OMOP/ddl/5.4/postgresql/OMOPCDM_postgresql_5.4_ddl.sql

550 lines
19 KiB
SQL

--postgresql CDM DDL Specification for OMOP Common Data Model 5.4
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.PERSON (
person_id integer NOT NULL,
gender_concept_id integer NOT NULL,
year_of_birth integer NOT NULL,
month_of_birth integer NULL,
day_of_birth integer NULL,
birth_datetime TIMESTAMP NULL,
race_concept_id integer NOT NULL,
ethnicity_concept_id integer NOT NULL,
location_id integer NULL,
provider_id integer NULL,
care_site_id integer NULL,
person_source_value varchar(50) NULL,
gender_source_value varchar(50) NULL,
gender_source_concept_id integer NULL,
race_source_value varchar(50) NULL,
race_source_concept_id integer NULL,
ethnicity_source_value varchar(50) NULL,
ethnicity_source_concept_id integer NULL );
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.OBSERVATION_PERIOD (
observation_period_id integer NOT NULL,
person_id integer NOT NULL,
observation_period_start_date date NOT NULL,
observation_period_end_date date NOT NULL,
period_type_concept_id integer NOT NULL );
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.VISIT_OCCURRENCE (
visit_occurrence_id integer NOT NULL,
person_id integer NOT NULL,
visit_concept_id integer NOT NULL,
visit_start_date date NOT NULL,
visit_start_datetime TIMESTAMP NULL,
visit_end_date date NOT NULL,
visit_end_datetime TIMESTAMP NULL,
visit_type_concept_id Integer NOT NULL,
provider_id integer NULL,
care_site_id integer NULL,
visit_source_value varchar(50) NULL,
visit_source_concept_id integer NULL,
admitted_from_concept_id integer NULL,
admitted_from_source_value varchar(50) NULL,
discharged_to_concept_id integer NULL,
discharged_to_source_value varchar(50) NULL,
preceding_visit_occurrence_id integer NULL );
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.VISIT_DETAIL (
visit_detail_id integer NOT NULL,
person_id integer NOT NULL,
visit_detail_concept_id integer NOT NULL,
visit_detail_start_date date NOT NULL,
visit_detail_start_datetime TIMESTAMP NULL,
visit_detail_end_date date NOT NULL,
visit_detail_end_datetime TIMESTAMP NULL,
visit_detail_type_concept_id integer NOT NULL,
provider_id integer NULL,
care_site_id integer NULL,
visit_detail_source_value varchar(50) NULL,
visit_detail_source_concept_id Integer NULL,
admitted_from_concept_id Integer NULL,
admitted_from_source_value Varchar(50) NULL,
discharged_to_source_value Varchar(50) NULL,
discharged_to_concept_id integer NULL,
preceding_visit_detail_id integer NULL,
parent_visit_detail_id integer NULL,
visit_occurrence_id integer NOT NULL );
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.CONDITION_OCCURRENCE (
condition_occurrence_id integer NOT NULL,
person_id integer NOT NULL,
condition_concept_id integer NOT NULL,
condition_start_date date NOT NULL,
condition_start_datetime TIMESTAMP NULL,
condition_end_date date NULL,
condition_end_datetime TIMESTAMP NULL,
condition_type_concept_id integer NOT NULL,
condition_status_concept_id integer NULL,
stop_reason varchar(20) NULL,
provider_id integer NULL,
visit_occurrence_id integer NULL,
visit_detail_id integer NULL,
condition_source_value varchar(50) NULL,
condition_source_concept_id integer NULL,
condition_status_source_value varchar(50) NULL );
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.DRUG_EXPOSURE (
drug_exposure_id integer NOT NULL,
person_id integer NOT NULL,
drug_concept_id integer NOT NULL,
drug_exposure_start_date date NOT NULL,
drug_exposure_start_datetime TIMESTAMP NULL,
drug_exposure_end_date date NOT NULL,
drug_exposure_end_datetime TIMESTAMP NULL,
verbatim_end_date date NULL,
drug_type_concept_id integer NOT NULL,
stop_reason varchar(20) NULL,
refills integer NULL,
quantity NUMERIC NULL,
days_supply integer NULL,
sig TEXT NULL,
route_concept_id integer NULL,
lot_number varchar(50) NULL,
provider_id integer NULL,
visit_occurrence_id integer NULL,
visit_detail_id integer NULL,
drug_source_value varchar(50) NULL,
drug_source_concept_id integer NULL,
route_source_value varchar(50) NULL,
dose_unit_source_value varchar(50) NULL );
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.PROCEDURE_OCCURRENCE (
procedure_occurrence_id integer NOT NULL,
person_id integer NOT NULL,
