736 lines
22 KiB
Plaintext
736 lines
22 KiB
Plaintext
/*********************************************************************************
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# Copyright 2017-11 Observational Health Data Sciences and Informatics
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#
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#
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# Licensed under the Apache License, Version 2.0 (the "License");
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# you may not use this file except in compliance with the License.
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# You may obtain a copy of the License at
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#
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# http://www.apache.org/licenses/LICENSE-2.0
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#
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# Unless required by applicable law or agreed to in writing, software
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# distributed under the License is distributed on an "AS IS" BASIS,
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# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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# See the License for the specific language governing permissions and
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# limitations under the License.
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********************************************************************************/
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/************************
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####### # # ####### ###### ##### ###### # # ####### #####
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# # ## ## # # # # # # # # ## ## # # # # #
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# # # # # # # # # # # # # # # # # # # # #
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# # # # # # # ###### # # # # # # # # ###### #####
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# # # # # # # # # # # # # # # ### #
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# # # # # # # # # # # # # # # # # ### # #
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####### # # ####### # ##### ###### # # ## ##### ### #####
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bigquery script to create OMOP common data model version 5.3
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last revised: 6-Nov-2017
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Authors: Patrick Ryan, Christian Reich, Clair Blacketer
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*************************/
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/************************
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Standardized vocabulary
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************************/
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create table concept (
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concept_id integer not null ,
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concept_name varchar(255) not null ,
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domain_id varchar(20) not null ,
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vocabulary_id varchar(20) not null ,
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concept_class_id varchar(20) not null ,
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standard_concept varchar(1) null ,
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concept_code varchar(50) not null ,
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valid_start_date date not null ,
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valid_end_date date not null ,
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invalid_reason varchar(1) null
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)
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;
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create table vocabulary (
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vocabulary_id varchar(20) not null,
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vocabulary_name varchar(255) not null,
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vocabulary_reference varchar(255) not null,
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vocabulary_version varchar(255) not null,
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vocabulary_concept_id integer not null
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)
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;
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create table domain (
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domain_id varchar(20) not null,
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domain_name varchar(255) not null,
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domain_concept_id integer not null
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)
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;
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create table concept_class (
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concept_class_id varchar(20) not null,
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concept_class_name varchar(255) not null,
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concept_class_concept_id integer not null
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)
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;
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create table concept_relationship (
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concept_id_1 integer not null,
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concept_id_2 integer not null,
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relationship_id varchar(20) not null,
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valid_start_date date not null,
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valid_end_date date not null,
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invalid_reason varchar(1) null
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)
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;
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create table relationship (
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relationship_id varchar(20) not null,
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relationship_name varchar(255) not null,
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is_hierarchical varchar(1) not null,
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defines_ancestry varchar(1) not null,
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reverse_relationship_id varchar(20) not null,
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relationship_concept_id integer not null
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)
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;
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create table concept_synonym (
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concept_id integer not null,
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concept_synonym_name varchar(1000) not null,
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language_concept_id integer not null
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)
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;
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create table concept_ancestor (
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ancestor_concept_id integer not null,
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descendant_concept_id integer not null,
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min_levels_of_separation integer not null,
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max_levels_of_separation integer not null
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)
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;
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create table source_to_concept_map (
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source_code varchar(50) not null,
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source_concept_id integer not null,
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source_vocabulary_id varchar(20) not null,
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source_code_description varchar(255) null,
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target_concept_id integer not null,
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target_vocabulary_id varchar(20) not null,
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valid_start_date date not null,
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valid_end_date date not null,
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invalid_reason varchar(1) null
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)
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;
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create table drug_strength (
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drug_concept_id integer not null,
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ingredient_concept_id integer not null,
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amount_value float null,
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amount_unit_concept_id integer null,
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numerator_value float null,
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numerator_unit_concept_id integer null,
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denominator_value float null,
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denominator_unit_concept_id integer null,
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box_size integer null,
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valid_start_date date not null,
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valid_end_date date not null,
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invalid_reason varchar(1) null
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)
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;
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create table cohort_definition (
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cohort_definition_id integer not null,
