mz-health/OMOP
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OMOP
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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 ohdsi.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 ohdsi.vocabulary (
vocabulary_id STRING not null,
vocabulary_name STRING not null,
vocabulary_reference STRING not null,
vocabulary_version STRING,
vocabulary_concept_id INT64 not null
)
;
--HINT DISTRIBUTE ON RANDOM
create table ohdsi.domain (
domain_id STRING not null,
domain_name STRING not null,
domain_concept_id INT64 not null
)
;
--HINT DISTRIBUTE ON RANDOM
create table ohdsi.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 ohdsi.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 ohdsi.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 ohdsi.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 ohdsi.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 ohdsi.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 ohdsi.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
)
;
/**************************
Standardized meta-data
***************************/
--HINT DISTRIBUTE ON RANDOM
create table ohdsi.cdm_source
(
cdm_source_name STRING not null ,
cdm_source_abbreviation STRING ,
cdm_holder STRING ,
source_description STRING ,
source_documentation_reference STRING ,
cdm_etl_reference STRING ,
source_release_date date null ,
cdm_release_date date null ,
cdm_version STRING ,
vocabulary_version STRING
)
;
--HINT DISTRIBUTE ON RANDOM
create table ohdsi.metadata
(
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 ,
metadata_date date null ,
metadata_datetime datetime null
)
;
insert into ohdsi.metadata (metadata_concept_id, metadata_type_concept_id, name, value_as_string, value_as_concept_id, metadata_date, metadata_datetime) --Added cdm version record
values (0,0,'CDM Version', '6.0',0,null,null)
;
/************************
Standardized clinical data
************************/
--HINT DISTRIBUTE_ON_KEY(person_id)
create table ohdsi.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,
death_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 not null,
race_source_value STRING,
race_source_concept_id INT64 not null,
ethnicity_source_value STRING,
ethnicity_source_concept_id INT64 not null
)
;
--HINT DISTRIBUTE_ON_KEY(person_id)
create table ohdsi.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 ohdsi.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 ,
anatomic_site_concept_id INT64 not null ,
disease_status_concept_id INT64 not null ,
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_KEY(person_id)
create table ohdsi.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,
care_site_id INT64,
visit_source_value STRING,
visit_source_concept_id INT64 not null ,
admitted_from_concept_id INT64 not null ,
admitted_from_source_value STRING ,
discharge_to_source_value STRING ,
discharge_to_concept_id INT64 not null ,
preceding_visit_occurrence_id INT64
)
;
--HINT DISTRIBUTE_ON_KEY(person_id)
create table ohdsi.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 ,
care_site_id INT64 ,
discharge_to_concept_id INT64 not null ,
admitted_from_concept_id INT64 not null ,
admitted_from_source_value STRING ,
visit_detail_source_value STRING ,
visit_detail_source_concept_id INT64 not null ,
discharge_to_source_value STRING ,
preceding_visit_detail_id INT64 ,
visit_detail_parent_id INT64 ,
visit_occurrence_id INT64 not null
)
;
--HINT DISTRIBUTE_ON_KEY(person_id)
create table ohdsi.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 ,
provider_id INT64 ,
visit_occurrence_id INT64 ,
visit_detail_id INT64 ,
procedure_source_value STRING ,
procedure_source_concept_id INT64 not null ,
modifier_source_value STRING
)
;
--HINT DISTRIBUTE_ON_KEY(person_id)
create table ohdsi.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 ,
refills INT64 ,
quantity FLOAT64 null ,
days_supply INT64 ,
sig STRING ,
route_concept_id INT64 not null ,
lot_number STRING ,
provider_id INT64 ,
visit_occurrence_id INT64 ,
visit_detail_id INT64 ,
drug_source_value STRING ,
drug_source_concept_id INT64 not null ,
route_source_value STRING ,
dose_unit_source_value STRING
)
;
--HINT DISTRIBUTE_ON_KEY(person_id)
create table ohdsi.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 ,
quantity INT64 ,
provider_id INT64 ,
visit_occurrence_id INT64 ,
visit_detail_id INT64 ,
device_source_value STRING ,
device_source_concept_id INT64 not null
)
;
--HINT DISTRIBUTE_ON_KEY(person_id)
create table ohdsi.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 ,
provider_id INT64 ,
visit_occurrence_id INT64 ,
visit_detail_id INT64 ,
condition_source_value STRING ,
condition_source_concept_id INT64 not null ,
condition_status_source_value STRING
)
;
--HINT DISTRIBUTE_ON_KEY(person_id)
create table ohdsi.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,
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 not null ,
unit_source_value STRING ,
