OMOP/Impala/OMOP CDM impala ddl.txt

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# Copyright 2017-11 Observational Health Data Sciences and Informatics

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# Licensed under the Apache License, Version 2.0 (the "License");

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impala script to create OMOP common data model version 5.3



last revised: 6-Nov-2017



Authors:  Patrick Ryan, Christian Reich, Clair Blacketer




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




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



Standardized vocabulary



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



CREATE TABLE concept (

	concept_id INTEGER,

	concept_name VARCHAR(255),

	domain_id VARCHAR(20),

	vocabulary_id VARCHAR(20),

  concept_class_id VARCHAR(20),

	standard_concept VARCHAR(1),

  concept_code VARCHAR(50),

  valid_start_date TIMESTAMP,

  valid_end_date TIMESTAMP,

  invalid_reason VARCHAR(1)

)

;



CREATE TABLE vocabulary (

    vocabulary_id VARCHAR(20),

    vocabulary_name VARCHAR(255),

    vocabulary_reference VARCHAR(255),
    vocabulary_version VARCHAR(255),

    vocabulary_concept_id INTEGER

)

;




CREATE TABLE domain (

    domain_id VARCHAR(20),

    domain_name VARCHAR(255),

    domain_concept_id INTEGER

)

;




CREATE TABLE concept_class (

    concept_class_id VARCHAR(20),

    concept_class_name VARCHAR(255),

    concept_class_concept_id INTEGER

)

;




CREATE TABLE concept_relationship (

    concept_id_1 INTEGER,

    concept_id_2 INTEGER,

    relationship_id VARCHAR(20),

    valid_start_date TIMESTAMP,

    valid_end_date TIMESTAMP,

    invalid_reason VARCHAR(1)

)

;




CREATE TABLE relationship (

    relationship_id VARCHAR(20),

    relationship_name VARCHAR(255),

    is_hierarchical VARCHAR(1),

    defines_ancestry VARCHAR(1),

    reverse_relationship_id VARCHAR(20),

    relationship_concept_id INTEGER

)

;




CREATE TABLE concept_synonym (

    concept_id INTEGER,

    concept_synonym_name STRING,

    language_concept_id INTEGER

)

;




CREATE TABLE concept_ancestor (

     ancestor_concept_id INTEGER,

     descendant_concept_id INTEGER,

     min_levels_of_separation INTEGER,

     max_levels_of_separation INTEGER

)

;




CREATE TABLE source_to_concept_map (

    source_code VARCHAR(50),

    source_concept_id INTEGER,

    source_vocabulary_id VARCHAR(20),

    source_code_description VARCHAR(255),

    target_concept_id INTEGER,

    target_vocabulary_id VARCHAR(20),

    valid_start_date TIMESTAMP,

    valid_end_date TIMESTAMP,

    invalid_reason VARCHAR(1)

)

;




CREATE TABLE drug_strength (

    drug_concept_id INTEGER,

    ingredient_concept_id INTEGER,

    amount_value FLOAT,

    amount_unit_concept_id INTEGER,

    numerator_value FLOAT,

    numerator_unit_concept_id INTEGER,

    denominator_value FLOAT,

    denominator_unit_concept_id INTEGER,

    box_size INTEGER,

    valid_start_date TIMESTAMP,

    valid_end_date TIMESTAMP,

    invalid_reason VARCHAR(1)

)

;




CREATE TABLE cohort_definition (

    cohort_definition_id INTEGER,

    cohort_definition_name VARCHAR(255),

    cohort_definition_description STRING,

    definition_type_concept_id INTEGER,

    cohort_definition_syntax STRING,

    subject_concept_id INTEGER,

    cohort_initiation_date TIMESTAMP

)

;




CREATE TABLE attribute_definition (

    attribute_definition_id INTEGER,

    attribute_name VARCHAR(255),

    attribute_description STRING,

    attribute_type_concept_id INTEGER,

    attribute_syntax STRING

)

;



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



Standardized meta-data



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



CREATE TABLE cdm_source
(

    cdm_source_name VARCHAR(255),

    cdm_source_abbreviation VARCHAR(25),

    cdm_holder VARCHAR(255),

    source_description STRING,

    source_documentation_reference VARCHAR(255),

    cdm_etl_reference VARCHAR(255),

    source_release_date TIMESTAMP,

    cdm_release_date TIMESTAMP,

    cdm_version VARCHAR(10),

    vocabulary_version VARCHAR(20)

)

;




CREATE TABLE "metadata"
(

    metadata_concept_id INTEGER,

    metadata_type_concept_id INTEGER,

    name VARCHAR(250),

    value_as_string VARCHAR(50),

    value_as_concept_id INTEGER,

    metadata_date TIMESTAMP,

    metadata_datetime TIMESTAMP

)

