520 lines
18 KiB
MySQL
520 lines
18 KiB
MySQL
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--@targetdialect 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 integer NOT NULL,
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gender_concept_id integer NOT NULL,
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year_of_birth integer NOT NULL,
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month_of_birth integer NULL,
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day_of_birth integer NULL,
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birth_datetime datetime NULL,
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race_concept_id integer NOT NULL,
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ethnicity_concept_id integer NOT NULL,
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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) NULL,
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gender_source_value varchar(50) NULL,
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gender_source_concept_id integer NULL,
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race_source_value varchar(50) NULL,
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race_source_concept_id integer NULL,
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ethnicity_source_value varchar(50) NULL,
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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 integer NOT NULL,
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person_id integer NOT NULL,
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observation_period_start_date date NOT NULL,
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observation_period_end_date date NOT NULL,
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period_type_concept_id integer NOT NULL );
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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 integer NOT NULL,
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person_id integer NOT NULL,
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visit_concept_id integer NOT NULL,
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visit_start_date date NOT NULL,
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visit_start_datetime datetime NULL,
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visit_end_date date NOT NULL,
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visit_end_datetime datetime NULL,
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visit_type_concept_id Integer NOT NULL,
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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) NULL,
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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) NULL,
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discharge_to_concept_id integer NULL,
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discharge_to_source_value varchar(50) NULL,
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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 integer NOT NULL,
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person_id integer NOT NULL,
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visit_detail_concept_id integer NOT NULL,
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visit_detail_start_date date NOT NULL,
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visit_detail_start_datetime datetime NULL,
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visit_detail_end_date date NOT NULL,
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visit_detail_end_datetime datetime NULL,
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visit_detail_type_concept_id integer NOT NULL,
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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) NULL,
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visit_detail_source_concept_id Integer NULL,
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admitted_from_source_value Varchar(50) NULL,
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admitted_from_concept_id Integer NULL,
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discharge_to_source_value Varchar(50) NULL,
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discharge_to_concept_id integer NULL,
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preceding_visit_detail_id integer NULL,
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visit_detail_parent_id integer NULL,
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visit_occurrence_id integer NOT NULL );
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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 integer NOT NULL,
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person_id integer NOT NULL,
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condition_concept_id integer NOT NULL,
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condition_start_date date NOT NULL,
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condition_start_datetime datetime NULL,
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condition_end_date date NULL,
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condition_end_datetime datetime NULL,
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condition_type_concept_id integer NOT NULL,
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condition_status_concept_id integer NULL,
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stop_reason varchar(20) 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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condition_source_value varchar(50) NULL,
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condition_source_concept_id integer NULL,
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condition_status_source_value varchar(50) NULL );
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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 integer NOT NULL,
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person_id integer NOT NULL,
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drug_concept_id integer NOT NULL,
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drug_exposure_start_date date NOT NULL,
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drug_exposure_start_datetime datetime NULL,
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drug_exposure_end_date date NOT NULL,
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drug_exposure_end_datetime datetime NULL,
