670 lines
20 KiB
Plaintext
670 lines
20 KiB
Plaintext
/*
|
|
Copyright 2018-08 Observational Health Data Sciences and Informatics
|
|
|
|
|
|
Licensed under the Apache License, Version 2.0 (the "License");
|
|
you may not use this file except in compliance with the License.
|
|
You may obtain a copy of the License at
|
|
|
|
http://www.apache.org/licenses/LICENSE-2.0
|
|
|
|
Unless required by applicable law or agreed to in writing, software
|
|
distributed under the License is distributed on an "AS IS" BASIS,
|
|
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
|
|
See the License for the specific language governing permissions and
|
|
limitations under the License.
|
|
|
|
OMOP CDM v6.0 DDL
|
|
|
|
bigquery script to create OMOP common data model version 6.0
|
|
|
|
last revised: 27-Aug-2018
|
|
|
|
Authors: Patrick Ryan, Christian Reich, Clair Blacketer
|
|
*/
|
|
|
|
#standardsql
|
|
create table 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 null ,
|
|
concept_code STRING not null ,
|
|
valid_start_date date not null ,
|
|
valid_end_date date not null ,
|
|
invalid_reason STRING null
|
|
)
|
|
;
|
|
|
|
|
|
create table vocabulary (
|
|
vocabulary_id STRING not null,
|
|
vocabulary_name STRING not null,
|
|
vocabulary_reference STRING not null,
|
|
vocabulary_version STRING null,
|
|
vocabulary_concept_id INT64 not null
|
|
)
|
|
;
|
|
|
|
|
|
create table domain (
|
|
domain_id STRING not null,
|
|
domain_name STRING not null,
|
|
domain_concept_id INT64 not null
|
|
)
|
|
;
|
|
|
|
|
|
create table concept_class (
|
|
concept_class_id STRING not null,
|
|
concept_class_name STRING not null,
|
|
concept_class_concept_id INT64 not null
|
|
)
|
|
;
|
|
|
|
|
|
create table 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 null
|
|
)
|
|
;
|
|
|
|
|
|
create table 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
|
|
)
|
|
;
|
|
|
|
|
|
create table concept_synonym (
|
|
concept_id INT64 not null,
|
|
concept_synonym_name STRING not null,
|
|
language_concept_id INT64 not null
|
|
)
|
|
;
|
|
|
|
|
|
create table 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
|
|
)
|
|
;
|
|
|
|
|
|
create table 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 null,
|
|
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 null
|
|
)
|
|
;
|
|
|
|
|
|
create table drug_strength (
|
|
drug_concept_id INT64 not null,
|
|
ingredient_concept_id INT64 not null,
|
|
amount_value FLOAT64 null,
|
|
amount_unit_concept_id INT64 null,
|
|
numerator_value FLOAT64 null,
|
|
numerator_unit_concept_id INT64 null,
|
|
denominator_value FLOAT64 null,
|
|
denominator_unit_concept_id INT64 null,
|
|
box_size INT64 null,
|
|
valid_start_date date not null,
|
|
valid_end_date date not null,
|
|
invalid_reason STRING null
|
|
)
|
|
;
|
|
|
|
|
|
create table cdm_source
|
|
(
|
|
cdm_source_name STRING not null ,
|
|
cdm_source_abbreviation STRING null ,
|
|
cdm_holder STRING null ,
|
|
source_description STRING null ,
|
|
source_documentation_reference STRING null ,
|
|
cdm_etl_reference STRING null ,
|
|
source_release_date date null ,
|
|
cdm_release_date date null ,
|
|
cdm_version STRING null ,
|
|
vocabulary_version STRING null
|
|
)
|
|
;
|
|
|
|
|
|
create table metadata
|
|
(
|
|
metadata_concept_id INT64 not null ,
|
|
metadata_type_concept_id INT64 not null ,
|
|
name STRING not null ,
|
|
value_as_string STRING null ,
|
|
value_as_concept_id INT64 null ,
|
|
metadata_date date null ,
|
|
metadata_datetime DATETIME null
|
|
)
|
|
;
|
|
|
|