value_source_value STRING,
modifier_of_event_id INT64,
modifier_of_field_concept_id INT64
)
;
--HINT DISTRIBUTE_ON_KEY(person_id)
create table ohdsi.note
(
note_id INT64 not null ,
person_id INT64 not null ,
note_event_id INT64 ,
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 ,
note_text STRING ,
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
)
;
--HINT DISTRIBUTE ON RANDOM
create table ohdsi.note_nlp
(
note_nlp_id INT64 not null ,
note_id INT64 not null ,
section_concept_id INT64 not null ,
snippet STRING ,
"offset" STRING ,
lexical_variant STRING not null ,
note_nlp_concept_id INT64 not null ,
nlp_system STRING ,
nlp_date date not null ,
nlp_datetime datetime null ,
term_exists STRING ,
term_temporal STRING ,
term_modifiers STRING ,
note_nlp_source_concept_id INT64 not null
)
;
--HINT DISTRIBUTE_ON_KEY(person_id)
create table ohdsi.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 ,
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 not null ,
unit_source_value STRING ,
qualifier_source_value STRING ,
observation_event_id INT64 ,
obs_event_field_concept_id INT64 not null ,
value_as_datetime datetime null
)
;
--HINT DISTRIBUTE ON KEY(person_id)
create table ohdsi.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 ,
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 ,
respondent_type_source_value STRING ,
timing_source_value STRING ,
collection_method_source_value STRING ,
survey_source_value STRING ,
survey_source_concept_id INT64 not null ,
survey_source_identifier STRING ,
validated_survey_concept_id INT64 not null ,
validated_survey_source_value STRING ,
survey_version_number STRING ,
visit_occurrence_id INT64 ,
visit_detail_id INT64 ,
response_visit_occurrence_id INT64
)
;
--HINT DISTRIBUTE ON RANDOM
create table ohdsi.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 ohdsi.episode (
episode_id INT64 not null,
person_id INT64 not null,
episode_start_datetime datetime not null,
episode_end_datetime datetime not null,
episode_concept_id INT64 not 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
)
;
-- Episode_Event
create table ohdsi.episode_event (
episode_id INT64 not null,
event_id INT64 not null,
event_field_concept_id INT64 not null
)
;
/************************
Standardized health system data
************************/
--HINT DISTRIBUTE ON RANDOM
create table ohdsi.location
(
location_id INT64 not null ,
address_1 STRING ,
address_2 STRING ,
city STRING ,
state STRING ,
zip STRING ,
county STRING ,
country STRING ,
location_source_value STRING ,
latitude FLOAT64 null ,
longitude FLOAT64 null ,
region_concept_id INT64
)
;
--HINT DISTRIBUTE ON RANDOM
create table ohdsi.location_history --Table added
(
location_history_id INT64 not null ,
location_id INT64 not null ,
relationship_type_concept_id INT64 not null ,
domain_id STRING not null ,
entity_id INT64 not null ,
start_date date not null ,
end_date date null
)
;
--HINT DISTRIBUTE ON RANDOM
create table ohdsi.care_site
(
care_site_id INT64 not null ,
care_site_name STRING ,
place_of_service_concept_id INT64 not null ,
location_id INT64 ,
care_site_source_value STRING ,
place_of_service_source_value STRING
)
;
--HINT DISTRIBUTE ON RANDOM
create table ohdsi.provider
(
provider_id INT64 not null ,
provider_name STRING ,
npi STRING ,
dea STRING ,
specialty_concept_id INT64 not null ,
care_site_id INT64 ,
year_of_birth INT64 ,
gender_concept_id INT64 not null ,
provider_source_value STRING ,
specialty_source_value STRING ,
specialty_source_concept_id INT64 not null ,
gender_source_value STRING ,
gender_source_concept_id INT64 not null
)
;
/************************
Standardized health economics
************************/
--HINT DISTRIBUTE_ON_KEY(person_id)
create table ohdsi.payer_plan_period
(
payer_plan_period_id INT64 not null ,
person_id INT64 not null ,
contract_person_id INT64 ,
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 ,
payer_source_concept_id INT64 not null ,
plan_source_value STRING ,
plan_source_concept_id INT64 not null ,
contract_source_value STRING ,
contract_source_concept_id INT64 not null ,
sponsor_source_value STRING ,
sponsor_source_concept_id INT64 not null ,
family_source_value STRING ,
stop_reason_source_value STRING ,
stop_reason_source_concept_id INT64 not null
)
;
--HINT DISTRIBUTE ON KEY(person_id)
create table ohdsi.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 ,
cost_source_concept_id INT64 not null ,
revenue_code_source_value STRING ,
drg_source_value STRING ,
payer_plan_period_id INT64
)
;
/************************
Standardized derived elements
************************/
--HINT DISTRIBUTE_ON_KEY(person_id)
create table ohdsi.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 ,
gap_days INT64
)
;
--HINT DISTRIBUTE_ON_KEY(person_id)
create table ohdsi.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 ohdsi.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
)
;
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