OMOP/inst/ddl/5.4/bigquery/OMOPCDM_bigquery_5.4_ddl.sql

550 lines
17 KiB
SQL

--bigquery CDM DDL Specification for OMOP Common Data Model 5.4
--HINT DISTRIBUTE ON KEY (person_id)
create table @cdmDatabaseSchema.person (
person_id INT64 not null,
gender_concept_id INT64 not null,
year_of_birth INT64 not null,
month_of_birth INT64,
day_of_birth INT64,
birth_datetime datetime null,
race_concept_id INT64 not null,
ethnicity_concept_id INT64 not null,
location_id INT64,
provider_id INT64,
care_site_id INT64,
person_source_value STRING,
gender_source_value STRING,
gender_source_concept_id INT64,
race_source_value STRING,
race_source_concept_id INT64,
ethnicity_source_value STRING,
ethnicity_source_concept_id INT64 );
--HINT DISTRIBUTE ON KEY (person_id)
create table @cdmDatabaseSchema.observation_period (
observation_period_id INT64 not null,
person_id INT64 not null,
observation_period_start_date date not null,
observation_period_end_date date not null,
period_type_concept_id INT64 not null );
--HINT DISTRIBUTE ON KEY (person_id)
create table @cdmDatabaseSchema.visit_occurrence (
visit_occurrence_id INT64 not null,
person_id INT64 not null,
visit_concept_id INT64 not null,
visit_start_date date not null,
visit_start_datetime datetime null,
visit_end_date date not null,
visit_end_datetime datetime null,
visit_type_concept_id INT64 not null,
provider_id INT64,
care_site_id INT64,
visit_source_value STRING,
visit_source_concept_id INT64,
admitted_from_concept_id INT64,
admitted_from_source_value STRING,
discharged_to_concept_id INT64,
discharged_to_source_value STRING,
preceding_visit_occurrence_id INT64 );
--HINT DISTRIBUTE ON KEY (person_id)
create table @cdmDatabaseSchema.visit_detail (
visit_detail_id INT64 not null,
person_id INT64 not null,
visit_detail_concept_id INT64 not null,
visit_detail_start_date date not null,
visit_detail_start_datetime datetime null,
visit_detail_end_date date not null,
visit_detail_end_datetime datetime null,
visit_detail_type_concept_id INT64 not null,
provider_id INT64,
care_site_id INT64,
visit_detail_source_value STRING,
visit_detail_source_concept_id INT64,
admitted_from_concept_id INT64,
admitted_from_source_value STRING,
discharged_to_source_value STRING,
discharged_to_concept_id INT64,
preceding_visit_detail_id INT64,
parent_visit_detail_id INT64,
visit_occurrence_id INT64 not null );
--HINT DISTRIBUTE ON KEY (person_id)
create table @cdmDatabaseSchema.condition_occurrence (
condition_occurrence_id INT64 not null,
person_id INT64 not null,
condition_concept_id INT64 not null,
condition_start_date date not null,
condition_start_datetime datetime null,
condition_end_date date null,
condition_end_datetime datetime null,
condition_type_concept_id INT64 not null,
condition_status_concept_id INT64,
stop_reason STRING,
provider_id INT64,
visit_occurrence_id INT64,
visit_detail_id INT64,
condition_source_value STRING,
condition_source_concept_id INT64,
condition_status_source_value STRING );
--HINT DISTRIBUTE ON KEY (person_id)
create table @cdmDatabaseSchema.drug_exposure (
drug_exposure_id INT64 not null,
person_id INT64 not null,
drug_concept_id INT64 not null,
drug_exposure_start_date date not null,
drug_exposure_start_datetime datetime null,
drug_exposure_end_date date not null,
drug_exposure_end_datetime datetime null,
verbatim_end_date date null,
drug_type_concept_id INT64 not null,
stop_reason STRING,
refills INT64,
quantity FLOAT64 null,
days_supply INT64,
sig STRING,
route_concept_id INT64,
lot_number STRING,
provider_id INT64,
visit_occurrence_id INT64,
visit_detail_id INT64,
drug_source_value STRING,
drug_source_concept_id INT64,
route_source_value STRING,
dose_unit_source_value STRING );
--HINT DISTRIBUTE ON KEY (person_id)
create table @cdmDatabaseSchema.procedure_occurrence (
procedure_occurrence_id INT64 not null,
person_id INT64 not null,
procedure_concept_id INT64 not null,
procedure_date date not null,
procedure_datetime datetime null,
procedure_end_date date null,
procedure_end_datetime datetime null,
procedure_type_concept_id INT64 not null,