;



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



Standardized clinical data



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



CREATE TABLE person
(

    person_id INTEGER,

    gender_concept_id INTEGER,

    year_of_birth INTEGER,

    month_of_birth INTEGER,

    day_of_birth INTEGER,

    birth_datetime TIMESTAMP,

    race_concept_id INTEGER,

    ethnicity_concept_id INTEGER,

    location_id INTEGER,

    provider_id INTEGER,

    care_site_id INTEGER,

    person_source_value VARCHAR(50),

    gender_source_value VARCHAR(50),

    gender_source_concept_id INTEGER,

    race_source_value VARCHAR(50),

    race_source_concept_id INTEGER,

    ethnicity_source_value VARCHAR(50),

    ethnicity_source_concept_id INTEGER

)

;




CREATE TABLE observation_period
(

    observation_period_id INTEGER,

    person_id INTEGER,

    observation_period_start_date TIMESTAMP,

    observation_period_end_date TIMESTAMP,

    period_type_concept_id INTEGER

)

;




CREATE TABLE specimen
(

    specimen_id INTEGER,
    person_id INTEGER,

    specimen_concept_id INTEGER,

    specimen_type_concept_id INTEGER,

    specimen_date TIMESTAMP,

    specimen_datetime TIMESTAMP,

    quantity FLOAT,

    unit_concept_id INTEGER,

    anatomic_site_concept_id INTEGER,

    disease_status_concept_id INTEGER,

    specimen_source_id VARCHAR(50),

    specimen_source_value VARCHAR(50),

    unit_source_value VARCHAR(50),

    anatomic_site_source_value VARCHAR(50),

    disease_status_source_value VARCHAR(50)

)

;



CREATE TABLE death
(

    person_id INTEGER,

    death_date TIMESTAMP,

    death_datetime TIMESTAMP,

    death_type_concept_id INTEGER,

    cause_concept_id INTEGER,

    cause_source_value VARCHAR(50),

    cause_source_concept_id INTEGER

)

;




CREATE TABLE visit_occurrence
(

    visit_occurrence_id INTEGER,

    person_id INTEGER,

    visit_concept_id INTEGER,

    visit_start_date TIMESTAMP,

    visit_start_datetime TIMESTAMP,

    visit_end_date TIMESTAMP,

    visit_end_datetime TIMESTAMP,

    visit_type_concept_id INTEGER,

    provider_id INTEGER,

    care_site_id INTEGER,

    visit_source_value VARCHAR(50),

    visit_source_concept_id INTEGER
,
    admitting_source_concept_id INTEGER,

    admitting_source_value VARCHAR(50),

    discharge_to_concept_id INTEGER,

    discharge_to_source_value VARCHAR(50),

    preceding_visit_occurrence_id INTEGER

)

;




CREATE TABLE visit_detail
(

    visit_detail_id INTEGER,

    person_id INTEGER,

    visit_detail_concept_id INTEGER,

    visit_start_date TIMESTAMP,

    visit_start_datetime TIMESTAMP,

    visit_end_date TIMESTAMP,

    visit_end_datetime TIMESTAMP,

    visit_type_concept_id INTEGER,

    provider_id INTEGER,

    care_site_id INTEGER,

    admitting_source_concept_id INTEGER,

    discharge_to_concept_id INTEGER,

    preceding_visit_detail_id INTEGER,

    visit_source_value VARCHAR(50),

    visit_source_concept_id INTEGER,

    admitting_source_value VARCHAR(50),

    discharge_to_source_value VARCHAR(50),

    visit_detail_parent_id INTEGER,

    visit_occurrence_id INTEGER

)

;




CREATE TABLE procedure_occurrence
(

    procedure_occurrence_id INTEGER,

    person_id INTEGER,

    procedure_concept_id INTEGER,

    procedure_date TIMESTAMP,

    procedure_datetime TIMESTAMP,

    procedure_type_concept_id INTEGER,

    modifier_concept_id INTEGER,

    quantity INTEGER,

    provider_id INTEGER,

    visit_occurrence_id INTEGER,

    visit_detail_id INTEGER,

    procedure_source_value VARCHAR(50),

    procedure_source_concept_id INTEGER,

    modifier_source_value VARCHAR(50)

)

;