insert into metadata (metadata_concept_id, metadata_type_concept_id, name, value_as_string, value_as_concept_id, metadata_date, measurement_datetime) --Added cdm version record
|
|
values (0, 0, 'CDM Version', '6.0', 0, NULL, NULL)
|
|
;
|
|
|
|
|
|
--HINT DISTRIBUTE_ON_KEY(person_id)
|
|
create table person
|
|
(
|
|
person_id INT64 not null , --INT64s added
|
|
gender_concept_id INT64 not null ,
|
|
year_of_birth INT64 not null ,
|
|
month_of_birth INT64 null,
|
|
day_of_birth INT64 null,
|
|
birth_datetime DATETIME null,
|
|
death_datetime DATETIME null,
|
|
race_concept_id INT64 not null,
|
|
ethnicity_concept_id INT64 not null,
|
|
location_id INT64 null,
|
|
provider_id INT64 null,
|
|
care_site_id INT64 null,
|
|
person_source_value STRING null,
|
|
gender_source_value STRING null,
|
|
gender_source_concept_id INT64 not null,
|
|
race_source_value STRING null,
|
|
race_source_concept_id INT64 not null,
|
|
ethnicity_source_value STRING null,
|
|
ethnicity_source_concept_id INT64 not null
|
|
)
|
|
;
|
|
|
|
|
|
--HINT DISTRIBUTE_ON_KEY(person_id)
|
|
create table 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 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 null ,
|
|
specimen_datetime DATETIME not null ,
|
|
quantity FLOAT64 null ,
|
|
unit_concept_id INT64 null ,
|
|
anatomic_site_concept_id INT64 not null ,
|
|
disease_status_concept_id INT64 not null ,
|
|
specimen_source_id STRING null ,
|
|
specimen_source_value STRING null ,
|
|
unit_source_value STRING null ,
|
|
anatomic_site_source_value STRING null ,
|
|
disease_status_source_value STRING null
|
|
)
|
|
;
|
|
|
|
|
|
--HINT DISTRIBUTE_ON_KEY(person_id)
|
|
create table visit_occurrence
|
|
(
|
|
visit_occurrence_id INT64 not null ,
|
|
person_id INT64 not null ,
|
|
visit_concept_id INT64 not null ,
|
|
visit_start_date date null ,
|
|
visit_start_datetime DATETIME not null ,
|
|
visit_end_date date null ,
|
|
visit_end_datetime DATETIME not null ,
|
|
visit_type_concept_id INT64 not null ,
|
|
provider_id INT64 null,
|
|
care_site_id INT64 null,
|
|
visit_source_value STRING null,
|
|
visit_source_concept_id INT64 not null ,
|
|
admitted_from_concept_id INT64 not NULL , /*Changed from admitting_source_* */
|
|
admitted_from_source_value STRING NULL ,
|
|
discharge_to_source_value STRING null ,
|
|
discharge_to_concept_id INT64 not null ,
|
|
preceding_visit_occurrence_id INT64 null
|
|
)
|
|
;
|
|
|
|
|
|
--HINT DISTRIBUTE_ON_KEY(person_id)
|
|
create table 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 null ,
|
|
visit_detail_start_datetime DATETIME not null ,
|
|
visit_detail_end_date date null ,
|
|
visit_detail_end_datetime DATETIME not null ,
|
|
visit_detail_type_concept_id INT64 not null ,
|
|
provider_id INT64 null ,
|
|
care_site_id INT64 null ,
|
|
discharge_to_concept_id INT64 not null ,
|
|
admitted_from_concept_id INT64 not NULL , /*Changed from admitting_source_* */
|
|
admitted_from_source_value STRING NULL ,
|
|
visit_detail_source_value STRING null ,
|
|
visit_detail_source_concept_id INT64 not null ,
|
|
discharge_to_source_value STRING null ,
|
|
preceding_visit_detail_id INT64 null ,
|
|
visit_detail_parent_id INT64 null ,
|
|
visit_occurrence_id INT64 not null
|
|
)
|
|
;
|
|
|
|
|
|
--HINT DISTRIBUTE_ON_KEY(person_id)
|
|
create table procedure_occurrence
|
|
(
|
|
procedure_occurrence_id INT64 not null ,
|
|
person_id INT64 not null ,
|
|
procedure_concept_id INT64 not null ,
|
|
procedure_date date null ,
|
|
procedure_datetime DATETIME not null ,
|
|
procedure_type_concept_id INT64 not null ,
|
|
modifier_concept_id INT64 not null ,
|
|
quantity INT64 null ,
|
|
