1318 lines
17 KiB
Plaintext
1318 lines
17 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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impala 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,
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concept_name VARCHAR(255),
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domain_id VARCHAR(20),
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vocabulary_id VARCHAR(20),
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concept_class_id VARCHAR(20),
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standard_concept VARCHAR(1),
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concept_code VARCHAR(50),
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valid_start_date TIMESTAMP,
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valid_end_date TIMESTAMP,
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invalid_reason VARCHAR(1)
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)
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;
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CREATE TABLE vocabulary (
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vocabulary_id VARCHAR(20),
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vocabulary_name VARCHAR(255),
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vocabulary_reference VARCHAR(255),
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vocabulary_version VARCHAR(255),
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vocabulary_concept_id INTEGER
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)
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;
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CREATE TABLE domain (
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domain_id VARCHAR(20),
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domain_name VARCHAR(255),
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domain_concept_id INTEGER
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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),
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concept_class_name VARCHAR(255),
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concept_class_concept_id INTEGER
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)
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;
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CREATE TABLE concept_relationship (
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concept_id_1 INTEGER,
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concept_id_2 INTEGER,
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relationship_id VARCHAR(20),
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valid_start_date TIMESTAMP,
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valid_end_date TIMESTAMP,
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invalid_reason VARCHAR(1)
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)
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;
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CREATE TABLE relationship (
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relationship_id VARCHAR(20),
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relationship_name VARCHAR(255),
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is_hierarchical VARCHAR(1),
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defines_ancestry VARCHAR(1),
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reverse_relationship_id VARCHAR(20),
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relationship_concept_id INTEGER
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)
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;
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CREATE TABLE concept_synonym (
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concept_id INTEGER,
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concept_synonym_name STRING,
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language_concept_id INTEGER
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)
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;
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CREATE TABLE concept_ancestor (
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ancestor_concept_id INTEGER,
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descendant_concept_id INTEGER,
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min_levels_of_separation INTEGER,
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max_levels_of_separation INTEGER
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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),
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source_concept_id INTEGER,
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source_vocabulary_id VARCHAR(20),
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source_code_description VARCHAR(255),
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target_concept_id INTEGER,
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target_vocabulary_id VARCHAR(20),
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valid_start_date TIMESTAMP,
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valid_end_date TIMESTAMP,
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invalid_reason VARCHAR(1)
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)
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;
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CREATE TABLE drug_strength (
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drug_concept_id INTEGER,
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ingredient_concept_id INTEGER,
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amount_value FLOAT,
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amount_unit_concept_id INTEGER,
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numerator_value FLOAT,
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numerator_unit_concept_id INTEGER,
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denominator_value FLOAT,
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denominator_unit_concept_id INTEGER,
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box_size INTEGER,
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valid_start_date TIMESTAMP,
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valid_end_date TIMESTAMP,
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invalid_reason VARCHAR(1)
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)