procedure_concept_id integer NOT NULL,
procedure_date date NOT NULL,
procedure_datetime TIMESTAMP NULL,
procedure_type_concept_id integer NOT NULL,
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) NULL,
procedure_source_concept_id integer NULL,
modifier_source_value varchar(50) NULL,
procedure_status_source_value varchar(50) NULL,
procedure_status_concept_id integer NOT NULL );
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.DEVICE_EXPOSURE (
device_exposure_id integer NOT NULL,
person_id integer NOT NULL,
device_concept_id integer NOT NULL,
device_exposure_start_date date NOT NULL,
device_exposure_start_datetime TIMESTAMP NULL,
device_exposure_end_date date NULL,
device_exposure_end_datetime TIMESTAMP NULL,
device_type_concept_id integer NOT NULL,
unique_device_id varchar(255) NULL,
production_id varchar(255) NULL,
quantity integer NULL,
provider_id integer NULL,
visit_occurrence_id integer NULL,
visit_detail_id integer NULL,
device_source_value varchar(50) NULL,
device_source_concept_id integer NULL,
unit_concept_id integer NULL,
unit_source_value varchar(50) NULL,
unit_source_concept_id integer NULL );
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.MEASUREMENT (
measurement_id integer NOT NULL,
person_id integer NOT NULL,
measurement_concept_id integer NOT NULL,
measurement_date date NOT NULL,
measurement_datetime TIMESTAMP NULL,
measurement_time varchar(10) NULL,
measurement_type_concept_id integer NOT NULL,
operator_concept_id integer NULL,
value_as_number NUMERIC NULL,
value_as_concept_id integer NULL,
unit_concept_id integer NULL,
range_low NUMERIC NULL,
range_high NUMERIC NULL,
provider_id integer NULL,
visit_occurrence_id integer NULL,
visit_detail_id integer NULL,
measurement_source_value varchar(50) NULL,
measurement_source_concept_id integer NULL,
unit_source_value varchar(50) NULL,
unit_source_concept_id integer NULL,
value_source_value varchar(50) NULL,
measurement_event_id bigint NULL,
meas_event_field_concept_id integer NULL );
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.OBSERVATION (
observation_id integer NOT NULL,
person_id integer NOT NULL,
observation_concept_id integer NOT NULL,
observation_date date NOT NULL,
observation_datetime TIMESTAMP NULL,
observation_type_concept_id integer NOT NULL,
value_as_number NUMERIC NULL,
value_as_string varchar(60) NULL,
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) NULL,
observation_source_concept_id integer NULL,
unit_source_value varchar(50) NULL,
qualifier_source_value varchar(50) NULL,
value_source_value varchar(50) NULL,
observation_event_id bigint NULL,
obs_event_field_concept_id integer NULL );
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.DEATH (
person_id integer NOT NULL,
death_date date NOT NULL,
death_datetime TIMESTAMP NULL,
death_type_concept_id integer NULL,
cause_concept_id integer NULL,
cause_source_value varchar(50) NULL,
cause_source_concept_id integer NULL );
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.NOTE (
note_id integer NOT NULL,
person_id integer NOT NULL,
note_event_id bigint NULL,
note_event_field_concept_id integer NULL,
note_date date NOT NULL,
note_datetime TIMESTAMP NULL,
note_type_concept_id integer NOT NULL,
note_class_concept_id integer NOT NULL,
note_title varchar(250) NULL,
note_text TEXT NOT NULL,
encoding_concept_id integer NOT NULL,
language_concept_id integer NOT NULL,
provider_id integer NULL,
visit_occurrence_id integer NULL,
visit_detail_id integer NULL,
note_source_value varchar(50) NULL );
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE @cdmDatabaseSchema.NOTE_NLP (
note_nlp_id integer NOT NULL,
note_id integer NOT NULL,
section_concept_id integer NULL,
snippet varchar(250) NULL,
"offset" varchar(50) NULL,
lexical_variant varchar(250) NOT NULL,
note_nlp_concept_id integer NULL,
note_nlp_source_concept_id integer NULL,
nlp_system varchar(250) NULL,
nlp_date date NOT NULL,
nlp_datetime TIMESTAMP NULL,
term_exists varchar(1) NULL,
term_temporal varchar(50) NULL,
term_modifiers varchar(2000) NULL );
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.SPECIMEN (
specimen_id integer NOT NULL,
person_id integer NOT NULL,
specimen_concept_id integer NOT NULL,
specimen_type_concept_id integer NOT NULL,