provider_id INT64 null ,
|
|
visit_occurrence_id INT64 null ,
|
|
visit_detail_id INT64 null ,
|
|
procedure_source_value STRING null ,
|
|
procedure_source_concept_id INT64 not null ,
|
|
modifier_source_value STRING null
|
|
)
|
|
;
|
|
|
|
|
|
--HINT DISTRIBUTE_ON_KEY(person_id)
|
|
create table drug_exposure
|
|
(
|
|
drug_exposure_id INT64 not null ,
|
|
person_id INT64 not null ,
|
|
drug_concept_id INT64 not null ,
|
|
drug_exposure_start_date date null ,
|
|
drug_exposure_start_datetime DATETIME not null ,
|
|
drug_exposure_end_date date null ,
|
|
drug_exposure_end_datetime DATETIME not null ,
|
|
verbatim_end_date date null ,
|
|
drug_type_concept_id INT64 not null ,
|
|
stop_reason STRING null ,
|
|
refills INT64 null ,
|
|
quantity FLOAT64 null ,
|
|
days_supply INT64 null ,
|
|
sig STRING null ,
|
|
route_concept_id INT64 not null ,
|
|
lot_number STRING null ,
|
|
provider_id INT64 null ,
|
|
visit_occurrence_id INT64 null ,
|
|
visit_detail_id INT64 null ,
|
|
drug_source_value STRING null ,
|
|
drug_source_concept_id INT64 not null ,
|
|
route_source_value STRING null ,
|
|
dose_unit_source_value STRING null
|
|
)
|
|
;
|
|
|
|
|
|
--HINT DISTRIBUTE_ON_KEY(person_id)
|
|
create table device_exposure
|
|
(
|
|
device_exposure_id INT64 not null ,
|
|
person_id INT64 not null ,
|
|
device_concept_id INT64 not null ,
|
|
device_exposure_start_date date null ,
|
|
device_exposure_start_datetime DATETIME not null ,
|
|
device_exposure_end_date date null ,
|
|
device_exposure_end_datetime DATETIME null ,
|
|
device_type_concept_id INT64 not null ,
|
|
unique_device_id STRING null ,
|
|
quantity INT64 null ,
|
|
provider_id INT64 null ,
|
|
visit_occurrence_id INT64 null ,
|
|
visit_detail_id INT64 null ,
|
|
device_source_value STRING null ,
|
|
device_source_concept_id INT64 not null
|
|
)
|
|
;
|
|
|
|
|
|
--HINT DISTRIBUTE_ON_KEY(person_id)
|
|
create table condition_occurrence
|
|
(
|
|
condition_occurrence_id INT64 not null ,
|
|
person_id INT64 not null ,
|
|
condition_concept_id INT64 not null ,
|
|
condition_start_date date null ,
|
|
condition_start_datetime DATETIME not null ,
|
|
condition_end_date date null ,
|
|
condition_end_datetime DATETIME null ,
|
|
condition_type_concept_id INT64 not null ,
|
|
condition_status_concept_id INT64 not null ,
|
|
stop_reason STRING null ,
|
|
provider_id INT64 null ,
|
|
visit_occurrence_id INT64 null ,
|
|
visit_detail_id INT64 null ,
|
|
condition_source_value STRING null ,
|
|
condition_source_concept_id INT64 not null ,
|
|
condition_status_source_value STRING null
|
|
)
|
|
;
|
|
|
|
|
|
--HINT DISTRIBUTE_ON_KEY(person_id)
|
|
create table measurement
|
|
(
|
|
measurement_id INT64 not null ,
|
|
person_id INT64 not null ,
|
|
measurement_concept_id INT64 not null ,
|
|
measurement_date date null ,
|
|
measurement_datetime DATETIME not null ,
|
|
measurement_time STRING null,
|
|
measurement_type_concept_id INT64 not null ,
|
|
operator_concept_id INT64 null ,
|
|
value_as_number FLOAT64 null ,
|
|
value_as_concept_id INT64 null ,
|
|
unit_concept_id INT64 null ,
|
|
range_low FLOAT64 null ,
|
|
range_high FLOAT64 null ,
|
|
provider_id INT64 null ,
|
|
visit_occurrence_id INT64 null ,
|
|
visit_detail_id INT64 null ,
|
|
measurement_source_value STRING null ,
|
|
measurement_source_concept_id INT64 not null ,
|
|
unit_source_value STRING null ,
|
|
value_source_value STRING null
|
|
)
|
|
;
|
|
|
|
|
|
--HINT DISTRIBUTE_ON_KEY(person_id)
|
|
create table note
|
|
(
|
|
note_id INT64 not null ,
|
|
person_id INT64 not null ,
|
|
note_event_id INT64 null ,
