471 lines
17 KiB
MySQL
471 lines
17 KiB
MySQL
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--sqlite CDM DDL Specification for OMOP Common Data Model 5.3
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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 REAL 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 TEXT NULL,
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gender_source_value TEXT NULL,
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gender_source_concept_id integer NULL,
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race_source_value TEXT NULL,
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race_source_concept_id integer NULL,
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ethnicity_source_value TEXT 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 REAL NULL,
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visit_end_date date NOT NULL,
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visit_end_datetime REAL 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 TEXT NULL,
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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 TEXT NULL,
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discharge_to_concept_id integer NULL,
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discharge_to_source_value TEXT 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 REAL NULL,
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visit_detail_end_date date NOT NULL,
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visit_detail_end_datetime REAL 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 TEXT NULL,
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visit_detail_source_concept_id Integer NULL,
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admitting_source_value TEXT NULL,
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admitting_source_concept_id Integer NULL,
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discharge_to_source_value TEXT 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 REAL NULL,
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condition_end_date date NULL,
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condition_end_datetime REAL 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 TEXT 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 TEXT NULL,
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condition_source_concept_id integer NULL,
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condition_status_source_value TEXT 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 REAL NULL,
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drug_exposure_end_date date NOT NULL,
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drug_exposure_end_datetime REAL 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 TEXT NULL,
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refills integer NULL,
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quantity REAL NULL,
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days_supply integer NULL,
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sig TEXT NULL,
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route_concept_id integer NULL,
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lot_number TEXT 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 TEXT NULL,
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drug_source_concept_id integer NULL,
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route_source_value TEXT NULL,
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dose_unit_source_value TEXT 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 REAL 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 TEXT NULL,
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procedure_source_concept_id integer NULL,
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modifier_source_value TEXT 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 REAL NULL,
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device_exposure_end_date date NULL,
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device_exposure_end_datetime REAL NULL,
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device_type_concept_id integer NOT NULL,
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unique_device_id TEXT 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 TEXT NULL,
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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 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 REAL NULL,
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measurement_time TEXT 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 REAL 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 REAL NULL,
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range_high REAL 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 TEXT NULL,
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measurement_source_concept_id integer NULL,
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unit_source_value TEXT NULL,
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value_source_value TEXT 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 REAL NULL,
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observation_type_concept_id integer NOT NULL,
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value_as_number REAL NULL,
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value_as_string TEXT 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 TEXT NULL,
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observation_source_concept_id integer NULL,
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unit_source_value TEXT NULL,
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qualifier_source_value TEXT 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 REAL 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 TEXT 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 REAL 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 TEXT NULL,
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note_text TEXT 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 TEXT 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 TEXT NULL,
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"offset" TEXT NULL,
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lexical_variant TEXT 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 TEXT NULL,
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nlp_date date NOT NULL,
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nlp_datetime REAL NULL,
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term_exists TEXT NULL,
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term_temporal TEXT NULL,
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term_modifiers TEXT 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 REAL NULL,
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quantity REAL 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 TEXT NULL,
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specimen_source_value TEXT NULL,
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unit_source_value TEXT NULL,
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anatomic_site_source_value TEXT NULL,
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disease_status_source_value TEXT 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 TEXT NULL,
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address_2 TEXT NULL,
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city TEXT NULL,
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state TEXT NULL,
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zip TEXT NULL,
