743 lines
23 KiB
Plaintext
743 lines
23 KiB
Plaintext
/*
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Copyright 2018-08 Observational Health Data Sciences and Informatics
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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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http://www.apache.org/licenses/LICENSE-2.0
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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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OMOP CDM v6.0 DDL
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bigquery script to create OMOP common data model version 6.0
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last revised: 27-Aug-2018
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Authors: Patrick Ryan, Christian Reich, Clair Blacketer
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*/
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#standardsql
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create table concept (
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concept_id INT64 not null ,
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concept_name STRING not null ,
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domain_id STRING not null ,
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vocabulary_id STRING not null ,
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concept_class_id STRING not null ,
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standard_concept STRING null ,
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concept_code STRING 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 STRING null
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)
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;
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create table vocabulary (
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vocabulary_id STRING not null,
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vocabulary_name STRING not null,
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vocabulary_reference STRING not null,
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vocabulary_version STRING not null,
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vocabulary_concept_id INT64 not null
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)
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;
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create table domain (
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domain_id STRING not null,
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domain_name STRING not null,
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domain_concept_id INT64 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 STRING not null,
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concept_class_name STRING not null,
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concept_class_concept_id INT64 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 INT64 not null,
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concept_id_2 INT64 not null,
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relationship_id STRING 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 STRING null
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)
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;
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create table relationship (
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relationship_id STRING not null,
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relationship_name STRING not null,
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is_hierarchical STRING not null,
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defines_ancestry STRING not null,
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reverse_relationship_id STRING not null,
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relationship_concept_id INT64 not null
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)
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;
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create table concept_synonym (
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concept_id INT64 not null,
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concept_synonym_name STRING not null,
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language_concept_id INT64 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 INT64 not null,
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descendant_concept_id INT64 not null,
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min_levels_of_separation INT64 not null,
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max_levels_of_separation INT64 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 STRING not null,
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source_concept_id INT64 not null,
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source_vocabulary_id STRING not null,
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source_code_description STRING null,
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target_concept_id INT64 not null,
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target_vocabulary_id STRING 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 STRING null
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)
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;
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create table drug_strength (
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drug_concept_id INT64 not null,
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ingredient_concept_id INT64 not null,
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amount_value FLOAT64 null,
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amount_unit_concept_id INT64 null,
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numerator_value FLOAT64 null,
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numerator_unit_concept_id INT64 null,
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denominator_value FLOAT64 null,
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denominator_unit_concept_id INT64 null,
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box_size INT64 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 STRING null
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)
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;
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create table cohort_definition (
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cohort_definition_id INT64 not null,
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cohort_definition_name STRING not null,
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cohort_definition_description STRING null,
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definition_type_concept_id INT64 not null,
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cohort_definition_syntax STRING null,
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subject_concept_id INT64 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 INT64 not null,
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attribute_name STRING not null,
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attribute_description STRING null,
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attribute_type_concept_id INT64 not null,
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attribute_syntax STRING null
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)
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;
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create table cdm_source
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(
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cdm_source_name STRING not null ,
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cdm_source_abbreviation STRING null ,
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cdm_holder STRING null ,
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source_description STRING null ,
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source_documentation_reference STRING null ,
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cdm_etl_reference STRING 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 STRING null ,
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vocabulary_version STRING 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 INT64 not null ,
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metadata_type_concept_id INT64 not null ,
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name STRING not null ,
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value_as_string STRING null ,
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value_as_concept_id INT64 null ,
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metadata_date date null ,
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metadata_datetime DATETIME null
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)
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;
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insert into metadata (name, value_as_string) --Added cdm version record
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values ('CDM Version', '6.0')
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;
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--HINT DISTRIBUTE_ON_KEY(person_id)
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create table person