CREATE TABLE drug_exposure
(

    drug_exposure_id INTEGER,

    person_id INTEGER,

    drug_concept_id INTEGER,

    drug_exposure_start_date TIMESTAMP,

    drug_exposure_start_datetime TIMESTAMP,

    drug_exposure_end_date TIMESTAMP,

    drug_exposure_end_datetime TIMESTAMP,

    verbatim_end_date TIMESTAMP,

    drug_type_concept_id INTEGER,

    stop_reason VARCHAR(20),

    refills INTEGER,

    quantity FLOAT,

    days_supply INTEGER,

    sig STRING,

    route_concept_id INTEGER,

    lot_number VARCHAR(50),

    provider_id INTEGER,

    visit_occurrence_id INTEGER,

    visit_detail_id INTEGER,

    drug_source_value VARCHAR(50),

    drug_source_concept_id INTEGER,

    route_source_value VARCHAR(50),

    dose_unit_source_value VARCHAR(50)

)

;




CREATE TABLE device_exposure
(

    device_exposure_id INTEGER,

    person_id INTEGER,

    device_concept_id INTEGER,

    device_exposure_start_date TIMESTAMP,

    device_exposure_start_datetime TIMESTAMP,

    device_exposure_end_date TIMESTAMP,

    device_exposure_end_datetime TIMESTAMP,

    device_type_concept_id INTEGER,

    unique_device_id VARCHAR(50),

    quantity INTEGER,

    provider_id INTEGER,

    visit_occurrence_id INTEGER,

    visit_detail_id INTEGER,

    device_source_value VARCHAR(100),

    device_source_concept_id INTEGER

)

;




CREATE TABLE condition_occurrence
(

    condition_occurrence_id INTEGER,

    person_id INTEGER,

    condition_concept_id INTEGER,

    condition_start_date TIMESTAMP,

    condition_start_datetime TIMESTAMP,

    condition_end_date TIMESTAMP,

    condition_end_datetime TIMESTAMP,

    condition_type_concept_id INTEGER,

    stop_reason VARCHAR(20),

    provider_id INTEGER,

    visit_occurrence_id INTEGER,

    visit_detail_id INTEGER,

    condition_source_value VARCHAR(50),

    condition_source_concept_id INTEGER,

    condition_status_source_value VARCHAR(50),

    condition_status_concept_id INTEGER

)

;




CREATE TABLE measurement
(

    measurement_id INTEGER,

    person_id INTEGER,

    measurement_concept_id INTEGER,

    measurement_date TIMESTAMP,

    measurement_time VARCHAR(10),

    measurement_type_concept_id INTEGER,

    operator_concept_id INTEGER,

    value_as_number FLOAT,

    value_as_concept_id INTEGER,

    unit_concept_id INTEGER,

    range_low FLOAT,

    range_high FLOAT,

    provider_id INTEGER,
    visit_occurrence_id INTEGER,

    visit_detail_id INTEGER,

    measurement_source_value VARCHAR(50),

    measurement_source_concept_id INTEGER,

    unit_source_value VARCHAR(50),

    value_source_value VARCHAR(50)

)

;




CREATE TABLE note
(

    note_id INTEGER,

    person_id INTEGER,

    note_date TIMESTAMP,

    note_datetime TIMESTAMP,

    note_type_concept_id INTEGER,

    note_class_concept_id INTEGER,

    note_title VARCHAR(250),

    note_text STRING,

    encoding_concept_id INTEGER,

    language_concept_id INTEGER,

    provider_id INTEGER,

    visit_occurrence_id INTEGER,

    visit_detail_id INTEGER,

    note_source_value VARCHAR(50)

)

;




CREATE TABLE note_nlp
(

    note_nlp_id INTEGER,

    note_id INTEGER,

    section_concept_id INTEGER,

    snippet VARCHAR(250),

    "offset" VARCHAR(250),

    lexical_variant VARCHAR(250),

    note_nlp_concept_id INTEGER,

    note_nlp_source_concept_id INTEGER,

    nlp_system VARCHAR(250),

    nlp_date TIMESTAMP,

    nlp_datetime TIMESTAMP,

    term_exists VARCHAR(1),

    term_temporal VARCHAR(50),

    term_modifiers VARCHAR(2000)

)

;




CREATE TABLE observation
(

    observation_id INTEGER,

    person_id INTEGER,

    observation_concept_id INTEGER,

    observation_date TIMESTAMP,

    observation_datetime TIMESTAMP,

    observation_type_concept_id INTEGER,

    value_as_number FLOAT,

    value_as_string VARCHAR(60),

    value_as_concept_id INTEGER,

    qualifier_concept_id INTEGER,

    unit_concept_id INTEGER,

    provider_id INTEGER,

    visit_occurrence_id INTEGER,

    visit_detail_id INTEGER,

    observation_source_value VARCHAR(50),

    observation_source_concept_id INTEGER,

    unit_source_value VARCHAR(50),

    qualifier_source_value VARCHAR(50)

