545 lines
16 KiB
MySQL
545 lines
16 KiB
MySQL
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--impala CDM DDL Specification for OMOP Common Data Model v5_3_1
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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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admitting_source_concept_id integer NULL,
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admitting_source_value VARCHAR(50),
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discharge_to_concept_id integer NULL,
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discharge_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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admitting_source_value VARCHAR(50),
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admitting_source_concept_id Integer NULL,
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discharge_to_source_value VARCHAR(50),
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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 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_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(50),
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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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--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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value_source_value VARCHAR(50) );
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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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--HINT DISTRIBUTE ON KEY (person_id)
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CREATE TABLE @cdmDatabaseSchema.DEATH (
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person_id integer NULL,
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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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--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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--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,
|
||
|
|
drug_concept_id INT,
|
||
|
|
drug_era_start_date TIMESTAMP,
|
||
|
|
drug_era_end_date TIMESTAMP,
|
||
|
|
drug_exposure_count integer NULL,
|
||
|
|
gap_days integer NULL );
|
||
|
|
|
||
|
|
--HINT DISTRIBUTE ON KEY (person_id)
|
||
|
|
CREATE TABLE @cdmDatabaseSchema.DOSE_ERA (
|
||
|
|
|
||
|
|
dose_era_id INT,
|
||
|
|
person_id INT,
|
||
|
|
drug_concept_id INT,
|
||
|
|
unit_concept_id INT,
|
||
|
|
dose_value FLOAT,
|
||
|
|
dose_era_start_date TIMESTAMP,
|
||
|
|
dose_era_end_date TIMESTAMP );
|
||
|
|
|
||
|
|
--HINT DISTRIBUTE ON KEY (person_id)
|
||
|
|
CREATE TABLE @cdmDatabaseSchema.CONDITION_ERA (
|
||
|
|
|
||
|
|
condition_era_id INT,
|
||
|
|
person_id INT,
|
||
|
|
condition_concept_id INT,
|
||
|
|
condition_era_start_date TIMESTAMP,
|
||
|
|
condition_era_end_date TIMESTAMP,
|
||
|
|
condition_occurrence_count integer NULL );
|
||
|
|
|
||
|
|
--HINT DISTRIBUTE ON RANDOM
|
||
|
|
CREATE TABLE @cdmDatabaseSchema.METADATA (
|
||
|
|
|
||
|
|
metadata_concept_id INT,
|
||
|
|
metadata_type_concept_id INT,
|
||
|
|
name VARCHAR(250),
|
||
|
|
value_as_string VARCHAR(250),
|
||
|
|
value_as_concept_id integer NULL,
|
||
|
|
metadata_date TIMESTAMP,
|
||
|
|
metadata_datetime TIMESTAMP );
|
||
|
|
|
||
|
|
--HINT DISTRIBUTE ON RANDOM
|
||
|
|
CREATE TABLE @cdmDatabaseSchema.CDM_SOURCE (
|
||
|
|
|
||
|
|
cdm_source_name VARCHAR(255),
|
||
|
|
cdm_source_abbreviation VARCHAR(25),
|
||
|
|
cdm_holder VARCHAR(255),
|
||
|
|
source_description VARCHAR(MAX),
|
||
|
|
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) );
|
||
|
|
|
||
|
|
--HINT DISTRIBUTE ON RANDOM
|
||
|
|
CREATE TABLE @cdmDatabaseSchema.CONCEPT (
|
||
|
|
|
||
|
|
concept_id INT,
|
||
|
|
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) );
|
||
|
|
|
||
|
|
--HINT DISTRIBUTE ON RANDOM
|
||
|
|
CREATE TABLE @cdmDatabaseSchema.VOCABULARY (
|
||
|
|
|
||
|
|
vocabulary_id VARCHAR(20),
|
||
|
|
vocabulary_name VARCHAR(255),
|
||
|
|
vocabulary_reference VARCHAR(255),
|
||
|
|
vocabulary_version VARCHAR(255),
|
||
|
|
vocabulary_concept_id INT );
|
||
|
|
|
||
|
|
--HINT DISTRIBUTE ON RANDOM
|
||
|
|
CREATE TABLE @cdmDatabaseSchema.DOMAIN (
|
||
|
|
|
||
|
|
domain_id VARCHAR(20),
|
||
|
|
domain_name VARCHAR(255),
|
||
|
|
domain_concept_id INT );
|
||
|
|
|
||
|
|
--HINT DISTRIBUTE ON RANDOM
|
||
|
|
CREATE TABLE @cdmDatabaseSchema.CONCEPT_CLASS (
|
||
|
|
|
||
|
|
concept_class_id VARCHAR(20),
|
||
|
|
concept_class_name VARCHAR(255),
|
||
|
|
concept_class_concept_id INT );
|
||
|
|
|
||
|
|
--HINT DISTRIBUTE ON RANDOM
|
||
|
|
CREATE TABLE @cdmDatabaseSchema.CONCEPT_RELATIONSHIP (
|
||
|
|
|
||
|
|
concept_id_1 INT,
|
||
|
|
concept_id_2 INT,
|
||
|
|
relationship_id VARCHAR(20),
|
||
|
|
valid_start_date TIMESTAMP,
|
||
|
|
valid_end_date TIMESTAMP,
|
||
|
|
invalid_reason VARCHAR(1) );
|
||
|
|
|
||
|
|
--HINT DISTRIBUTE ON RANDOM
|
||
|
|
CREATE TABLE @cdmDatabaseSchema.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 INT );
|
||
|
|
|
||
|
|
--HINT DISTRIBUTE ON RANDOM
|
||
|
|
CREATE TABLE @cdmDatabaseSchema.CONCEPT_SYNONYM (
|
||
|
|
|
||
|
|
concept_id INT,
|
||
|
|
concept_synonym_name VARCHAR(1000),
|
||
|
|
language_concept_id INT );
|
||
|
|
|
||
|
|
--HINT DISTRIBUTE ON RANDOM
|
||
|
|
CREATE TABLE @cdmDatabaseSchema.CONCEPT_ANCESTOR (
|
||
|
|
|
||
|
|
ancestor_concept_id INT,
|
||
|
|
descendant_concept_id INT,
|
||
|
|
min_levels_of_separation INT,
|
||
|
|
max_levels_of_separation INT );
|
||
|
|
|
||
|
|
--HINT DISTRIBUTE ON RANDOM
|
||
|
|
CREATE TABLE @cdmDatabaseSchema.SOURCE_TO_CONCEPT_MAP (
|
||
|
|
|
||
|
|
source_code VARCHAR(50),
|
||
|
|
source_concept_id INT,
|
||
|
|
source_vocabulary_id VARCHAR(20),
|
||
|
|
source_code_description VARCHAR(255),
|
||
|
|
target_concept_id INT,
|
||
|
|
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_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 );
|
||
|
|
|
||
|
|
--HINT DISTRIBUTE ON RANDOM
|
||
|
|
CREATE TABLE @cdmDatabaseSchema.ATTRIBUTE_DEFINITION (
|
||
|
|
|
||
|
|
attribute_definition_id INT,
|
||
|
|
attribute_name VARCHAR(255),
|
||
|
|
attribute_description VARCHAR(MAX),
|
||
|
|
attribute_type_concept_id INT,
|
||
|
|
attribute_syntax VARCHAR(MAX) );
|