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(
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person_id INT64 not null , --INT64s added
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gender_concept_id INT64 not null ,
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year_of_birth INT64 not null ,
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month_of_birth INT64 null,
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day_of_birth INT64 null,
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birth_datetime DATETIME null,
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race_concept_id INT64 not null,
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ethnicity_concept_id INT64 not null,
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location_id INT64 null,
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provider_id INT64 null,
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care_site_id INT64 null,
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person_source_value STRING null,
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gender_source_value STRING null,
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gender_source_concept_id INT64 null,
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race_source_value STRING null,
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race_source_concept_id INT64 null,
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ethnicity_source_value STRING null,
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ethnicity_source_concept_id INT64 null
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)
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;
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--HINT DISTRIBUTE_ON_KEY(person_id)
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create table observation_period
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(
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observation_period_id INT64 not null ,
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person_id INT64 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 INT64 not null
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)
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;
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--HINT DISTRIBUTE_ON_KEY(person_id)
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create table specimen
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(
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specimen_id INT64 not null ,
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person_id INT64 not null ,
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specimen_concept_id INT64 not null ,
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specimen_type_concept_id INT64 not null ,
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specimen_date date null ,
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specimen_datetime DATETIME not null ,
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quantity FLOAT64 null ,
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unit_concept_id INT64 null ,
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anatomic_site_concept_id INT64 null ,
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disease_status_concept_id INT64 null ,
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specimen_source_id STRING null ,
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specimen_source_value STRING null ,
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unit_source_value STRING null ,
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anatomic_site_source_value STRING null ,
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disease_status_source_value STRING null
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)
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;
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--HINT DISTRIBUTE_ON_KEY(person_id)
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create table death
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(
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person_id INT64 not null ,
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death_date date null ,
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death_datetime DATETIME not null ,
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death_type_concept_id INT64 not null ,
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cause_concept_id INT64 null ,
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cause_source_value STRING null,
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cause_source_concept_id INT64 null
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)
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;
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--HINT DISTRIBUTE_ON_KEY(person_id)
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create table visit_occurrence
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(
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visit_occurrence_id INT64 not null ,
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person_id INT64 not null ,
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visit_concept_id INT64 not null ,
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visit_start_date date null ,
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visit_start_datetime DATETIME not null ,
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visit_end_date date null ,
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visit_end_datetime DATETIME not null ,
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visit_type_concept_id INT64 not null ,
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provider_id INT64 null,
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care_site_id INT64 null,
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visit_source_value STRING null,
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visit_source_concept_id INT64 null ,
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admitted_from_concept_id INT64 NULL , /*Changed from admitting_source_* */
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admitted_from_source_value STRING NULL ,
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discharge_to_source_value STRING null ,
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discharge_to_concept_id INT64 null ,
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preceding_visit_occurrence_id INT64 null
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)
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;
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--HINT DISTRIBUTE_ON_KEY(person_id)
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create table visit_detail
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(
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visit_detail_id INT64 not null ,
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person_id INT64 not null ,
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visit_detail_concept_id INT64 not null ,
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visit_detail_start_date date null ,
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visit_detail_start_datetime DATETIME not null ,
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visit_detail_end_date date null ,
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visit_detail_end_datetime DATETIME not null ,
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visit_detail_type_concept_id INT64 not null ,
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provider_id INT64 null ,
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care_site_id INT64 null ,
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discharge_to_concept_id INT64 null ,
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admitted_from_concept_id INT64 NULL , /*Changed from admitting_source_* */
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admitted_from_source_value STRING NULL ,
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visit_detail_source_value STRING null ,
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visit_detail_source_concept_id INT64 null ,
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discharge_to_source_value STRING null ,
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preceding_visit_detail_id INT64 null ,
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visit_detail_parent_id INT64 null ,
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visit_occurrence_id INT64 not null
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)
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;
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--HINT DISTRIBUTE_ON_KEY(person_id)
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create table procedure_occurrence
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(
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procedure_occurrence_id INT64 not null ,
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person_id INT64 not null ,
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procedure_concept_id INT64 not null ,
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procedure_date date null ,
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procedure_datetime DATETIME not null ,
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procedure_type_concept_id INT64 not null ,
