OMOP/output/bigquery/OMOP CDM bigquery ddl.txt

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/*********************************************************************************
# 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.
********************************************************************************/
/************************
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bigquery script to create OMOP common data model version 6.0
last revised: 27-Aug-2018
Authors: Patrick Ryan, Christian Reich, Clair Blacketer
*************************/
/************************
Standardized vocabulary
************************/
--HINT DISTRIBUTE ON RANDOM
create table 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 vocabulary (
vocabulary_id varchar(20) not null,
vocabulary_name varchar(255) not null,
vocabulary_reference varchar(255) not null,
vocabulary_version varchar(255) not null,
vocabulary_concept_id integer not null
)
;
--HINT DISTRIBUTE ON RANDOM
create table 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 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 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 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 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 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 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 drug_strength (
drug_concept_id integer not null,
ingredient_concept_id integer not null,
amount_value float null,
amount_unit_concept_id integer null,
numerator_value float null,
numerator_unit_concept_id integer null,
denominator_value float 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 cohort_definition (
cohort_definition_id integer not null,
cohort_definition_name varchar(255) not null,
cohort_definition_description varchar(max) null,
definition_type_concept_id integer not null,
cohort_definition_syntax varchar(max) null,
subject_concept_id integer not null,
cohort_initiation_date date null
)
;
--HINT DISTRIBUTE ON RANDOM
create table attribute_definition (
attribute_definition_id integer not null,
attribute_name varchar(255) not null,
attribute_description varchar(max) null,
attribute_type_concept_id integer not null,
attribute_syntax varchar(max) null
)
;
/**************************
Standardized meta-data
***************************/
--HINT DISTRIBUTE ON RANDOM
create table cdm_source
(
cdm_source_name varchar(255) not null ,
cdm_source_abbreviation varchar(25) null ,
cdm_holder varchar(255) null ,
source_description varchar(max) null ,
source_documentation_reference varchar(255) null ,
cdm_etl_reference varchar(255) null ,
source_release_date date null ,
cdm_release_date date null ,
cdm_version varchar(10) null ,
vocabulary_version varchar(20) null
)
;
--HINT DISTRIBUTE ON RANDOM
create table metadata
(
metadata_concept_id integer not null ,
metadata_type_concept_id integer not null ,
name varchar(250) not null ,
value_as_string varchar(max) null ,
value_as_concept_id integer null ,
metadata_date date null ,
metadata_datetime datetime2 null
)
;
insert into metadata (name, value_as_string) --Added cdm version record
values ('CDM Version', '6.0')
;
/************************
Standardized clinical data
************************/
--HINT DISTRIBUTE_ON_KEY(person_id)
create table person
(
person_id bigint not null , --BIGINTs added
gender_concept_id integer not null ,
year_of_birth integer not null ,
month_of_birth integer null,
day_of_birth integer null,
birth_datetime datetime2 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 observation_period
(
observation_period_id bigint not null ,
person_id bigint 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 specimen
(
specimen_id bigint not null ,
person_id bigint not null ,
specimen_concept_id integer not null ,
specimen_type_concept_id integer not null ,
specimen_date date null ,
specimen_datetime datetime2 not null ,
quantity float 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_KEY(person_id)
create table death
(
person_id bigint not null ,
death_date date null ,
death_datetime datetime2 not null ,
death_type_concept_id integer not 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 visit_occurrence
(
visit_occurrence_id bigint not null ,
person_id bigint not null ,
visit_concept_id integer not null ,
visit_start_date date null ,
visit_start_datetime datetime2 not null ,
visit_end_date date null ,
visit_end_datetime datetime2 not 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 , /*Changed from admitting_source_* */
admitted_from_source_value varchar(50) null ,
discharge_to_source_value varchar(50) null ,
discharge_to_concept_id integer null ,
preceding_visit_occurrence_id integer null
)
;
--HINT DISTRIBUTE_ON_KEY(person_id)
create table visit_detail
(
visit_detail_id bigint not null ,
person_id bigint not null ,
visit_detail_concept_id integer not null ,
visit_detail_start_date date null ,
visit_detail_start_datetime datetime2 not null ,
visit_detail_end_date date null ,
visit_detail_end_datetime datetime2 not null ,
visit_detail_type_concept_id integer not null ,
provider_id integer null ,
care_site_id integer null ,
discharge_to_concept_id integer null ,