|
|
note_event_field_concept_id INT64 not NULL ,
|
|
note_date date null ,
|
|
note_datetime DATETIME not null ,
|
|
note_type_concept_id INT64 not null ,
|
|
note_class_concept_id INT64 not null ,
|
|
note_title STRING null ,
|
|
note_text STRING null ,
|
|
encoding_concept_id INT64 not null ,
|
|
language_concept_id INT64 not null ,
|
|
provider_id INT64 null ,
|
|
visit_occurrence_id INT64 null ,
|
|
visit_detail_id INT64 null ,
|
|
note_source_value STRING null
|
|
)
|
|
;
|
|
|
|
|
|
|
|
create table note_nlp
|
|
(
|
|
note_nlp_id INT64 not null ,
|
|
note_id INT64 not null ,
|
|
section_concept_id INT64 not null ,
|
|
snippet STRING null ,
|
|
"offset" STRING null ,
|
|
lexical_variant STRING not null ,
|
|
note_nlp_concept_id INT64 not null ,
|
|
nlp_system STRING null ,
|
|
nlp_date date not null ,
|
|
nlp_datetime DATETIME null ,
|
|
term_exists STRING null ,
|
|
term_temporal STRING null ,
|
|
term_modifiers STRING null ,
|
|
note_nlp_source_concept_id INT64 not null
|
|
)
|
|
;
|
|
|
|
|
|
--HINT DISTRIBUTE_ON_KEY(person_id)
|
|
create table observation
|
|
(
|
|
observation_id INT64 not null ,
|
|
person_id INT64 not null ,
|
|
observation_concept_id INT64 not null ,
|
|
observation_date date null ,
|
|
observation_datetime DATETIME not null ,
|
|
observation_type_concept_id INT64 not null ,
|
|
value_as_number FLOAT64 null ,
|
|
value_as_string STRING null ,
|
|
value_as_concept_id INT64 null ,
|
|
qualifier_concept_id INT64 null ,
|
|
unit_concept_id INT64 null ,
|
|
provider_id INT64 null ,
|
|
visit_occurrence_id INT64 null ,
|
|
visit_detail_id INT64 null ,
|
|
observation_source_value STRING null ,
|
|
observation_source_concept_id INT64 not null ,
|
|
unit_source_value STRING null ,
|
|
qualifier_source_value STRING null ,
|
|
observation_event_id INT64 null ,
|
|
obs_event_field_concept_id INT64 not NULL ,
|
|
value_as_datetime DATETIME null
|
|
)
|
|
;
|
|
|
|
|
|
create table survey_conduct
|
|
(
|
|
survey_conduct_id INT64 not null ,
|
|
person_id INT64 not null ,
|
|
survey_concept_id INT64 not null ,
|
|
survey_start_date date null ,
|
|
survey_start_datetime DATETIME null ,
|
|
survey_end_date date null ,
|
|
survey_end_datetime DATETIME not null ,
|
|
provider_id INT64 null ,
|
|
assisted_concept_id INT64 not null ,
|
|
respondent_type_concept_id INT64 not null ,
|
|
timing_concept_id INT64 not null ,
|
|
collection_method_concept_id INT64 not null ,
|
|
assisted_source_value STRING null ,
|
|
respondent_type_source_value STRING null ,
|
|
timing_source_value STRING null ,
|
|
collection_method_source_value STRING null ,
|
|
survey_source_value STRING null ,
|
|
survey_source_concept_id INT64 not null ,
|
|
survey_source_identifier STRING null ,
|
|
validated_survey_concept_id INT64 not null ,
|
|
validated_survey_source_value STRING null ,
|
|
survey_version_number STRING null ,
|
|
visit_occurrence_id INT64 null ,
|
|
visit_detail_id INT64 null ,
|
|
response_visit_occurrence_id INT64 null
|
|
)
|
|
;
|
|
|
|
|
|
create table 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
|
|
)
|
|
;
|
|
|
|
|
|
create table location
|
|
(
|
|
location_id INT64 not null ,
|
|
address_1 STRING null ,
|
|
address_2 STRING null ,
|
|
city STRING null ,
|
|
state STRING null ,
|
|
zip STRING null ,
|
|
county STRING null ,
|
|
country STRING null ,
|
|
location_source_value STRING null ,
|
|
latitude FLOAT64 null ,
|
|
longitude FLOAT64 null
|
|
)
|
|
;
|
|
|
|
|
|
create table location_history
|
|
(
|
|
location_history_id INT64 not null ,
|
|
location_id INT64 not null ,
|
|