specimen_date date NOT NULL,
specimen_datetime TIMESTAMP NULL,
quantity NUMERIC NULL,
unit_concept_id integer NULL,
anatomic_site_concept_id integer NULL,
disease_status_concept_id integer NULL,
specimen_source_id varchar(50) NULL,
specimen_source_value varchar(50) NULL,
unit_source_value varchar(50) NULL,
anatomic_site_source_value varchar(50) NULL,
disease_status_source_value varchar(50) NULL );
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE @cdmDatabaseSchema.FACT_RELATIONSHIP (
domain_concept_id_1 integer NOT NULL,
fact_id_1 integer NOT NULL,
domain_concept_id_2 integer NOT NULL,
fact_id_2 integer NOT NULL,
relationship_concept_id integer NOT NULL );
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE @cdmDatabaseSchema.LOCATION (
location_id integer NOT NULL,
address_1 varchar(50) NULL,
address_2 varchar(50) NULL,
city varchar(50) NULL,
state varchar(2) NULL,
zip varchar(9) NULL,
county varchar(20) NULL,
location_source_value varchar(50) NULL,
country_concept_id integer NULL,
country_source_value varchar(80) NULL,
latitude NUMERIC NULL,
longitude NUMERIC NULL );
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE @cdmDatabaseSchema.CARE_SITE (
care_site_id integer NOT NULL,
care_site_name varchar(255) NULL,
place_of_service_concept_id integer NULL,
location_id integer NULL,
care_site_source_value varchar(50) NULL,
place_of_service_source_value varchar(50) NULL );
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE @cdmDatabaseSchema.PROVIDER (
provider_id integer NOT NULL,
provider_name varchar(255) NULL,
npi varchar(20) NULL,
dea varchar(20) NULL,
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) NULL,
specialty_source_value varchar(50) NULL,
specialty_source_concept_id integer NULL,
gender_source_value varchar(50) NULL,
gender_source_concept_id integer NULL );
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.PAYER_PLAN_PERIOD (
payer_plan_period_id integer NOT NULL,
person_id integer NOT NULL,
payer_plan_period_start_date date NOT NULL,
payer_plan_period_end_date date NOT NULL,
payer_concept_id integer NULL,
payer_source_value varchar(50) NULL,
payer_source_concept_id integer NULL,
plan_concept_id integer NULL,
plan_source_value varchar(50) NULL,
plan_source_concept_id integer NULL,
sponsor_concept_id integer NULL,
sponsor_source_value varchar(50) NULL,
sponsor_source_concept_id integer NULL,
family_source_value varchar(50) NULL,
stop_reason_concept_id integer NULL,
stop_reason_source_value varchar(50) NULL,
stop_reason_source_concept_id integer NULL );
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE @cdmDatabaseSchema.COST (
cost_id integer NOT NULL,
cost_event_id integer NOT NULL,
cost_domain_id varchar(20) NOT NULL,
cost_type_concept_id integer NOT NULL,
currency_concept_id integer NULL,
total_charge NUMERIC NULL,
total_cost NUMERIC NULL,
total_paid NUMERIC NULL,
paid_by_payer NUMERIC NULL,
paid_by_patient NUMERIC NULL,
paid_patient_copay NUMERIC NULL,
paid_patient_coinsurance NUMERIC NULL,
paid_patient_deductible NUMERIC NULL,
paid_by_primary NUMERIC NULL,
paid_ingredient_cost NUMERIC NULL,
paid_dispensing_fee NUMERIC NULL,
payer_plan_period_id integer NULL,
amount_allowed NUMERIC NULL,
revenue_code_concept_id integer NULL,
revenue_code_source_value varchar(50) NULL,
drg_concept_id integer NULL,
drg_source_value varchar(3) NULL );
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.DRUG_ERA (
drug_era_id integer NOT NULL,
person_id integer NOT NULL,
drug_concept_id integer NOT NULL,
drug_era_start_date TIMESTAMP NOT NULL,
drug_era_end_date TIMESTAMP NOT NULL,
drug_exposure_count integer NULL,
gap_days integer NULL );
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.DOSE_ERA (
dose_era_id integer NOT NULL,
person_id integer NOT NULL,
drug_concept_id integer NOT NULL,
unit_concept_id integer NOT NULL,
dose_value NUMERIC NOT NULL,
dose_era_start_date TIMESTAMP NOT NULL,
dose_era_end_date TIMESTAMP NOT NULL );
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.CONDITION_ERA (
condition_era_id integer NOT NULL,
person_id integer NOT NULL,
condition_concept_id integer NOT NULL,
condition_era_start_date TIMESTAMP NOT NULL,
condition_era_end_date TIMESTAMP NOT NULL,
condition_occurrence_count integer NULL );