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cohort_definition_name varchar(255) not null,
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cohort_definition_description varchar(max) null,
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definition_type_concept_id integer not null,
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cohort_definition_syntax varchar(max) null,
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subject_concept_id integer not null,
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cohort_initiation_date date null
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)
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;
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create table attribute_definition (
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attribute_definition_id integer not null,
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attribute_name varchar(255) not null,
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attribute_description varchar(max) null,
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attribute_type_concept_id integer not null,
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attribute_syntax varchar(max) null
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)
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;
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/**************************
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Standardized meta-data
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***************************/
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create table cdm_source
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(
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cdm_source_name varchar(255) not null ,
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cdm_source_abbreviation varchar(25) null ,
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cdm_holder varchar(255) null ,
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source_description varchar(max) null ,
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source_documentation_reference varchar(255) null ,
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cdm_etl_reference varchar(255) null ,
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source_release_date date null ,
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cdm_release_date date null ,
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cdm_version varchar(10) null ,
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vocabulary_version varchar(20) null
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)
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;
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create table metadata
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(
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metadata_concept_id integer not null ,
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metadata_type_concept_id integer not null ,
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name varchar(250) not null ,
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value_as_string nvarchar null ,
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value_as_concept_id integer null ,
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metadata_date date null ,
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metadata_datetime datetime2 null
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)
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;
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/************************
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Standardized clinical data
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************************/
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create table person
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(
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person_id integer not null ,
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gender_concept_id integer not null ,
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year_of_birth integer not null ,
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month_of_birth integer null,
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day_of_birth integer null,
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birth_datetime datetime2 null,
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race_concept_id integer not null,
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ethnicity_concept_id integer not null,
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location_id integer null,
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provider_id integer null,
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care_site_id integer null,
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person_source_value varchar(50) null,
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gender_source_value varchar(50) null,
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gender_source_concept_id integer null,
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race_source_value varchar(50) null,
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race_source_concept_id integer null,
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ethnicity_source_value varchar(50) null,
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ethnicity_source_concept_id integer null
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)
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;
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create table observation_period
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(
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observation_period_id integer not null ,
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person_id integer not null ,
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observation_period_start_date date not null ,
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observation_period_end_date date not null ,
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period_type_concept_id integer not null
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)
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;
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create table specimen
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(
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specimen_id integer not null ,
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person_id integer not null ,
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specimen_concept_id integer not null ,
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specimen_type_concept_id integer not null ,
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specimen_date date not null ,
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specimen_datetime datetime2 null ,
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quantity float null ,
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unit_concept_id integer null ,
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anatomic_site_concept_id integer null ,
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disease_status_concept_id integer null ,
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specimen_source_id varchar(50) null ,
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specimen_source_value varchar(50) null ,
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unit_source_value varchar(50) null ,
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anatomic_site_source_value varchar(50) null ,
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disease_status_source_value varchar(50) null
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)
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;
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create table death
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(
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person_id integer not null ,
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death_date date not null ,
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death_datetime datetime2 null ,
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death_type_concept_id integer not null ,
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cause_concept_id integer null ,
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cause_source_value varchar(50) null,
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cause_source_concept_id integer null
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)
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;
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create table visit_occurrence
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(
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visit_occurrence_id integer not null ,
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person_id integer not null ,
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visit_concept_id integer not null ,
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visit_start_date date not null ,
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visit_start_datetime datetime2 null ,
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visit_end_date date not null ,
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visit_end_datetime datetime2 null ,
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visit_type_concept_id integer not null ,
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provider_id integer null,
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care_site_id integer null,
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visit_source_value varchar(50) null,
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visit_source_concept_id integer null
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admitting_source_concept_id integer null ,
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admitting_source_value varchar(50) null ,
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discharge_to_concept_id integer(50) null ,
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discharge_to_source_value varchar(50) null ,
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preceding_visit_occurrence_id integer null
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)
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;