modifier_concept_id INT64,
quantity INT64,
provider_id INT64,
visit_occurrence_id INT64,
visit_detail_id INT64,
procedure_source_value STRING,
procedure_source_concept_id INT64,
modifier_source_value STRING );
--HINT DISTRIBUTE ON KEY (person_id)
create table @cdmDatabaseSchema.device_exposure (
device_exposure_id INT64 not null,
person_id INT64 not null,
device_concept_id INT64 not null,
device_exposure_start_date date not null,
device_exposure_start_datetime datetime null,
device_exposure_end_date date null,
device_exposure_end_datetime datetime null,
device_type_concept_id INT64 not null,
unique_device_id STRING,
production_id STRING,
quantity INT64,
provider_id INT64,
visit_occurrence_id INT64,
visit_detail_id INT64,
device_source_value STRING,
device_source_concept_id INT64,
unit_concept_id INT64,
unit_source_value STRING,
unit_source_concept_id INT64 );
--HINT DISTRIBUTE ON KEY (person_id)
create table @cdmDatabaseSchema.measurement (
measurement_id INT64 not null,
person_id INT64 not null,
measurement_concept_id INT64 not null,
measurement_date date not null,
measurement_datetime datetime null,
measurement_time STRING,
measurement_type_concept_id INT64 not null,
operator_concept_id INT64,
value_as_number FLOAT64 null,
value_as_concept_id INT64,
unit_concept_id INT64,
range_low FLOAT64 null,
range_high FLOAT64 null,
provider_id INT64,
visit_occurrence_id INT64,
visit_detail_id INT64,
measurement_source_value STRING,
measurement_source_concept_id INT64,
unit_source_value STRING,
unit_source_concept_id INT64,
value_source_value STRING,
measurement_event_id INT64,
meas_event_field_concept_id INT64 );
--HINT DISTRIBUTE ON KEY (person_id)
create table @cdmDatabaseSchema.observation (
observation_id INT64 not null,
person_id INT64 not null,
observation_concept_id INT64 not null,
observation_date date not null,
observation_datetime datetime null,
observation_type_concept_id INT64 not null,
value_as_number FLOAT64 null,
value_as_string STRING,
value_as_concept_id INT64,
qualifier_concept_id INT64,
unit_concept_id INT64,
provider_id INT64,
visit_occurrence_id INT64,
visit_detail_id INT64,
observation_source_value STRING,
observation_source_concept_id INT64,
unit_source_value STRING,
qualifier_source_value STRING,
value_source_value STRING,
observation_event_id INT64,
obs_event_field_concept_id INT64 );
--HINT DISTRIBUTE ON KEY (person_id)
create table @cdmDatabaseSchema.death (
person_id INT64 not null,
death_date date not null,
death_datetime datetime null,
death_type_concept_id INT64,
cause_concept_id INT64,
cause_source_value STRING,
cause_source_concept_id INT64 );
--HINT DISTRIBUTE ON KEY (person_id)
create table @cdmDatabaseSchema.note (
note_id INT64 not null,
person_id INT64 not null,
note_date date not null,
note_datetime datetime null,
note_type_concept_id INT64 not null,
note_class_concept_id INT64 not null,
note_title STRING,
note_text STRING not null,
encoding_concept_id INT64 not null,
language_concept_id INT64 not null,
provider_id INT64,
visit_occurrence_id INT64,
visit_detail_id INT64,
note_source_value STRING,
note_event_id INT64,
note_event_field_concept_id INT64 );
--HINT DISTRIBUTE ON RANDOM
create table @cdmDatabaseSchema.note_nlp (
note_nlp_id INT64 not null,
note_id INT64 not null,
section_concept_id INT64,
snippet STRING,
"offset" STRING,
lexical_variant STRING not null,
note_nlp_concept_id INT64,
note_nlp_source_concept_id INT64,
nlp_system STRING,
nlp_date date not null,
nlp_datetime datetime null,
term_exists STRING,
term_temporal STRING,
term_modifiers STRING );
--HINT DISTRIBUTE ON KEY (person_id)
create table @cdmDatabaseSchema.specimen (
specimen_id INT64 not null,
person_id INT64 not null,
specimen_concept_id INT64 not null,
specimen_type_concept_id INT64 not null,
specimen_date date not null,
specimen_datetime datetime null,
quantity FLOAT64 null,
unit_concept_id INT64,
anatomic_site_concept_id INT64,
disease_status_concept_id INT64,
specimen_source_id STRING,
specimen_source_value STRING,
unit_source_value STRING,
anatomic_site_source_value STRING,
disease_status_source_value STRING );
