OMOP/inst/ddl/5.4/impala/OMOPCDM_impala_5.4_ddl.sql

511 lines
17 KiB
SQL

--impala CDM DDL Specification for OMOP Common Data Model 5.4
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.person (
person_id INT,
gender_concept_id INT,
year_of_birth INT,
month_of_birth integer NULL,
day_of_birth integer NULL,
birth_datetime TIMESTAMP,
race_concept_id INT,
ethnicity_concept_id INT,
location_id integer NULL,
provider_id integer NULL,
care_site_id integer NULL,
person_source_value VARCHAR(50),
gender_source_value VARCHAR(50),
gender_source_concept_id integer NULL,
race_source_value VARCHAR(50),
race_source_concept_id integer NULL,
ethnicity_source_value VARCHAR(50),
ethnicity_source_concept_id integer NULL );
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.observation_period (
observation_period_id INT,
person_id INT,
observation_period_start_date TIMESTAMP,
observation_period_end_date TIMESTAMP,
period_type_concept_id INT );
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.visit_occurrence (
visit_occurrence_id INT,
person_id INT,
visit_concept_id INT,
visit_start_date TIMESTAMP,
visit_start_datetime TIMESTAMP,
visit_end_date TIMESTAMP,
visit_end_datetime TIMESTAMP,
visit_type_concept_id INT,
provider_id integer NULL,
care_site_id integer NULL,
visit_source_value VARCHAR(50),
visit_source_concept_id integer NULL,
admitted_from_concept_id integer NULL,
admitted_from_source_value VARCHAR(50),
discharged_to_concept_id integer NULL,
discharged_to_source_value VARCHAR(50),
preceding_visit_occurrence_id integer NULL );
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.visit_detail (
visit_detail_id INT,
person_id INT,
visit_detail_concept_id INT,
visit_detail_start_date TIMESTAMP,
visit_detail_start_datetime TIMESTAMP,
visit_detail_end_date TIMESTAMP,
visit_detail_end_datetime TIMESTAMP,
visit_detail_type_concept_id INT,
provider_id integer NULL,
care_site_id integer NULL,
visit_detail_source_value VARCHAR(50),
visit_detail_source_concept_id Integer NULL,
admitted_from_concept_id Integer NULL,
admitted_from_source_value VARCHAR(50),
discharged_to_source_value VARCHAR(50),
discharged_to_concept_id integer NULL,
preceding_visit_detail_id integer NULL,
parent_visit_detail_id integer NULL,
visit_occurrence_id INT );
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.condition_occurrence (
condition_occurrence_id INT,
person_id INT,
condition_concept_id INT,
condition_start_date TIMESTAMP,
condition_start_datetime TIMESTAMP,
condition_end_date TIMESTAMP,
condition_end_datetime TIMESTAMP,
condition_type_concept_id INT,
condition_status_concept_id integer NULL,
stop_reason VARCHAR(20),
provider_id integer NULL,
visit_occurrence_id integer NULL,
visit_detail_id integer NULL,
condition_source_value VARCHAR(50),
condition_source_concept_id integer NULL,
condition_status_source_value VARCHAR(50) );
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.drug_exposure (
drug_exposure_id INT,
person_id INT,
drug_concept_id INT,
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 INT,
stop_reason VARCHAR(20),
refills integer NULL,
quantity FLOAT,
days_supply integer NULL,
sig VARCHAR(MAX),
route_concept_id integer NULL,
lot_number VARCHAR(50),
provider_id integer NULL,
visit_occurrence_id integer NULL,
visit_detail_id integer NULL,
drug_source_value VARCHAR(50),
drug_source_concept_id integer NULL,
route_source_value VARCHAR(50),
dose_unit_source_value VARCHAR(50) );
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.procedure_occurrence (
procedure_occurrence_id INT,
person_id INT,
procedure_concept_id INT,
procedure_date TIMESTAMP,
procedure_datetime TIMESTAMP,
procedure_end_date TIMESTAMP,
procedure_end_datetime TIMESTAMP,
procedure_type_concept_id INT,
modifier_concept_id integer NULL,
quantity integer NULL,
provider_id integer NULL,
visit_occurrence_id integer NULL,
visit_detail_id integer NULL,