admitted_from_concept_id integer null , /*Changed from admitting_source_* */
admitted_from_source_value varchar(50) null ,
visit_detail_source_value varchar(50) null ,
visit_detail_source_concept_id integer null ,
discharge_to_source_value varchar(50) null ,
preceding_visit_detail_id bigint null ,
visit_detail_parent_id bigint null ,
visit_occurrence_id bigint not null
)
;
--HINT DISTRIBUTE_ON_KEY(person_id)
create table procedure_occurrence
(
procedure_occurrence_id bigint not null ,
person_id bigint not null ,
procedure_concept_id integer not null ,
procedure_date date null ,
procedure_datetime datetime2 not 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 ,
)
;
--HINT DISTRIBUTE_ON_KEY(person_id)
create table drug_exposure
(
drug_exposure_id bigint not null ,
person_id bigint not null ,
drug_concept_id integer not null ,
drug_exposure_start_date date null ,
drug_exposure_start_datetime datetime2 not null ,
drug_exposure_end_date date null ,
drug_exposure_end_datetime datetime2 not null ,
verbatim_end_date date null ,
drug_type_concept_id integer not null ,
stop_reason varchar(20) null ,
refills integer null ,
quantity float null ,
days_supply integer null ,
sig varchar(max) 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 device_exposure
(
device_exposure_id bigint not null ,
person_id bigint not null ,
device_concept_id integer not null ,
device_exposure_start_date date null ,
device_exposure_start_datetime datetime2 not null ,
device_exposure_end_date date null ,
device_exposure_end_datetime datetime2 null ,
device_type_concept_id integer not null ,
unique_device_id varchar(50) null ,
quantity integer null ,
provider_id integer null ,
visit_occurrence_id integer null ,
visit_detail_id integer null ,
device_source_value varchar(100) null ,
device_source_concept_id integer null
)
;
--HINT DISTRIBUTE_ON_KEY(person_id)
create table condition_occurrence
(
condition_occurrence_id bigint not null ,
person_id bigint not null ,
condition_concept_id integer not null ,
condition_start_date date null ,
condition_start_datetime datetime2 not null ,
condition_end_date date null ,
condition_end_datetime datetime2 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 measurement
(
measurement_id bigint not null ,
person_id bigint not null ,
measurement_concept_id integer not null ,
measurement_date date null ,
measurement_datetime datetime2 not null ,
measurement_time varchar(10) null,
measurement_type_concept_id integer not null ,
operator_concept_id integer null ,
value_as_number float null ,
value_as_concept_id integer null ,
unit_concept_id integer null ,
range_low float null ,
range_high float 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 ,
value_source_value varchar(50) null
)
;
--HINT DISTRIBUTE_ON_KEY(person_id)
create table note
(
note_id bigint not null ,
person_id bigint not null ,
note_event_id bigint null , --This and the field below added
note_domain_id varchar(20) null , --This field may be removed in favor of the one below
--note_event_table_concept_id INTEGER NULL , --This may be added based on 9/4 meeting
note_date date null ,
note_datetime datetime2 not null ,
note_type_concept_id integer not null ,
note_class_concept_id integer not null ,
note_title varchar(250) null ,
note_text varchar(max) 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 note_nlp
(
note_nlp_id bigint not null ,
note_id bigint not null ,
section_concept_id integer null ,
snippet varchar(250) null ,
"offset" varchar(250) null ,
lexical_variant varchar(250) not null ,
note_nlp_concept_id integer null ,
nlp_system varchar(250) null ,
nlp_date date not null ,
nlp_datetime datetime2 null ,
term_exists varchar(1) null ,
term_temporal varchar(50) null ,
term_modifiers varchar(2000) null ,
note_nlp_source_concept_id integer null
)
;
--HINT DISTRIBUTE_ON_KEY(person_id)
create table observation
(
observation_id bigint not null ,
person_id bigint not null ,
observation_concept_id integer not null ,
observation_date date null ,
observation_datetime datetime2 not null ,
observation_type_concept_id integer not null ,
value_as_number float 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 bigint null ,
visit_detail_id bigint 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 ,
observation_event_id bigint null , /* This will link back to the event table (SURVEY) on SURVEY_OCCURRENCE_ID, changed name to comply with COST and NOTE*/
observation_event_domain_id varchar(20) null ,
--obs_event_table_concept_id INTEGER NULL , /* Changed name to comply with COST and NOTE. Had to use 'obs' for oracle restriction, may be added on 9/4*/
value_as_datetime datetime2 null
)
;
--HINT DISTRIBUTE ON KEY(person_id)
create table survey_conduct --Table added
(
survey_conduct_id bigint not null ,
person_id bigint not null ,
survey_concept_id integer not null ,
survey_start_date date null ,
survey_start_datetime datetime2 null ,
survey_end_date date null ,
survey_end_datetime datetime2 not null ,
provider_id bigint null ,
assisted_concept_id integer null ,
respondent_type_concept_id integer null ,
timing_concept_id integer null ,
collection_method_concept_id integer null ,
assisted_source_value varchar(50) null ,