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county TEXT NULL,
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location_source_value TEXT 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 TEXT 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 TEXT NULL,
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place_of_service_source_value TEXT 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 TEXT NULL,
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npi TEXT NULL,
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dea TEXT 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 TEXT NULL,
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specialty_source_value TEXT NULL,
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specialty_source_concept_id integer NULL,
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gender_source_value TEXT 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 TEXT 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 TEXT 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 TEXT NULL,
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sponsor_source_concept_id integer NULL,
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family_source_value TEXT NULL,
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stop_reason_concept_id integer NULL,
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stop_reason_source_value TEXT 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 TEXT 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 REAL NULL,
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total_cost REAL NULL,
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total_paid REAL NULL,
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paid_by_payer REAL NULL,
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paid_by_patient REAL NULL,
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paid_patient_copay REAL NULL,
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paid_patient_coinsurance REAL NULL,
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paid_patient_deductible REAL NULL,
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paid_by_primary REAL NULL,
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paid_ingredient_cost REAL NULL,
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paid_dispensing_fee REAL NULL,
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payer_plan_period_id integer NULL,
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amount_allowed REAL NULL,
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revenue_code_concept_id integer NULL,
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revenue_code_source_value TEXT NULL,
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drg_concept_id integer NULL,
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drg_source_value TEXT NULL );
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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 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_era_start_date date NOT NULL,
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drug_era_end_date date NOT NULL,
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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 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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unit_concept_id integer NOT NULL,
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dose_value REAL NOT NULL,
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dose_era_start_date date NOT NULL,
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dose_era_end_date date NOT NULL );
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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 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_era_start_date date NOT NULL,
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condition_era_end_date date NOT NULL,
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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 TEXT NOT NULL,
|
||
|
|
value_as_string TEXT NULL,
|
||
|
|
value_as_concept_id integer NULL,
|
||
|
|
metadata_date date NULL,
|
||
|
|
metadata_datetime REAL NULL );
|
||
|
|
--HINT DISTRIBUTE ON RANDOM
|
||
|
|
CREATE TABLE @cdmDatabaseSchema.cdm_source (
|
||
|
|
cdm_source_name TEXT NOT NULL,
|
||
|
|
cdm_source_abbreviation TEXT NULL,
|
||
|
|
cdm_holder TEXT NULL,
|
||
|
|
source_description TEXT NULL,
|
||
|
|
source_documentation_reference TEXT NULL,
|
||
|
|
cdm_etl_reference TEXT NULL,
|
||
|
|
source_release_date date NULL,
|
||
|
|
cdm_release_date date NULL,
|
||
|
|
cdm_version TEXT NULL,
|
||
|
|
vocabulary_version TEXT NULL );
|
||
|
|
--HINT DISTRIBUTE ON RANDOM
|
||
|
|
CREATE TABLE @cdmDatabaseSchema.concept (
|
||
|
|
concept_id integer NOT NULL,
|
||
|
|
concept_name TEXT NOT NULL,
|
||
|
|
domain_id TEXT NOT NULL,
|
||
|
|
vocabulary_id TEXT NOT NULL,
|
||
|
|
concept_class_id TEXT NOT NULL,
|
||
|
|
standard_concept TEXT NULL,
|
||
|
|
concept_code TEXT NOT NULL,
|
||
|
|
valid_start_date date NOT NULL,
|
||
|
|
valid_end_date date NOT NULL,
|
||
|
|
invalid_reason TEXT NULL );
|
||
|
|
--HINT DISTRIBUTE ON RANDOM
|
||
|
|
CREATE TABLE @cdmDatabaseSchema.vocabulary (
|
||
|
|
vocabulary_id TEXT NOT NULL,
|
||
|
|
vocabulary_name TEXT NOT NULL,
|
||
|
|
vocabulary_reference TEXT NOT NULL,
|
||
|
|
vocabulary_version TEXT NULL,
|
||
|
|
vocabulary_concept_id integer NOT NULL );
|
||
|
|
--HINT DISTRIBUTE ON RANDOM
|
||
|
|
CREATE TABLE @cdmDatabaseSchema.domain (
|
||
|
|
domain_id TEXT NOT NULL,
|
||
|
|
domain_name TEXT NOT NULL,
|
||
|
|
domain_concept_id integer NOT NULL );
|
||
|
|
--HINT DISTRIBUTE ON RANDOM
|
||
|
|
CREATE TABLE @cdmDatabaseSchema.concept_class (
|
||
|
|
concept_class_id TEXT NOT NULL,
|
||
|
|
concept_class_name TEXT 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 TEXT NOT NULL,
|
||
|
|
valid_start_date date NOT NULL,
|
||
|
|
valid_end_date date NOT NULL,
|
||
|
|
invalid_reason TEXT NULL );
|
||
|
|
--HINT DISTRIBUTE ON RANDOM
|
||
|
|
CREATE TABLE @cdmDatabaseSchema.relationship (
|
||
|
|
relationship_id TEXT NOT NULL,
|
||
|
|
relationship_name TEXT NOT NULL,
|
||
|
|
is_hierarchical TEXT NOT NULL,
|
||
|
|
defines_ancestry TEXT NOT NULL,
|
||
|
|
reverse_relationship_id TEXT 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 TEXT 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 TEXT NOT NULL,
|
||
|
|
source_concept_id integer NOT NULL,
|
||
|
|
source_vocabulary_id TEXT NOT NULL,
|
||
|
|
source_code_description TEXT NULL,
|
||
|
|
target_concept_id integer NOT NULL,
|
||
|
|
target_vocabulary_id TEXT NOT NULL,
|
||
|
|
valid_start_date date NOT NULL,
|
||
|
|
valid_end_date date NOT NULL,
|
||
|
|
invalid_reason TEXT NULL );
|
||
|
|
--HINT DISTRIBUTE ON RANDOM
|
||
|
|
CREATE TABLE @cdmDatabaseSchema.drug_strength (
|
||
|
|
drug_concept_id integer NOT NULL,
|
||
|
|
ingredient_concept_id integer NOT NULL,
|
||
|
|
amount_value REAL NULL,
|
||
|
|
amount_unit_concept_id integer NULL,
|
||
|
|
numerator_value REAL NULL,
|
||
|
|
numerator_unit_concept_id integer NULL,
|
||
|
|
denominator_value REAL 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 TEXT NULL );
|
||
|
|
--HINT DISTRIBUTE ON RANDOM
|
||
|
|
CREATE TABLE @cdmDatabaseSchema.cohort_definition (
|
||
|
|
cohort_definition_id integer NOT NULL,
|
||
|
|
cohort_definition_name TEXT NOT NULL,
|
||
|
|
cohort_definition_description TEXT NULL,
|
||
|
|
definition_type_concept_id integer NOT NULL,
|
||
|
|
cohort_definition_syntax TEXT 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 TEXT NOT NULL,
|
||
|
|
attribute_description TEXT NULL,
|
||
|
|
attribute_type_concept_id integer NOT NULL,
|
||
|
|
attribute_syntax TEXT NULL );
|