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modifier_concept_id INT64 null ,
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quantity INT64 null ,
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provider_id INT64 null ,
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visit_occurrence_id INT64 null ,
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visit_detail_id INT64 null ,
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procedure_source_value STRING null ,
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procedure_source_concept_id INT64 null ,
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modifier_source_value STRING null ,
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)
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;
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--HINT DISTRIBUTE_ON_KEY(person_id)
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create table drug_exposure
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(
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drug_exposure_id INT64 not null ,
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person_id INT64 not null ,
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drug_concept_id INT64 not null ,
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drug_exposure_start_date date null ,
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drug_exposure_start_datetime DATETIME not null ,
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drug_exposure_end_date date null ,
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drug_exposure_end_datetime DATETIME not null ,
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verbatim_end_date date null ,
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drug_type_concept_id INT64 not null ,
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stop_reason STRING null ,
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refills INT64 null ,
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quantity FLOAT64 null ,
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days_supply INT64 null ,
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sig STRING null ,
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route_concept_id INT64 null ,
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lot_number STRING null ,
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provider_id INT64 null ,
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visit_occurrence_id INT64 null ,
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visit_detail_id INT64 null ,
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drug_source_value STRING null ,
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drug_source_concept_id INT64 null ,
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route_source_value STRING null ,
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dose_unit_source_value STRING null
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)
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;
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--HINT DISTRIBUTE_ON_KEY(person_id)
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create table device_exposure
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(
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device_exposure_id INT64 not null ,
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person_id INT64 not null ,
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device_concept_id INT64 not null ,
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device_exposure_start_date date null ,
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device_exposure_start_datetime DATETIME not null ,
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device_exposure_end_date date null ,
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device_exposure_end_datetime DATETIME null ,
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device_type_concept_id INT64 not null ,
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unique_device_id STRING null ,
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quantity INT64 null ,
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provider_id INT64 null ,
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visit_occurrence_id INT64 null ,
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visit_detail_id INT64 null ,
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device_source_value STRING null ,
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device_source_concept_id INT64 null
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)
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;
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--HINT DISTRIBUTE_ON_KEY(person_id)
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create table condition_occurrence
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(
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condition_occurrence_id INT64 not null ,
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person_id INT64 not null ,
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condition_concept_id INT64 not null ,
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condition_start_date date null ,
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condition_start_datetime DATETIME not null ,
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condition_end_date date null ,
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condition_end_datetime DATETIME null ,
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condition_type_concept_id INT64 not null ,
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condition_status_concept_id INT64 null ,
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stop_reason STRING null ,
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provider_id INT64 null ,
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visit_occurrence_id INT64 null ,
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visit_detail_id INT64 null ,
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condition_source_value STRING null ,
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condition_source_concept_id INT64 null ,
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condition_status_source_value STRING null
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)
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;
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--HINT DISTRIBUTE_ON_KEY(person_id)
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create table measurement
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(
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measurement_id INT64 not null ,
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person_id INT64 not null ,
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measurement_concept_id INT64 not null ,
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measurement_date date null ,
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measurement_datetime DATETIME not null ,
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measurement_time STRING null,
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measurement_type_concept_id INT64 not null ,
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operator_concept_id INT64 null ,
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value_as_number FLOAT64 null ,
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value_as_concept_id INT64 null ,
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unit_concept_id INT64 null ,
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range_low FLOAT64 null ,
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range_high FLOAT64 null ,
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provider_id INT64 null ,
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visit_occurrence_id INT64 null ,
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visit_detail_id INT64 null ,
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measurement_source_value STRING null ,
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measurement_source_concept_id INT64 null ,
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unit_source_value STRING null ,
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value_source_value STRING null
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)
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;
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--HINT DISTRIBUTE_ON_KEY(person_id)
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create table note
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(
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note_id INT64 not null ,
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person_id INT64 not null ,
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note_event_id INT64 null , --This and the field below added
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note_domain_id STRING null , --This field may be removed in favor of the one below
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--note_event_table_concept_id INT64 NULL , --This may be added based on 9/4 meeting
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note_date date null ,
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note_datetime DATETIME not null ,
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note_type_concept_id INT64 not null ,