procedure_source_value VARCHAR(50),
procedure_source_concept_id integer NULL,
modifier_source_value VARCHAR(50) );
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.device_exposure (
device_exposure_id INT,
person_id INT,
device_concept_id INT,
device_exposure_start_date TIMESTAMP,
device_exposure_start_datetime TIMESTAMP,
device_exposure_end_date TIMESTAMP,
device_exposure_end_datetime TIMESTAMP,
device_type_concept_id INT,
unique_device_id VARCHAR(255),
production_id VARCHAR(255),
quantity integer NULL,
provider_id integer NULL,
visit_occurrence_id integer NULL,
visit_detail_id integer NULL,
device_source_value VARCHAR(50),
device_source_concept_id integer NULL,
unit_concept_id integer NULL,
unit_source_value VARCHAR(50),
unit_source_concept_id integer NULL );
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.measurement (
measurement_id INT,
person_id INT,
measurement_concept_id INT,
measurement_date TIMESTAMP,
measurement_datetime TIMESTAMP,
measurement_time VARCHAR(10),
measurement_type_concept_id INT,
operator_concept_id integer NULL,
value_as_number FLOAT,
value_as_concept_id integer NULL,
unit_concept_id integer NULL,
range_low FLOAT,
range_high FLOAT,
provider_id integer NULL,
visit_occurrence_id integer NULL,
visit_detail_id integer NULL,
measurement_source_value VARCHAR(50),
measurement_source_concept_id integer NULL,
unit_source_value VARCHAR(50),
unit_source_concept_id integer NULL,
value_source_value VARCHAR(50),
measurement_event_id integer NULL,
meas_event_field_concept_id integer NULL );
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.observation (
observation_id INT,
person_id INT,
observation_concept_id INT,
observation_date TIMESTAMP,
observation_datetime TIMESTAMP,
observation_type_concept_id INT,
value_as_number FLOAT,
value_as_string VARCHAR(60),
value_as_concept_id Integer NULL,
qualifier_concept_id integer NULL,
unit_concept_id integer NULL,
provider_id integer NULL,
visit_occurrence_id integer NULL,
visit_detail_id integer NULL,
observation_source_value VARCHAR(50),
observation_source_concept_id integer NULL,
unit_source_value VARCHAR(50),
qualifier_source_value VARCHAR(50),
value_source_value VARCHAR(50),
observation_event_id integer NULL,
obs_event_field_concept_id integer NULL );
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.death (
person_id INT,
death_date TIMESTAMP,
death_datetime TIMESTAMP,
death_type_concept_id integer NULL,
cause_concept_id integer NULL,
cause_source_value VARCHAR(50),
cause_source_concept_id integer NULL );
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.note (
note_id INT,
person_id INT,
note_date TIMESTAMP,
note_datetime TIMESTAMP,
note_type_concept_id INT,
note_class_concept_id INT,
note_title VARCHAR(250),
note_text VARCHAR(MAX),
encoding_concept_id INT,
language_concept_id INT,
provider_id integer NULL,
visit_occurrence_id integer NULL,
visit_detail_id integer NULL,
note_source_value VARCHAR(50),
note_event_id integer NULL,
note_event_field_concept_id integer NULL );
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE @cdmDatabaseSchema.note_nlp (
note_nlp_id INT,
note_id INT,
section_concept_id integer NULL,
snippet VARCHAR(250),
"offset" VARCHAR(50),
lexical_variant VARCHAR(250),
note_nlp_concept_id integer NULL,
note_nlp_source_concept_id integer NULL,
nlp_system VARCHAR(250),
nlp_date TIMESTAMP,
nlp_datetime TIMESTAMP,
term_exists VARCHAR(1),
term_temporal VARCHAR(50),
term_modifiers VARCHAR(2000) );
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.specimen (
specimen_id INT,
person_id INT,
specimen_concept_id INT,
specimen_type_concept_id INT,
specimen_date TIMESTAMP,
specimen_datetime TIMESTAMP,
quantity FLOAT,
unit_concept_id integer NULL,
anatomic_site_concept_id integer NULL,
disease_status_concept_id integer NULL,
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) );