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verbatim_end_date date NULL,
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drug_type_concept_id integer NOT NULL,
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stop_reason varchar(20) NULL,
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refills integer NULL,
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quantity float NULL,
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days_supply integer NULL,
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sig varchar(MAX) NULL,
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route_concept_id integer NULL,
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lot_number varchar(50) 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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drug_source_value varchar(50) NULL,
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drug_source_concept_id integer NULL,
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route_source_value varchar(50) NULL,
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dose_unit_source_value varchar(50) NULL );
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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 integer NOT NULL,
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person_id integer NOT NULL,
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procedure_concept_id integer NOT NULL,
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procedure_date date NOT NULL,
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procedure_datetime datetime NULL,
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procedure_type_concept_id integer NOT NULL,
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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) NULL,
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procedure_source_concept_id integer NULL,
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modifier_source_value varchar(50) NULL,
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procedure_status_source_value varchar(50) NULL,
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procedure_status_concept_id integer NOT NULL );
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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 integer NOT NULL,
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person_id integer NOT NULL,
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device_concept_id integer NOT NULL,
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device_exposure_start_date date NOT NULL,
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device_exposure_start_datetime datetime NULL,
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device_exposure_end_date date NULL,
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device_exposure_end_datetime datetime NULL,
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device_type_concept_id integer NOT NULL,
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unique_device_id varchar(255) NULL,
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production_id varchar(255) 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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device_source_value varchar(50) NULL,
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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) NULL,
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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 integer NOT NULL,
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person_id integer NOT NULL,
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measurement_concept_id integer NOT NULL,
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measurement_date date NOT NULL,
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measurement_datetime datetime NULL,
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measurement_time varchar(10) NULL,
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measurement_type_concept_id integer NOT NULL,
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operator_concept_id integer NULL,
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value_as_number float NULL,
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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 NULL,
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range_high float 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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measurement_source_value varchar(50) NULL,
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measurement_source_concept_id integer NULL,
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unit_source_value varchar(50) NULL,
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value_source_value varchar(50) 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 integer NOT NULL,
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person_id integer NOT NULL,
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observation_concept_id integer NOT NULL,
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observation_date date NOT NULL,
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observation_datetime datetime NULL,
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observation_type_concept_id integer NOT NULL,
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value_as_number float NULL,
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value_as_string varchar(60) NULL,
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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) NULL,
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observation_source_concept_id integer NULL,
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unit_source_value varchar(50) NULL,
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qualifier_source_value varchar(50) NULL,
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value_source_value varchar(50) 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 integer NOT NULL,
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death_date date NOT NULL,
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death_datetime datetime NULL,
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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) NULL,
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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 integer NOT NULL,
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person_id integer NOT NULL,
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note_date date NOT NULL,
