definition_id INT,
|
|
cohort_definition_name VARCHAR(255),
|
|
cohort_definition_description VARCHAR(MAX),
|
|
definition_type_concept_id INT,
|
|
cohort_definition_syntax VARCHAR(MAX),
|
|
subject_concept_id INT,
|
|
cohort_initiation_date TIMESTAMP ); |