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;
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CREATE TABLE cohort_definition (
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cohort_definition_id INTEGER,
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cohort_definition_name VARCHAR(255),
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cohort_definition_description STRING,
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definition_type_concept_id INTEGER,
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cohort_definition_syntax STRING,
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subject_concept_id INTEGER,
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cohort_initiation_date TIMESTAMP
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)
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;
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CREATE TABLE attribute_definition (
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attribute_definition_id INTEGER,
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attribute_name VARCHAR(255),
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attribute_description STRING,
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attribute_type_concept_id INTEGER,
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attribute_syntax STRING
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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),
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cdm_source_abbreviation VARCHAR(25),
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cdm_holder VARCHAR(255),
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source_description STRING,
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source_documentation_reference VARCHAR(255),
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cdm_etl_reference VARCHAR(255),
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source_release_date TIMESTAMP,
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cdm_release_date TIMESTAMP,
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cdm_version VARCHAR(10),
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vocabulary_version VARCHAR(20)
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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,
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metadata_type_concept_id INTEGER,
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name VARCHAR(250),
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value_as_string VARCHAR(50),
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value_as_concept_id INTEGER,
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metadata_date TIMESTAMP,
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metadata_datetime TIMESTAMP
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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,
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gender_concept_id INTEGER,
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year_of_birth INTEGER,
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month_of_birth INTEGER,
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day_of_birth INTEGER,
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birth_datetime TIMESTAMP,
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race_concept_id INTEGER,
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ethnicity_concept_id INTEGER,
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location_id INTEGER,
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provider_id INTEGER,
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care_site_id INTEGER,
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person_source_value VARCHAR(50),
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gender_source_value VARCHAR(50),
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gender_source_concept_id INTEGER,
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race_source_value VARCHAR(50),
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race_source_concept_id INTEGER,
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ethnicity_source_value VARCHAR(50),
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ethnicity_source_concept_id INTEGER
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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,
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person_id INTEGER,
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observation_period_start_date TIMESTAMP,
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observation_period_end_date TIMESTAMP,
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period_type_concept_id INTEGER
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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,
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person_id INTEGER,
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specimen_concept_id INTEGER,
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specimen_type_concept_id INTEGER,
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specimen_date TIMESTAMP,
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specimen_datetime TIMESTAMP,
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quantity FLOAT,
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unit_concept_id INTEGER,
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anatomic_site_concept_id INTEGER,
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disease_status_concept_id INTEGER,
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specimen_source_id VARCHAR(50),
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specimen_source_value VARCHAR(50),
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unit_source_value VARCHAR(50),
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anatomic_site_source_value VARCHAR(50),
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disease_status_source_value VARCHAR(50)
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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,
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death_date TIMESTAMP,
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death_datetime TIMESTAMP,
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death_type_concept_id INTEGER,
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cause_concept_id INTEGER,
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cause_source_value VARCHAR(50),