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note_datetime datetime NULL,
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note_type_concept_id integer NOT NULL,
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note_class_concept_id integer NOT NULL,
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note_title varchar(250) NULL,
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note_text varchar(MAX) NOT NULL,
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encoding_concept_id integer NOT NULL,
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language_concept_id integer NOT 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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note_source_value varchar(50) 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 integer NOT NULL,
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note_id integer NOT NULL,
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section_concept_id integer NULL,
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snippet varchar(250) NULL,
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"offset" varchar(50) NULL,
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lexical_variant varchar(250) NOT NULL,
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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) NULL,
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nlp_date date NOT NULL,
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nlp_datetime datetime NULL,
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term_exists varchar(1) NULL,
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term_temporal varchar(50) NULL,
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term_modifiers varchar(2000) NULL );
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--HINT DISTRIBUTE ON KEY (person_id)
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CREATE TABLE @cdmDatabaseSchema.SPECIMEN (
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specimen_id integer NOT NULL,
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person_id integer NOT NULL,
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specimen_concept_id integer NOT NULL,
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specimen_type_concept_id integer NOT NULL,
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specimen_date date NOT NULL,
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specimen_datetime datetime NULL,
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quantity float NULL,
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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) NULL,
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specimen_source_value varchar(50) NULL,
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unit_source_value varchar(50) NULL,
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anatomic_site_source_value varchar(50) NULL,
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disease_status_source_value varchar(50) NULL );
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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 integer NOT NULL,
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fact_id_1 integer NOT NULL,
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domain_concept_id_2 integer NOT NULL,
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fact_id_2 integer NOT NULL,
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relationship_concept_id integer NOT NULL );
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--HINT DISTRIBUTE ON RANDOM
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CREATE TABLE @cdmDatabaseSchema.LOCATION (
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location_id integer NOT NULL,
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address_1 varchar(50) NULL,
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address_2 varchar(50) NULL,
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city varchar(50) NULL,
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state varchar(2) NULL,
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zip varchar(9) NULL,
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county varchar(20) NULL,
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location_source_value varchar(50) NULL,
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country_concept_id integer NULL,
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country_source_value varchar(80) NULL,
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latitude float NULL,
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longitude float NULL );
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--HINT DISTRIBUTE ON RANDOM
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CREATE TABLE @cdmDatabaseSchema.CARE_SITE (
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care_site_id integer NOT NULL,
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care_site_name varchar(255) NULL,
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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) NULL,
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place_of_service_source_value varchar(50) NULL );
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--HINT DISTRIBUTE ON RANDOM
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CREATE TABLE @cdmDatabaseSchema.PROVIDER (
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provider_id integer NOT NULL,
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provider_name varchar(255) NULL,
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npi varchar(20) NULL,
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dea varchar(20) NULL,
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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) NULL,
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specialty_source_value varchar(50) NULL,
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specialty_source_concept_id integer NULL,
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gender_source_value varchar(50) NULL,
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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 integer NOT NULL,
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person_id integer NOT NULL,
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payer_plan_period_start_date date NOT NULL,
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payer_plan_period_end_date date NOT NULL,
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payer_concept_id integer NULL,