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note_class_concept_id INT64 not null ,
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note_title STRING null ,
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note_text STRING null ,
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encoding_concept_id INT64 not null ,
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language_concept_id INT64 not null ,
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provider_id INT64 null ,
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visit_occurrence_id INT64 null ,
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visit_detail_id INT64 null ,
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note_source_value STRING 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 INT64 not null ,
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note_id INT64 not null ,
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section_concept_id INT64 null ,
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snippet STRING null ,
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"offset" STRING null ,
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lexical_variant STRING not null ,
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note_nlp_concept_id INT64 null ,
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nlp_system STRING null ,
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nlp_date date not null ,
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nlp_datetime DATETIME null ,
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term_exists STRING null ,
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term_temporal STRING null ,
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term_modifiers STRING null ,
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note_nlp_source_concept_id INT64 null
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)
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;
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--HINT DISTRIBUTE_ON_KEY(person_id)
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create table observation
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(
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observation_id INT64 not null ,
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person_id INT64 not null ,
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observation_concept_id INT64 not null ,
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observation_date date null ,
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observation_datetime DATETIME not null ,
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observation_type_concept_id INT64 not null ,
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value_as_number FLOAT64 null ,
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value_as_string STRING null ,
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value_as_concept_id INT64 null ,
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qualifier_concept_id INT64 null ,
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unit_concept_id INT64 null ,
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provider_id INT64 null ,
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visit_occurrence_id INT64 null ,
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visit_detail_id INT64 null ,
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observation_source_value STRING null ,
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observation_source_concept_id INT64 null ,
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unit_source_value STRING null ,
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qualifier_source_value STRING null ,
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observation_event_id INT64 null , /* This will link back to the event table (SURVEY) on SURVEY_OCCURRENCE_ID, changed name to comply with COST and NOTE*/
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observation_event_domain_id STRING null ,
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--obs_event_table_concept_id INT64 NULL , /* Changed name to comply with COST and NOTE. This should be 'Survey'. Had to use 'obs' for oracle restriction, may be added on 9/4*/
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value_as_datetime DATETIME null
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)
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;
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create table survey_conduct /*Should this be SURVEY_OCCURRENCE instead to comply with the other tables?*/
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(
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survey_conduct_id INT64 not null ,
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person_id INT64 not null ,
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survey_concept_id INT64 not null ,
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survey_start_date date null ,
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survey_start_datetime DATETIME null ,
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survey_end_date date null ,
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survey_end_datetime DATETIME not null ,
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provider_id INT64 null ,
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assisted_concept_id INT64 null ,
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respondent_type_concept_id INT64 null ,
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timing_concept_id INT64 null ,
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collection_method_concept_id INT64 null ,
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assisted_source_value STRING null ,
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respondent_type_source_value STRING null ,
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timing_source_value STRING null ,
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collection_method_source_value STRING null ,
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survey_source_value STRING null ,
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survey_source_concept_id INT64 null ,
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survey_source_identifier STRING null ,
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validated_survey_concept_id INT64 null ,
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validated_survey_source_value STRING null ,
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|
survey_version_number STRING null ,
|
|
visit_occurrence_id INT64 null ,
|
|
visit_detail_id INT64 null ,
|
|
response_to_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 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 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 null ,
|
|
care_site_id INT64 null ,
|
|
year_of_birth INT64 null ,
|
|
gender_concept_id INT64 null ,
|
|
provider_source_value STRING null ,
|
|
specialty_source_value STRING null ,
|
|
specialty_source_concept_id INT64 null ,
|
|
gender_source_value STRING null ,
|
|
gender_source_concept_id INT64 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 null ,
|
|
plan_concept_id INT64 null ,
|
|
contract_concept_id INT64 null ,
|
|
sponsor_concept_id INT64 null ,
|
|
stop_reason_concept_id INT64 null ,
|
|
payer_source_value STRING null ,
|
|
payer_source_concept_id INT64 null ,
|
|
plan_source_value STRING null ,
|
|
plan_source_concept_id INT64 null ,
|
|
contract_source_value STRING null ,
|
|
contract_source_concept_id INT64 null ,
|
|
sponsor_source_value STRING null ,
|
|
sponsor_source_concept_id INT64 null ,
|
|
family_source_value STRING null ,
|
|
stop_reason_source_value STRING null ,
|
|
stop_reason_source_concept_id INT64 null
|
|
)
|
|
;
|
|
|
|
|
|
create table cost
|
|
(
|
|
cost_id INT64 not null ,
|
|
person_id INT64 not null,
|
|
cost_event_id INT64 not null ,
|
|
cost_domain_id STRING not null ,
|
|
--cost_event_table_concept_id INT64 NOT NULL , /*This is still in discussion and most likely will replace cost_domain_id at 9/4 meeting*/
|
|
cost_concept_id INT64 not null ,
|
|
cost_type_concept_id INT64 not null ,
|
|
currency_concept_id INT64 null ,
|
|
cost FLOAT64 null ,
|
|
incurred_date date not null ,
|
|
billed_date date null ,
|
|
paid_date date null ,
|
|
revenue_code_concept_id INT64 null ,
|
|
drg_concept_id INT64 null ,
|
|
cost_source_value STRING null ,
|
|
cost_source_concept_id INT64 null ,
|
|
revenue_code_source_value STRING null ,
|
|
drg_source_value STRING null ,
|
|
payer_plan_period_id INT64 null
|
|
)
|
|
;
|
|
|
|
|
|
|
|
|
|
--HINT DISTRIBUTE_ON_KEY(subject_id)
|
|
create table cohort
|
|
(
|
|
cohort_definition_id INT64 not null ,
|
|
subject_id INT64 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 INT64 not null ,
|
|
subject_id INT64 not null ,
|
|
cohort_start_date date not null ,
|
|
cohort_end_date date not null ,
|
|
attribute_definition_id INT64 not null ,
|
|
value_as_number FLOAT64 null ,
|
|
value_as_concept_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_date date not null ,
|
|
drug_era_end_date date 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_date date not null ,
|
|
dose_era_end_date date 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_date date not null ,
|
|
condition_era_end_date date not null ,
|
|
condition_occurrence_count INT64 null
|
|
)
|
|
;
|