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE @cdmDatabaseSchema.fact_relationship (
domain_concept_id_1 INT,
fact_id_1 INT,
domain_concept_id_2 INT,
fact_id_2 INT,
relationship_concept_id INT );
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE @cdmDatabaseSchema.`location` (
location_id INT,
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),
country_concept_id integer NULL,
country_source_value VARCHAR(80),
latitude FLOAT,
longitude FLOAT );
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE @cdmDatabaseSchema.care_site (
care_site_id INT,
care_site_name VARCHAR(255),
place_of_service_concept_id integer NULL,
location_id integer NULL,
care_site_source_value VARCHAR(50),
place_of_service_source_value VARCHAR(50) );
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE @cdmDatabaseSchema.provider (
provider_id INT,
provider_name VARCHAR(255),
npi VARCHAR(20),
dea VARCHAR(20),
specialty_concept_id integer NULL,
care_site_id integer NULL,
year_of_birth integer NULL,
gender_concept_id integer NULL,
provider_source_value VARCHAR(50),
specialty_source_value VARCHAR(50),
specialty_source_concept_id integer NULL,
gender_source_value VARCHAR(50),
gender_source_concept_id integer NULL );
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.payer_plan_period (
payer_plan_period_id INT,
person_id INT,
payer_plan_period_start_date TIMESTAMP,
payer_plan_period_end_date TIMESTAMP,
payer_concept_id integer NULL,
payer_source_value VARCHAR(50),
payer_source_concept_id integer NULL,
plan_concept_id integer NULL,
plan_source_value VARCHAR(50),
plan_source_concept_id integer NULL,
sponsor_concept_id integer NULL,
sponsor_source_value VARCHAR(50),
sponsor_source_concept_id integer NULL,
family_source_value VARCHAR(50),
stop_reason_concept_id integer NULL,
stop_reason_source_value VARCHAR(50),
stop_reason_source_concept_id integer NULL );
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE @cdmDatabaseSchema.cost (
cost_id INT,
cost_event_id INT,
cost_domain_id VARCHAR(20),
cost_type_concept_id INT,
currency_concept_id integer NULL,
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 NULL,
amount_allowed FLOAT,
revenue_code_concept_id integer NULL,
revenue_code_source_value VARCHAR(50),
drg_concept_id integer NULL,
drg_source_value VARCHAR(3) );
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.drug_era (
drug_era_id INT,
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 KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.episode (
episode_id INT,
person_id INT,
episode_concept_id INT,
episode_start_date TIMESTAMP,
episode_start_datetime TIMESTAMP,
episode_end_date TIMESTAMP,
episode_end_datetime TIMESTAMP,
episode_parent_id integer NULL,
episode_number integer NULL,
episode_object_concept_id INT,
episode_type_concept_id INT,
episode_source_value VARCHAR(50),
episode_source_concept_id integer NULL );
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE @cdmDatabaseSchema.episode_event (
episode_id INT,
event_id INT,
episode_event_field_concept_id INT );
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE @cdmDatabaseSchema.metadata (
metadata_id INT,
metadata_concept_id INT,
metadata_type_concept_id INT,
name VARCHAR(250),
value_as_string VARCHAR(250),
value_as_concept_id integer NULL,
value_as_number FLOAT,
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),
cdm_version_concept_id INT,
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 (
cohort_definition_id INT,
subject_id INT,
cohort_start_date TIMESTAMP,
cohort_end_date TIMESTAMP );
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE @cdmDatabaseSchema.cohort_definition (
cohort_definition_id INT,
cohort_definition_name VARCHAR(255),
cohort_definition_description VARCHAR(MAX),
definition_type_concept_id INT,
cohort_definition_syntax VARCHAR(MAX),
subject_concept_id INT,
cohort_initiation_date TIMESTAMP );