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payer_source_value varchar(50) NULL,
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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) NULL,
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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) NULL,
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sponsor_source_concept_id integer NULL,
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family_source_value varchar(50) NULL,
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stop_reason_concept_id integer NULL,
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stop_reason_source_value varchar(50) NULL,
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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 integer NOT NULL,
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cost_event_id integer NOT NULL,
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cost_domain_id varchar(20) NOT NULL,
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cost_type_concept_id integer NOT NULL,
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currency_concept_id integer NULL,
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total_charge float NULL,
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total_cost float NULL,
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total_paid float NULL,
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paid_by_payer float NULL,
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paid_by_patient float NULL,
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paid_patient_copay float NULL,
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paid_patient_coinsurance float NULL,
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paid_patient_deductible float NULL,
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paid_by_primary float NULL,
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paid_ingredient_cost float NULL,
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paid_dispensing_fee float NULL,
|
||
|
|
payer_plan_period_id integer NULL,
|
||
|
|
amount_allowed float NULL,
|
||
|
|
revenue_code_concept_id integer NULL,
|
||
|
|
revenue_code_source_value varchar(50) NULL,
|
||
|
|
drg_concept_id integer NULL,
|
||
|
|
drg_source_value varchar(3) NULL );
|
||
|
|
|
||
|
|
--HINT DISTRIBUTE ON KEY (person_id)
|
||
|
|
CREATE TABLE @cdmDatabaseSchema.DRUG_ERA (
|
||
|
|
drug_era_id integer NOT NULL,
|
||
|
|
person_id integer NOT NULL,
|
||
|
|
drug_concept_id integer NOT NULL,
|
||
|
|
drug_era_start_date datetime NOT NULL,
|
||
|
|
drug_era_end_date datetime NOT NULL,
|
||
|
|
drug_exposure_count integer NULL,
|
||
|
|
gap_days integer NULL );
|
||
|
|
|
||
|
|
--HINT DISTRIBUTE ON KEY (person_id)
|
||
|
|
CREATE TABLE @cdmDatabaseSchema.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 datetime NOT NULL,
|
||
|
|
dose_era_end_date datetime NOT NULL );
|
||
|
|
|
||
|
|
--HINT DISTRIBUTE ON KEY (person_id)
|
||
|
|
CREATE TABLE @cdmDatabaseSchema.CONDITION_ERA (
|
||
|
|
condition_era_id integer NOT NULL,
|
||
|
|
person_id integer NOT NULL,
|
||
|
|
condition_concept_id integer NOT NULL,
|
||
|
|
condition_era_start_date datetime NOT NULL,
|
||
|
|
condition_era_end_date datetime NOT NULL,
|
||
|
|
condition_occurrence_count integer NULL );
|
||
|
|
|
||
|
|
--HINT DISTRIBUTE ON RANDOM
|
||
|
|
CREATE TABLE @cdmDatabaseSchema.METADATA (
|
||
|
|
metadata_concept_id integer NOT NULL,
|
||
|
|
metadata_type_concept_id integer NOT NULL,
|
||
|
|
name varchar(250) NOT NULL,
|
||
|
|
value_as_string varchar(250) NULL,
|
||
|
|
value_as_concept_id integer NULL,
|
||
|
|
metadata_date date NULL,
|
||
|
|
metadata_datetime datetime NULL );
|
||
|
|
|
||
|
|
--HINT DISTRIBUTE ON RANDOM
|
||
|
|
CREATE TABLE @cdmDatabaseSchema.CDM_SOURCE (
|
||
|
|
cdm_source_name varchar(255) NOT NULL,
|
||
|
|
cdm_source_abbreviation varchar(25) NOT NULL,
|
||
|
|
cdm_holder varchar(255) NOT NULL,
|
||
|
|
source_description varchar(MAX) NULL,
|
||
|
|
source_documentation_reference varchar(255) NULL,
|
||
|
|
cdm_etl_reference varchar(255) NULL,
|
||
|
|
source_release_date date NOT NULL,
|
||
|
|
cdm_release_date date NOT NULL,
|
||
|
|
cdm_version varchar(10) NULL,
|
||
|
|
cdm_version_concept_id integer NOT NULL,
|
||
|
|
vocabulary_version varchar(20) NOT NULL );
|
||
|
|
|
||
|
|
--HINT DISTRIBUTE ON RANDOM
|
||
|
|
CREATE TABLE @cdmDatabaseSchema.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 );
|
||
|
|
|
||
|
|
--HINT DISTRIBUTE ON RANDOM
|
||
|
|
CREATE TABLE @cdmDatabaseSchema.VOCABULARY (
|
||
|
|
vocabulary_id varchar(20) NOT NULL,
|
||
|
|
vocabulary_name varchar(255) NOT NULL,
|
||
|
|
vocabulary_reference varchar(255) NOT NULL,
|
||
|
|
vocabulary_version varchar(255) NULL,
|
||
|
|
vocabulary_concept_id integer NOT NULL );
|
||
|
|
|
||
|
|
--HINT DISTRIBUTE ON RANDOM
|
||
|
|
CREATE TABLE @cdmDatabaseSchema.DOMAIN (
|
||
|
|
domain_id varchar(20) NOT NULL,
|
||
|
|
domain_name varchar(255) NOT NULL,
|
||
|
|
domain_concept_id integer NOT NULL );
|
||
|
|
|
||
|
|
--HINT DISTRIBUTE ON RANDOM
|
||
|
|
CREATE TABLE @cdmDatabaseSchema.CONCEPT_CLASS (
|
||
|
|
concept_class_id varchar(20) NOT NULL,
|
||
|
|
concept_class_name varchar(255) NOT NULL,
|
||
|
|
concept_class_concept_id integer NOT NULL );
|
||
|
|
|
||
|
|
--HINT DISTRIBUTE ON RANDOM
|
||
|
|
CREATE TABLE @cdmDatabaseSchema.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 );
|
||
|
|
|
||
|
|
--HINT DISTRIBUTE ON RANDOM
|
||
|
|
CREATE TABLE @cdmDatabaseSchema.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 );
|
||
|
|
|
||
|
|
--HINT DISTRIBUTE ON RANDOM
|
||
|
|
CREATE TABLE @cdmDatabaseSchema.CONCEPT_SYNONYM (
|
||
|
|
concept_id integer NOT NULL,
|
||
|
|
concept_synonym_name varchar(1000) NOT NULL,
|
||
|
|
language_concept_id integer NOT NULL );
|
||
|
|
|
||
|
|
--HINT DISTRIBUTE ON RANDOM
|
||
|
|
CREATE TABLE @cdmDatabaseSchema.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 );
|
||
|
|
|
||
|
|
--HINT DISTRIBUTE ON RANDOM
|
||
|
|
CREATE TABLE @cdmDatabaseSchema.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 );
|
||
|
|
|
||
|
|
--HINT DISTRIBUTE ON RANDOM
|
||
|
|
CREATE TABLE @cdmDatabaseSchema.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 );
|
||
|
|
|
||
|
|
--HINT DISTRIBUTE ON RANDOM
|
||
|
|
CREATE TABLE @cdmDatabaseSchema.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 );
|
||
|
|
|
||
|
|
--HINT DISTRIBUTE ON RANDOM
|
||
|
|
CREATE TABLE @cdmDatabaseSchema.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 );
|