respondent_type_source_value varchar(100) null ,
timing_source_value varchar(100) null ,
collection_method_source_value varchar(100) null ,
survey_source_value varchar(100) null ,
survey_source_concept_id integer null ,
survey_source_identifier varchar(100) null ,
validated_survey_concept_id integer null ,
validated_survey_source_value varchar(100) null ,
survey_version_number varchar(20) null ,
visit_occurrence_id bigint null ,
visit_detail_id bigint null ,
response_to_visit_occurrence_id bigint null
)
;
--HINT DISTRIBUTE ON RANDOM
create table fact_relationship
(
domain_concept_id_1 integer not null ,
fact_id_1 bigint not null ,
domain_concept_id_2 integer not null ,
fact_id_2 bigint not null ,
relationship_concept_id integer not null
)
;
/************************
Standardized health system data
************************/
--HINT DISTRIBUTE ON RANDOM
create table location
(
location_id bigint 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 ,
country varchar(100) null ,
location_source_value varchar(50) null ,
latitude float null ,
longitude float null
)
;
--HINT DISTRIBUTE ON RANDOM
create table location_history --Table added
(
location_history_id bigint not null ,
location_id bigint not null ,
relationship_type_concept_id integer null , --Recent addition based on github discussion
domain_id varchar(50) not null ,
entity_id bigint not null ,
start_date date not null ,
end_date date null
)
;
--HINT DISTRIBUTE ON RANDOM
create table care_site
(
care_site_id bigint not null ,
care_site_name varchar(255) null ,
place_of_service_concept_id integer null ,
location_id bigint null ,
care_site_source_value varchar(50) null ,
place_of_service_source_value varchar(50) null
)
;
--HINT DISTRIBUTE ON RANDOM
create table provider
(
provider_id bigint not null ,
provider_name varchar(255) null ,
npi varchar(20) null ,
dea varchar(20) null ,
specialty_concept_id integer null ,
care_site_id bigint 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
)
;
/************************
Standardized health economics
************************/
--HINT DISTRIBUTE_ON_KEY(person_id)
create table payer_plan_period
(
payer_plan_period_id bigint not null ,
person_id bigint not null ,
contract_person_id bigint null ,
payer_plan_period_start_date date not null ,
payer_plan_period_end_date date not null ,
payer_concept_id integer null ,
plan_concept_id integer null ,
contract_concept_id integer null ,
sponsor_concept_id integer null ,
stop_reason_concept_id integer null ,
payer_source_value varchar(50) null ,
payer_source_concept_id integer null ,
plan_source_value varchar(50) null ,
plan_source_concept_id integer null ,
contract_source_value varchar(50) null ,
contract_source_concept_id integer null ,
sponsor_source_value varchar(50) null ,
sponsor_source_concept_id integer null ,
family_source_value varchar(50) null ,
stop_reason_source_value varchar(50) null ,
stop_reason_source_concept_id integer null
)
;
--HINT DISTRIBUTE ON KEY(person_id)
create table cost
(
cost_id bigint not null ,
person_id bigint not null,
cost_event_id bigint not null ,
cost_domain_id varchar(20) not null ,
--cost_event_table_concept_id INTEGER NOT NULL , /*This is still in discussion and most likely will replace cost_domain_id at 9/4 meeting*/
cost_concept_id integer not null ,
cost_type_concept_id integer not null ,
currency_concept_id integer null ,
cost float null ,
incurred_date date not null ,
billed_date date null ,
paid_date date null ,
revenue_code_concept_id integer null ,
drg_concept_id integer null ,
cost_source_value varchar(50) null ,
cost_source_concept_id integer null ,
revenue_code_source_value varchar(50) null ,
drg_source_value varchar(3) null ,
payer_plan_period_id bigint null
)
;
/************************
Standardized derived elements
************************/
--HINT DISTRIBUTE_ON_KEY(subject_id)
create table cohort
(
cohort_definition_id bigint not null ,
subject_id bigint not null ,
cohort_start_date date not null ,
cohort_end_date date not null
)
;
--HINT DISTRIBUTE_ON_KEY(subject_id)
create table cohort_attribute
(
cohort_definition_id bigint not null ,
subject_id bigint not null ,
cohort_start_date date not null ,
cohort_end_date date not null ,
attribute_definition_id bigint not null ,
value_as_number float null ,
value_as_concept_id integer null
)
;
--HINT DISTRIBUTE_ON_KEY(person_id)
create table drug_era
(
drug_era_id bigint not null ,
person_id bigint not null ,
drug_concept_id integer not null ,
drug_era_start_date date not null ,
drug_era_end_date date not null ,
drug_exposure_count integer null ,
gap_days integer null
)
;
--HINT DISTRIBUTE_ON_KEY(person_id)
create table dose_era
(
dose_era_id bigint not null ,
person_id bigint not null ,
drug_concept_id integer not null ,
unit_concept_id integer not null ,
dose_value float not null ,
dose_era_start_date date not null ,
dose_era_end_date date not null
)
;
--HINT DISTRIBUTE_ON_KEY(person_id)
create table condition_era
(
condition_era_id bigint not null ,
person_id bigint not null ,
condition_concept_id integer not null ,
condition_era_start_date date not null ,
condition_era_end_date date not null ,
condition_occurrence_count integer null
)
;