)

;




CREATE TABLE fact_relationship
(

    domain_concept_id_1 INTEGER,

    fact_id_1 INTEGER,

    domain_concept_id_2 INTEGER,

    fact_id_2 INTEGER,

    relationship_concept_id INTEGER

)

;




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



Standardized health system data



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



CREATE TABLE "location"
(

    location_id INTEGER,

    address_1 VARCHAR(50),

    address_2 VARCHAR(50),

    city VARCHAR(50),

    state VARCHAR(2),

    zip VARCHAR(9),

    county VARCHAR(20),

    location_source_value VARCHAR(50)

)

;




CREATE TABLE care_site
(

    care_site_id INTEGER,

    care_site_name VARCHAR(255),

    place_of_service_concept_id INTEGER,

    location_id INTEGER,

    care_site_source_value VARCHAR(50),

    place_of_service_source_value VARCHAR(50)

)

;




CREATE TABLE provider
(

    provider_id INTEGER,

    provider_name VARCHAR(255),

    NPI VARCHAR(20),

    DEA VARCHAR(20),

    specialty_concept_id INTEGER,
    care_site_id INTEGER,

    year_of_birth INTEGER,

    gender_concept_id INTEGER,

    provider_source_value VARCHAR(50),

    specialty_source_value VARCHAR(50),

    specialty_source_concept_id INTEGER,

    gender_source_value VARCHAR(50),

    gender_source_concept_id INTEGER

)

;



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



Standardized health economics



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




CREATE TABLE payer_plan_period
(

    payer_plan_period_id INTEGER,

    person_id INTEGER,

    payer_plan_period_start_date TIMESTAMP,

    payer_plan_period_end_date TIMESTAMP,

    payer_concept_id INTEGER,

    payer_source_value VARCHAR(50),

    payer_source_concept_id INTEGER,

    plan_concept_id INTEGER,

    plan_source_value VARCHAR(50),

    plan_source_concept_id INTEGER,

    sponsor_concept_id INTEGER,

    sponsor_source_value VARCHAR(50),

    sponsor_source_concept_id INTEGER,

    family_source_value VARCHAR(50),

    stop_reason_concept_id INTEGER,

    stop_reason_source_value VARCHAR(50),

    stop_reason_source_concept_id INTEGER
)

;




CREATE TABLE cost
(

    cost_id INTEGER,

    cost_event_id INTEGER,

    cost_domain_id VARCHAR(20),

    cost_type_concept_id INTEGER,

    currency_concept_id INTEGER,

    total_charge FLOAT,

    total_cost FLOAT,

    total_paid FLOAT,

    paid_by_payer FLOAT,

    paid_by_patient FLOAT,

    paid_patient_copay FLOAT,

    paid_patient_coinsurance FLOAT,

    paid_patient_deductible FLOAT,

    paid_by_primary FLOAT,

    paid_ingredient_cost FLOAT,

    paid_dispensing_fee FLOAT,

    payer_plan_period_id INTEGER,

    amount_allowed FLOAT,

    revenue_code_concept_id INTEGER,

    reveue_code_source_value VARCHAR(50),

    drg_concept_id INTEGER,

    drg_source_value VARCHAR(3)

)

;



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



Standardized derived elements



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



CREATE TABLE cohort
(

    cohort_definition_id INTEGER,

    subject_id INTEGER,

    cohort_start_date TIMESTAMP,

    cohort_end_date TIMESTAMP

)

;




CREATE TABLE cohort_attribute
(

    cohort_definition_id INTEGER,

    cohort_start_date TIMESTAMP,

    cohort_end_date TIMESTAMP,

    subject_id INTEGER,

    attribute_definition_id INTEGER,

    value_as_number FLOAT,

    value_as_concept_id INTEGER

)

;




CREATE TABLE drug_era
(

    drug_era_id INTEGER,

    person_id INTEGER,

    drug_concept_id INTEGER,

    drug_era_start_date TIMESTAMP,

    drug_era_end_date TIMESTAMP,

    drug_exposure_count INTEGER,

    gap_days INTEGER

)

;




CREATE TABLE dose_era
(

    dose_era_id INTEGER,

    person_id INTEGER,

    drug_concept_id INTEGER,

    unit_concept_id INTEGER,

    dose_value FLOAT,

    dose_era_start_date TIMESTAMP,

    dose_era_end_date TIMESTAMP

)

;


CREATE TABLE condition_era
(

    condition_era_id INTEGER,

    person_id INTEGER,

    condition_concept_id INTEGER,

    condition_era_start_date TIMESTAMP,

    condition_era_end_date TIMESTAMP,

    condition_occurrence_count INTEGER
)
;