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create table visit_detail
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(
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visit_detail_id integer not null ,
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person_id integer not null ,
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visit_detail_concept_id integer not null ,
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visit_start_date date not null ,
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visit_start_datetime datetime2 null ,
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visit_end_date date not null ,
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visit_end_datetime datetime2 null ,
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visit_type_concept_id integer not null ,
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provider_id integer null ,
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care_site_id integer null ,
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admitting_source_concept_id integer null ,
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discharge_to_concept_id integer null ,
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preceding_visit_detail_id integer null ,
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visit_source_value varchar(50) null ,
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visit_source_concept_id integer null ,
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admitting_source_value varchar(50) null ,
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discharge_to_source_value varchar(50) null ,
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visit_detail_parent_id integer null ,
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visit_occurrence_id integer not null
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)
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;
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create table procedure_occurrence
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(
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procedure_occurrence_id integer not null ,
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person_id integer not null ,
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procedure_concept_id integer not null ,
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procedure_date date not null ,
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procedure_datetime datetime2 null ,
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procedure_type_concept_id integer not null ,
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modifier_concept_id integer null ,
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quantity integer null ,
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provider_id integer null ,
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visit_occurrence_id integer null ,
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visit_detail_id integer null ,
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procedure_source_value varchar(50) null ,
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procedure_source_concept_id integer null ,
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modifier_source_value varchar(50) null
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)
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;
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create table drug_exposure
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(
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drug_exposure_id integer not null ,
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person_id integer not null ,
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drug_concept_id integer not null ,
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drug_exposure_start_date date not null ,
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drug_exposure_start_datetime datetime2 null ,
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drug_exposure_end_date date not null ,
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drug_exposure_end_datetime datetime2 null ,
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verbatim_end_date date null ,
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drug_type_concept_id integer not null ,
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stop_reason varchar(20) null ,
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refills integer null ,
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quantity float null ,
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days_supply integer null ,
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sig varchar(max) null ,
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route_concept_id integer null ,
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lot_number varchar(50) null ,
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provider_id integer null ,
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visit_occurrence_id integer null ,
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visit_detail_id integer null ,
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drug_source_value varchar(50) null ,
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drug_source_concept_id integer null ,
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route_source_value varchar(50) null ,
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dose_unit_source_value varchar(50) null
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)
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;
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create table device_exposure
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(
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device_exposure_id integer not null ,
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person_id integer not null ,
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device_concept_id integer not null ,
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device_exposure_start_date date not null ,
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device_exposure_start_datetime datetime2 null ,
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device_exposure_end_date date null ,
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device_exposure_end_datetime datetime2 null ,
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device_type_concept_id integer not null ,
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unique_device_id varchar(50) null ,
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quantity integer null ,
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provider_id integer null ,
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visit_occurrence_id integer null ,
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visit_detail_id integer null ,
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device_source_value varchar(100) null ,
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device_source_concept_id integer null
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)
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;
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create table condition_occurrence
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(
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condition_occurrence_id integer not null ,
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person_id integer not null ,
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condition_concept_id integer not null ,
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condition_start_date date not null ,
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condition_start_datetime datetime2 null ,
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condition_end_date date null ,
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condition_end_datetime datetime2 null ,
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condition_type_concept_id integer not null ,
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stop_reason varchar(20) null ,
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provider_id integer null ,
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visit_occurrence_id integer null ,
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visit_detail_id integer null ,
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condition_source_value varchar(50) null ,
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condition_source_concept_id integer null ,
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condition_status_source_value varchar(50) null ,
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condition_status_concept_id integer null
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)
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;
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create table measurement
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(
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measurement_id integer not null ,
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person_id integer not null ,
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measurement_concept_id integer not null ,
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measurement_date date not null ,
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measurement_time varchar(10) null ,
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measurement_datetime datetime2 null ,
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measurement_type_concept_id integer not null ,
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operator_concept_id integer null ,
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value_as_number float null ,
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value_as_concept_id integer null ,
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unit_concept_id integer null ,
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range_low float null ,
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range_high float null ,
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provider_id integer null ,
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visit_occurrence_id integer null ,
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visit_detail_id integer null ,
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measurement_source_value varchar(50) null ,