relationship_type_concept_id INT64 not null , --Recent addition based on github discussion
|
|
domain_id STRING not null ,
|
|
entity_id INT64 not null ,
|
|
start_date date not null ,
|
|
end_date date null
|
|
)
|
|
;
|
|
|
|
|
|
create table care_site
|
|
(
|
|
care_site_id INT64 not null ,
|
|
care_site_name STRING null ,
|
|
place_of_service_concept_id INT64 not null ,
|
|
location_id INT64 null ,
|
|
care_site_source_value STRING null ,
|
|
place_of_service_source_value STRING null
|
|
)
|
|
;
|
|
|
|
|
|
create table provider
|
|
(
|
|
provider_id INT64 not null ,
|
|
provider_name STRING null ,
|
|
npi STRING null ,
|
|
dea STRING null ,
|
|
specialty_concept_id INT64 not null ,
|
|
care_site_id INT64 null ,
|
|
year_of_birth INT64 null ,
|
|
gender_concept_id INT64 not null ,
|
|
provider_source_value STRING null ,
|
|
specialty_source_value STRING null ,
|
|
specialty_source_concept_id INT64 not null ,
|
|
gender_source_value STRING null ,
|
|
gender_source_concept_id INT64 not null
|
|
)
|
|
;
|
|
|
|
|
|
--HINT DISTRIBUTE_ON_KEY(person_id)
|
|
create table payer_plan_period
|
|
(
|
|
payer_plan_period_id INT64 not null ,
|
|
person_id INT64 not null ,
|
|
contract_person_id INT64 null ,
|
|
payer_plan_period_start_date date not null ,
|
|
payer_plan_period_end_date date not null ,
|
|
payer_concept_id INT64 not null ,
|
|
plan_concept_id INT64 not null ,
|
|
contract_concept_id INT64 not null ,
|
|
sponsor_concept_id INT64 not null ,
|
|
stop_reason_concept_id INT64 not null ,
|
|
payer_source_value STRING null ,
|
|
payer_source_concept_id INT64 not null ,
|
|
plan_source_value STRING null ,
|
|
plan_source_concept_id INT64 not null ,
|
|
contract_source_value STRING null ,
|
|
contract_source_concept_id INT64 not null ,
|
|
sponsor_source_value STRING null ,
|
|
sponsor_source_concept_id INT64 not null ,
|
|
family_source_value STRING null ,
|
|
stop_reason_source_value STRING null ,
|
|
stop_reason_source_concept_id INT64 not null
|
|
)
|
|
;
|
|
|
|
|
|
create table cost
|
|
(
|
|
cost_id INT64 not null ,
|
|
person_id INT64 not null,
|
|
cost_event_id INT64 not null ,
|
|
cost_event_field_concept_id INT64 NOT NULL ,
|
|
cost_concept_id INT64 not null ,
|
|
cost_type_concept_id INT64 not null ,
|
|
currency_concept_id INT64 not null ,
|
|
cost FLOAT64 null ,
|
|
incurred_date date not null ,
|
|
billed_date date null ,
|
|
paid_date date null ,
|
|
revenue_code_concept_id INT64 not null ,
|
|
drg_concept_id INT64 not null ,
|
|
cost_source_value STRING null ,
|
|
cost_source_concept_id INT64 not null ,
|
|
revenue_code_source_value STRING null ,
|
|
drg_source_value STRING null ,
|
|
payer_plan_period_id INT64 null
|
|
)
|
|
;
|
|
|
|
|
|
--HINT DISTRIBUTE_ON_KEY(person_id)
|
|
create table drug_era
|
|
(
|
|
drug_era_id INT64 not null ,
|
|
person_id INT64 not null ,
|
|
drug_concept_id INT64 not null ,
|
|
drug_era_start_datetime datetime not null ,
|
|
drug_era_end_datetime datetime not null ,
|
|
drug_exposure_count INT64 null ,
|
|
gap_days INT64 null
|
|
)
|
|
;
|
|
|
|
|
|
--HINT DISTRIBUTE_ON_KEY(person_id)
|
|
create table 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_datetime datetime not null ,
|
|
dose_era_end_datetime datetime not null
|
|
)
|
|
;
|
|
|
|
|
|
--HINT DISTRIBUTE_ON_KEY(person_id)
|
|
create table condition_era
|
|
(
|
|
condition_era_id INT64 not null ,
|
|
person_id INT64 not null ,
|
|
condition_concept_id INT64 not null ,
|
|
condition_era_start_datetime datetime not null ,
|
|
condition_era_end_datetime datetime not null ,
|
|
condition_occurrence_count INT64 null
|
|
)
|
|
;
|