--HINT DISTRIBUTE ON RANDOM
create table @cdmDatabaseSchema.fact_relationship (
domain_concept_id_1 INT64 not null,
fact_id_1 INT64 not null,
domain_concept_id_2 INT64 not null,
fact_id_2 INT64 not null,
relationship_concept_id INT64 not null );
--HINT DISTRIBUTE ON RANDOM
create table @cdmDatabaseSchema.location (
location_id INT64 not null,
address_1 STRING,
address_2 STRING,
city STRING,
state STRING,
zip STRING,
county STRING,
location_source_value STRING,
country_concept_id INT64,
country_source_value STRING,
latitude FLOAT64 null,
longitude FLOAT64 null );
--HINT DISTRIBUTE ON RANDOM
create table @cdmDatabaseSchema.care_site (
care_site_id INT64 not null,
care_site_name STRING,
place_of_service_concept_id INT64,
location_id INT64,
care_site_source_value STRING,
place_of_service_source_value STRING );
--HINT DISTRIBUTE ON RANDOM
create table @cdmDatabaseSchema.provider (
provider_id INT64 not null,
provider_name STRING,
npi STRING,
dea STRING,
specialty_concept_id INT64,
care_site_id INT64,
year_of_birth INT64,
gender_concept_id INT64,
provider_source_value STRING,
specialty_source_value STRING,
specialty_source_concept_id INT64,
gender_source_value STRING,
gender_source_concept_id INT64 );
--HINT DISTRIBUTE ON KEY (person_id)
create table @cdmDatabaseSchema.payer_plan_period (
payer_plan_period_id INT64 not null,
person_id INT64 not null,
payer_plan_period_start_date date not null,
payer_plan_period_end_date date not null,
payer_concept_id INT64,
payer_source_value STRING,
payer_source_concept_id INT64,
plan_concept_id INT64,
plan_source_value STRING,
plan_source_concept_id INT64,
sponsor_concept_id INT64,
sponsor_source_value STRING,
sponsor_source_concept_id INT64,
family_source_value STRING,
stop_reason_concept_id INT64,
stop_reason_source_value STRING,
stop_reason_source_concept_id INT64 );
--HINT DISTRIBUTE ON RANDOM
create table @cdmDatabaseSchema.cost (
cost_id INT64 not null,
cost_event_id INT64 not null,
cost_domain_id STRING not null,
cost_type_concept_id INT64 not null,
currency_concept_id INT64,
total_charge FLOAT64 null,
total_cost FLOAT64 null,
total_paid FLOAT64 null,
paid_by_payer FLOAT64 null,
paid_by_patient FLOAT64 null,
paid_patient_copay FLOAT64 null,
paid_patient_coinsurance FLOAT64 null,
paid_patient_deductible FLOAT64 null,
paid_by_primary FLOAT64 null,
paid_ingredient_cost FLOAT64 null,
paid_dispensing_fee FLOAT64 null,
payer_plan_period_id INT64,
amount_allowed FLOAT64 null,
revenue_code_concept_id INT64,
revenue_code_source_value STRING,
drg_concept_id INT64,
drg_source_value STRING );
--HINT DISTRIBUTE ON KEY (person_id)
create table @cdmDatabaseSchema.drug_era (
drug_era_id INT64 not null,
person_id INT64 not null,
drug_concept_id INT64 not null,
drug_era_start_date date not null,
drug_era_end_date date not null,
drug_exposure_count INT64,
gap_days INT64 );
--HINT DISTRIBUTE ON KEY (person_id)
create table @cdmDatabaseSchema.dose_era (
dose_era_id INT64 not null,
person_id INT64 not null,
drug_concept_id INT64 not null,
unit_concept_id INT64 not null,
dose_value FLOAT64 not null,
dose_era_start_date date not null,
dose_era_end_date date not null );
--HINT DISTRIBUTE ON KEY (person_id)
create table @cdmDatabaseSchema.condition_era (
condition_era_id INT64 not null,
person_id INT64 not null,
condition_concept_id INT64 not null,
condition_era_start_date date not null,
condition_era_end_date date not null,
condition_occurrence_count INT64 );
--HINT DISTRIBUTE ON KEY (person_id)
create table @cdmDatabaseSchema.episode (
episode_id INT64 not null,
person_id INT64 not null,
episode_concept_id INT64 not null,
episode_start_date date not null,
episode_start_datetime datetime null,
episode_end_date date null,
episode_end_datetime datetime null,
episode_parent_id INT64,
episode_number INT64,
episode_object_concept_id INT64 not null,
episode_type_concept_id INT64 not null,
episode_source_value STRING,
episode_source_concept_id INT64 );
--HINT DISTRIBUTE ON RANDOM
create table @cdmDatabaseSchema.episode_event (
episode_id INT64 not null,
event_id INT64 not null,