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measurement_source_concept_id integer null ,
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unit_source_value varchar(50) null ,
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value_source_value varchar(50) null
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)
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;
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create table note
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(
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note_id integer not null ,
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person_id integer not null ,
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note_date date not null ,
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note_datetime datetime2 null ,
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note_type_concept_id integer not null ,
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note_class_concept_id integer not null ,
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note_title varchar(250) null ,
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note_text varchar(max) null ,
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encoding_concept_id integer not null ,
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language_concept_id integer not null ,
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provider_id integer null ,
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visit_occurrence_id integer null ,
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visit_detail_id integer null ,
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note_source_value varchar(50) null
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)
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;
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create table note_nlp
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(
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note_nlp_id bigint not null ,
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note_id integer not null ,
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section_concept_id integer null ,
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snippet varchar(250) null ,
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offset varchar(250) null ,
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lexical_variant varchar(250) not null ,
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note_nlp_concept_id integer null ,
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note_nlp_source_concept_id integer null ,
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nlp_system varchar(250) null ,
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nlp_date date not null ,
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nlp_datetime datetime2 null ,
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term_exists varchar(1) null ,
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term_temporal varchar(50) null ,
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term_modifiers varchar(2000) null
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)
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;
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create table observation
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(
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observation_id integer not null ,
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person_id integer not null ,
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observation_concept_id integer not null ,
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observation_date date not null ,
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observation_datetime datetime2 null ,
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observation_type_concept_id integer not null ,
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value_as_number float null ,
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value_as_string varchar(60) null ,
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value_as_concept_id integer null ,
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qualifier_concept_id integer null ,
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unit_concept_id integer null ,
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provider_id integer null ,
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visit_occurrence_id integer null ,
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visit_detail_id integer null ,
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observation_source_value varchar(50) null ,
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observation_source_concept_id integer null ,
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unit_source_value varchar(50) null ,
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qualifier_source_value varchar(50) null
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)
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;
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create table fact_relationship
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(
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domain_concept_id_1 integer not null ,
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fact_id_1 integer not null ,
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domain_concept_id_2 integer not null ,
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fact_id_2 integer not null ,
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relationship_concept_id integer not null
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)
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;
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/************************
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Standardized health system data
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************************/
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create table location
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(
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location_id integer not null ,
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address_1 varchar(50) null ,
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address_2 varchar(50) null ,
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city varchar(50) null ,
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state varchar(2) null ,
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zip varchar(9) null ,
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county varchar(20) null ,
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location_source_value varchar(50) null
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)
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;
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create table care_site
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(
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care_site_id integer not null ,
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care_site_name varchar(255) null ,
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place_of_service_concept_id integer null ,
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location_id integer null ,
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care_site_source_value varchar(50) null ,
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place_of_service_source_value varchar(50) null
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)
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;
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|
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create table provider
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|
(
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provider_id integer not null ,
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provider_name varchar(255) null ,
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npi varchar(20) null ,
|
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dea varchar(20) null ,
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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
|
|
)
|
|
;
|
|
|
|
|
|
|
|
|
|
/************************
|
|
|
|
Standardized health economics
|
|
|
|
************************/
|
|
|
|
|
|
create table 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 integer null ,
|
|
stop_reason_source_concept_id integer null
|
|
)
|
|
;
|
|
|
|
|
|
create table 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 float null ,
|
|
total_cost float null ,
|
|
total_paid float null ,
|
|
paid_by_payer float null ,
|
|
paid_by_patient float null ,
|
|
paid_patient_copay float null ,
|
|
paid_patient_coinsurance float null ,
|
|
paid_patient_deductible float null ,
|
|
paid_by_primary float null ,
|
|
paid_ingredient_cost float null ,
|
|
paid_dispensing_fee float null ,
|
|
payer_plan_period_id integer null ,
|
|
amount_allowed float null ,
|
|
revenue_code_concept_id integer null ,
|
|
reveue_code_source_value varchar(50) null,
|
|
drg_concept_id integer null,
|
|
drg_source_value varchar(3) null
|
|
)
|
|
;
|
|
|
|
|
|
|
|
|
|
|
|
/************************
|
|
|
|
Standardized derived elements
|
|
|
|
************************/
|
|
|
|
create table cohort
|
|
(
|
|
cohort_definition_id integer not null ,
|
|
subject_id integer not null ,
|
|
cohort_start_date date not null ,
|
|
cohort_end_date date not null
|
|
)
|
|
;
|
|
|
|
|
|
create table cohort_attribute
|
|
(
|
|
cohort_definition_id integer not null ,
|
|
cohort_start_date date not null ,
|
|
cohort_end_date date not null ,
|
|
subject_id integer not null ,
|
|
attribute_definition_id integer not null ,
|
|
value_as_number float null ,
|
|
value_as_concept_id integer null
|
|
)
|
|
;
|
|
|
|
|
|
|
|
|
|
create table drug_era
|
|
(
|
|
drug_era_id integer not null ,
|
|
person_id integer 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
|
|
)
|
|
;
|
|
|
|
|
|
create table 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 float not null ,
|
|
dose_era_start_date date not null ,
|
|
dose_era_end_date date not null
|
|
)
|
|
;
|
|
|
|
|
|
|
|
|
|
create table condition_era
|
|
(
|
|
condition_era_id integer not null ,
|
|
person_id integer 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
|
|
)
|
|
;
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|