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cause_source_concept_id INTEGER
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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,
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person_id INTEGER,
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visit_concept_id INTEGER,
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visit_start_date TIMESTAMP,
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visit_start_datetime TIMESTAMP,
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visit_end_date TIMESTAMP,
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visit_end_datetime TIMESTAMP,
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visit_type_concept_id INTEGER,
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provider_id INTEGER,
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care_site_id INTEGER,
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visit_source_value VARCHAR(50),
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visit_source_concept_id INTEGER
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admitting_source_concept_id INTEGER,
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admitting_source_value VARCHAR(50),
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discharge_to_concept_id INTEGER,
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discharge_to_source_value VARCHAR(50),
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preceding_visit_occurrence_id INTEGER
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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,
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person_id INTEGER,
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visit_detail_concept_id INTEGER,
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visit_start_date TIMESTAMP,
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visit_start_datetime TIMESTAMP,
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visit_end_date TIMESTAMP,
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visit_end_datetime TIMESTAMP,
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visit_type_concept_id INTEGER,
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provider_id INTEGER,
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care_site_id INTEGER,
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admitting_source_concept_id INTEGER,
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discharge_to_concept_id INTEGER,
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preceding_visit_detail_id INTEGER,
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visit_source_value VARCHAR(50),
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visit_source_concept_id INTEGER,
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admitting_source_value VARCHAR(50),
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discharge_to_source_value VARCHAR(50),
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visit_detail_parent_id INTEGER,
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visit_occurrence_id INTEGER
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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,
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person_id INTEGER,
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procedure_concept_id INTEGER,
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procedure_date TIMESTAMP,
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procedure_datetime TIMESTAMP,
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procedure_type_concept_id INTEGER,
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modifier_concept_id INTEGER,
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quantity INTEGER,
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provider_id INTEGER,
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visit_occurrence_id INTEGER,
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visit_detail_id INTEGER,
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procedure_source_value VARCHAR(50),
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procedure_source_concept_id INTEGER,
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modifier_source_value VARCHAR(50)
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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,
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person_id INTEGER,
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drug_concept_id INTEGER,
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drug_exposure_start_date TIMESTAMP,
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drug_exposure_start_datetime TIMESTAMP,
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drug_exposure_end_date TIMESTAMP,
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drug_exposure_end_datetime TIMESTAMP,
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verbatim_end_date TIMESTAMP,
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drug_type_concept_id INTEGER,
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stop_reason VARCHAR(20),
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refills INTEGER,
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quantity FLOAT,
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days_supply INTEGER,
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sig STRING,
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route_concept_id INTEGER,
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lot_number VARCHAR(50),
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provider_id INTEGER,
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visit_occurrence_id INTEGER,
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visit_detail_id INTEGER,
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drug_source_value VARCHAR(50),
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drug_source_concept_id INTEGER,
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route_source_value VARCHAR(50),
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dose_unit_source_value VARCHAR(50)
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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,
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person_id INTEGER,
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device_concept_id INTEGER,
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device_exposure_start_date TIMESTAMP,
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device_exposure_start_datetime TIMESTAMP,