episode_event_field_concept_id INT64 not null );
--HINT DISTRIBUTE ON RANDOM
create table @cdmDatabaseSchema.metadata (
metadata_id INT64 not null,
metadata_concept_id INT64 not null,
metadata_type_concept_id INT64 not null,
name STRING not null,
value_as_string STRING,
value_as_concept_id INT64,
value_as_number FLOAT64 null,
metadata_date date null,
metadata_datetime datetime null );
--HINT DISTRIBUTE ON RANDOM
create table @cdmDatabaseSchema.cdm_source (
cdm_source_name STRING not null,
cdm_source_abbreviation STRING not null,
cdm_holder STRING not null,
source_description STRING,
source_documentation_reference STRING,
cdm_etl_reference STRING,
source_release_date date not null,
cdm_release_date date not null,
cdm_version STRING,
cdm_version_concept_id INT64 not null,
vocabulary_version STRING not null );
--HINT DISTRIBUTE ON RANDOM
create table @cdmDatabaseSchema.concept (
concept_id INT64 not null,
concept_name STRING not null,
domain_id STRING not null,
vocabulary_id STRING not null,
concept_class_id STRING not null,
standard_concept STRING,
concept_code STRING not null,
valid_start_date date not null,
valid_end_date date not null,
invalid_reason STRING );
--HINT DISTRIBUTE ON RANDOM
create table @cdmDatabaseSchema.vocabulary (
vocabulary_id STRING not null,
vocabulary_name STRING not null,
vocabulary_reference STRING,
vocabulary_version STRING,
vocabulary_concept_id INT64 not null );
--HINT DISTRIBUTE ON RANDOM
create table @cdmDatabaseSchema.domain (
domain_id STRING not null,
domain_name STRING not null,
domain_concept_id INT64 not null );
--HINT DISTRIBUTE ON RANDOM
create table @cdmDatabaseSchema.concept_class (
concept_class_id STRING not null,
concept_class_name STRING not null,
concept_class_concept_id INT64 not null );
--HINT DISTRIBUTE ON RANDOM
create table @cdmDatabaseSchema.concept_relationship (
concept_id_1 INT64 not null,
concept_id_2 INT64 not null,
relationship_id STRING not null,
valid_start_date date not null,
valid_end_date date not null,
invalid_reason STRING );
--HINT DISTRIBUTE ON RANDOM
create table @cdmDatabaseSchema.relationship (
relationship_id STRING not null,
relationship_name STRING not null,
is_hierarchical STRING not null,
defines_ancestry STRING not null,
reverse_relationship_id STRING not null,
relationship_concept_id INT64 not null );
--HINT DISTRIBUTE ON RANDOM
create table @cdmDatabaseSchema.concept_synonym (
concept_id INT64 not null,
concept_synonym_name STRING not null,
language_concept_id INT64 not null );
--HINT DISTRIBUTE ON RANDOM
create table @cdmDatabaseSchema.concept_ancestor (
ancestor_concept_id INT64 not null,
descendant_concept_id INT64 not null,
min_levels_of_separation INT64 not null,
max_levels_of_separation INT64 not null );
--HINT DISTRIBUTE ON RANDOM
create table @cdmDatabaseSchema.source_to_concept_map (
source_code STRING not null,
source_concept_id INT64 not null,
source_vocabulary_id STRING not null,
source_code_description STRING,
target_concept_id INT64 not null,
target_vocabulary_id STRING not null,
valid_start_date date not null,
valid_end_date date not null,
invalid_reason STRING );
--HINT DISTRIBUTE ON RANDOM
create table @cdmDatabaseSchema.drug_strength (
drug_concept_id INT64 not null,
ingredient_concept_id INT64 not null,
amount_value FLOAT64 null,
amount_unit_concept_id INT64,
numerator_value FLOAT64 null,
numerator_unit_concept_id INT64,
denominator_value FLOAT64 null,
denominator_unit_concept_id INT64,
box_size INT64,
valid_start_date date not null,
valid_end_date date not null,
invalid_reason STRING );
--HINT DISTRIBUTE ON RANDOM
create table @cdmDatabaseSchema.cohort (
cohort_definition_id INT64 not null,
subject_id INT64 not null,
cohort_start_date date not null,
cohort_end_date date not null );
--HINT DISTRIBUTE ON RANDOM
create table @cdmDatabaseSchema.cohort_definition (
cohort_definition_id INT64 not null,
cohort_definition_name STRING not null,
cohort_definition_description STRING,
definition_type_concept_id INT64 not null,
cohort_definition_syntax STRING,
subject_concept_id INT64 not null,
cohort_initiation_date date null );