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.EPISODE (
episode_id integer NOT NULL,
person_id integer NOT NULL,
episode_concept_id integer NOT NULL,
episode_start_date date NOT NULL,
episode_start_datetime TIMESTAMP NULL,
episode_end_date date NULL,
episode_end_datetime TIMESTAMP NULL,
episode_parent_id integer NULL,
episode_number integer NULL,
episode_object_concept_id integer NOT NULL,
episode_type_concept_id integer NOT NULL,
episode_source_value varchar(50) NULL,
episode_source_concept_id integer NULL );
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE @cdmDatabaseSchema.EPISODE_EVENT (
episode_id integer NOT NULL,
event_id integer NOT NULL,
episode_event_field_concept_id integer NOT NULL );
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE @cdmDatabaseSchema.METADATA (
metadata_id integer NOT NULL,
metadata_concept_id integer NOT NULL,
metadata_type_concept_id integer NOT NULL,
name varchar(250) NOT NULL,
value_as_string varchar(250) NULL,
value_as_concept_id integer NULL,
value_as_number NUMERIC NULL,
metadata_date date NULL,
metadata_datetime TIMESTAMP NULL );
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE @cdmDatabaseSchema.CDM_SOURCE (
cdm_source_name varchar(255) NOT NULL,
cdm_source_abbreviation varchar(25) NOT NULL,
cdm_holder varchar(255) NOT NULL,
source_description TEXT NULL,
source_documentation_reference varchar(255) NULL,
cdm_etl_reference varchar(255) NULL,
source_release_date date NOT NULL,
cdm_release_date date NOT NULL,
cdm_version varchar(10) NULL,
cdm_version_concept_id integer NOT NULL,
vocabulary_version varchar(20) NOT NULL );
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE @cdmDatabaseSchema.CONCEPT (
concept_id integer NOT NULL,
concept_name varchar(255) NOT NULL,
domain_id varchar(20) NOT NULL,
vocabulary_id varchar(20) NOT NULL,
concept_class_id varchar(20) NOT NULL,
standard_concept varchar(1) NULL,
concept_code varchar(50) NOT NULL,
valid_start_date date NOT NULL,
valid_end_date date NOT NULL,
invalid_reason varchar(1) NULL );
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE @cdmDatabaseSchema.VOCABULARY (
vocabulary_id varchar(20) NOT NULL,
vocabulary_name varchar(255) NOT NULL,
vocabulary_reference varchar(255) NOT NULL,
vocabulary_version varchar(255) NULL,
vocabulary_concept_id integer NOT NULL );
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE @cdmDatabaseSchema.DOMAIN (
domain_id varchar(20) NOT NULL,
domain_name varchar(255) NOT NULL,
domain_concept_id integer NOT NULL );
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE @cdmDatabaseSchema.CONCEPT_CLASS (
concept_class_id varchar(20) NOT NULL,
concept_class_name varchar(255) 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 varchar(20) NOT NULL,
valid_start_date date NOT NULL,
valid_end_date date NOT NULL,
invalid_reason varchar(1) NULL );
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE @cdmDatabaseSchema.RELATIONSHIP (
relationship_id varchar(20) NOT NULL,
relationship_name varchar(255) NOT NULL,
is_hierarchical varchar(1) NOT NULL,
defines_ancestry varchar(1) NOT NULL,
reverse_relationship_id varchar(20) 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 varchar(1000) 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 varchar(50) NOT NULL,
source_concept_id integer NOT NULL,
source_vocabulary_id varchar(20) NOT NULL,
source_code_description varchar(255) NULL,
target_concept_id integer NOT NULL,
target_vocabulary_id varchar(20) NOT NULL,
valid_start_date date NOT NULL,
valid_end_date date NOT NULL,
invalid_reason varchar(1) NULL );
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE @cdmDatabaseSchema.DRUG_STRENGTH (
drug_concept_id integer NOT NULL,
ingredient_concept_id integer NOT NULL,
amount_value NUMERIC NULL,
amount_unit_concept_id integer NULL,
numerator_value NUMERIC NULL,
numerator_unit_concept_id integer NULL,
denominator_value NUMERIC 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 varchar(1) NULL );
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE @cdmDatabaseSchema.COHORT (
cohort_definition_id integer NOT NULL,
subject_id integer 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 integer NOT NULL,
cohort_definition_name varchar(255) 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 );