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device_exposure_end_date TIMESTAMP,
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device_exposure_end_datetime TIMESTAMP,
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device_type_concept_id INTEGER,
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unique_device_id VARCHAR(50),
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quantity INTEGER,
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provider_id INTEGER,
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visit_occurrence_id INTEGER,
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visit_detail_id INTEGER,
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device_source_value VARCHAR(100),
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device_source_concept_id INTEGER
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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,
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person_id INTEGER,
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condition_concept_id INTEGER,
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condition_start_date TIMESTAMP,
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condition_start_datetime TIMESTAMP,
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condition_end_date TIMESTAMP,
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condition_end_datetime TIMESTAMP,
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condition_type_concept_id INTEGER,
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stop_reason VARCHAR(20),
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provider_id INTEGER,
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visit_occurrence_id INTEGER,
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visit_detail_id INTEGER,
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condition_source_value VARCHAR(50),
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condition_source_concept_id INTEGER,
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condition_status_source_value VARCHAR(50),
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condition_status_concept_id INTEGER
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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,
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person_id INTEGER,
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measurement_concept_id INTEGER,
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measurement_date TIMESTAMP,
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measurement_datetime TIMESTAMP,
|
|
|
|
measurement_time VARCHAR(10),
|
|
|
|
measurement_type_concept_id INTEGER,
|
|
|
|
operator_concept_id INTEGER,
|
|
|
|
value_as_number FLOAT,
|
|
|
|
value_as_concept_id INTEGER,
|
|
|
|
unit_concept_id INTEGER,
|
|
|
|
range_low FLOAT,
|
|
|
|
range_high FLOAT,
|
|
|
|
provider_id INTEGER,
|
|
visit_occurrence_id INTEGER,
|
|
|
|
visit_detail_id INTEGER,
|
|
|
|
measurement_source_value VARCHAR(50),
|
|
|
|
measurement_source_concept_id INTEGER,
|
|
|
|
unit_source_value VARCHAR(50),
|
|
|
|
value_source_value VARCHAR(50)
|
|
|
|
)
|
|
|
|
;
|
|
|
|
|
|
|
|
|
|
CREATE TABLE note
|
|
(
|
|
|
|
note_id INTEGER,
|
|
|
|
person_id INTEGER,
|
|
|
|
note_date TIMESTAMP,
|
|
|
|
note_datetime TIMESTAMP,
|
|
|
|
note_type_concept_id INTEGER,
|
|
|
|
note_class_concept_id INTEGER,
|
|
|
|
note_title VARCHAR(250),
|
|
|
|
note_text STRING,
|
|
|
|
encoding_concept_id INTEGER,
|
|
|
|
language_concept_id INTEGER,
|
|
|
|
provider_id INTEGER,
|
|
|
|
visit_occurrence_id INTEGER,
|
|
|
|
visit_detail_id INTEGER,
|
|
|
|
note_source_value VARCHAR(50)
|
|
|
|
)
|
|
|
|
;
|
|
|
|
|
|
|
|
|
|
CREATE TABLE note_nlp
|
|
(
|
|
|
|
note_nlp_id INTEGER,
|
|
|
|
note_id INTEGER,
|
|
|
|
section_concept_id INTEGER,
|
|
|
|
snippet VARCHAR(250),
|
|
|
|
`offset` VARCHAR(250),
|
|
|
|
lexical_variant VARCHAR(250),
|
|
|
|
note_nlp_concept_id INTEGER,
|
|
|
|
note_nlp_source_concept_id INTEGER,
|
|
|
|
nlp_system VARCHAR(250),
|
|
|
|
nlp_date TIMESTAMP,
|
|
|
|
nlp_datetime TIMESTAMP,
|
|
|
|
term_exists VARCHAR(1),
|
|
|
|
term_temporal VARCHAR(50),
|
|
|
|
term_modifiers VARCHAR(2000)
|
|
|
|
)
|
|
|
|
;
|
|
|
|
|
|
|
|
|
|
CREATE TABLE observation
|
|
(
|
|
|
|
observation_id INTEGER,
|
|
|
|
person_id INTEGER,
|
|
|
|
observation_concept_id INTEGER,
|
|
|
|
observation_date TIMESTAMP,
|
|
|
|
observation_datetime TIMESTAMP,
|
|
|
|
observation_type_concept_id INTEGER,
|
|
|
|
value_as_number FLOAT,
|
|
|
|
value_as_string VARCHAR(60),
|
|
|
|
value_as_concept_id INTEGER,
|
|
|
|
qualifier_concept_id INTEGER,
|
|
|
|
unit_concept_id INTEGER,
|
|
|
|
provider_id INTEGER,
|
|
|
|
visit_occurrence_id INTEGER,
|
|
|
|
visit_detail_id INTEGER,
|
|
|
|
observation_source_value VARCHAR(50),
|
|
|
|
observation_source_concept_id INTEGER,
|
|
|
|
unit_source_value VARCHAR(50),
|
|
|
|
qualifier_source_value VARCHAR(50)
|
|
|
|
)
|
|
|
|
;
|
|
|
|
|
|
|
|
|
|
CREATE TABLE fact_relationship
|
|
(
|
|
|
|
domain_concept_id_1 INTEGER,
|
|
|
|
fact_id_1 INTEGER,
|
|
|
|
domain_concept_id_2 INTEGER,
|
|
|
|
fact_id_2 INTEGER,
|
|
|
|
relationship_concept_id INTEGER
|
|
|
|
)
|
|
|
|
;
|
|
|
|
|
|
|
|
|
|
/************************
|
|
|
|
|
|
|
|
Standardized health system data
|
|
|
|
|
|
|
|
************************/
|
|
|
|
|
|
|
|
CREATE TABLE `location`
|
|
(
|
|
|
|
location_id INTEGER,
|
|
|
|
address_1 VARCHAR(50),
|
|
|
|
address_2 VARCHAR(50),
|
|
|
|
city VARCHAR(50),
|
|
|
|
state VARCHAR(2),
|
|
|
|
zip VARCHAR(9),
|
|
|
|
county VARCHAR(20),
|
|
|
|
location_source_value VARCHAR(50)
|
|
|
|
)
|
|
|
|
;
|
|
|
|
|
|
|
|
|
|
CREATE TABLE care_site
|
|
(
|
|
|
|
care_site_id INTEGER,
|
|
|
|
care_site_name VARCHAR(255),
|
|
|
|
place_of_service_concept_id INTEGER,
|
|
|
|
location_id INTEGER,
|
|
|
|
care_site_source_value VARCHAR(50),
|
|
|
|
place_of_service_source_value VARCHAR(50)
|
|
|
|
)
|
|
|
|
;
|
|
|
|
|
|
|
|
|
|
CREATE TABLE provider
|
|
(
|
|
|
|
provider_id INTEGER,
|
|
|
|
provider_name VARCHAR(255),
|
|
|
|
NPI VARCHAR(20),
|
|
|
|
DEA VARCHAR(20),
|
|
|
|
specialty_concept_id INTEGER,
|
|
care_site_id INTEGER,
|
|
|
|
year_of_birth INTEGER,
|
|
|
|
gender_concept_id INTEGER,
|
|
|
|
provider_source_value VARCHAR(50),
|
|
|
|
specialty_source_value VARCHAR(50),
|
|
|
|
specialty_source_concept_id INTEGER,
|
|
|
|
gender_source_value VARCHAR(50),
|
|
|
|
gender_source_concept_id INTEGER
|
|
|
|
)
|
|
|
|
;
|
|
|
|
|
|
|
|
/************************
|
|
|
|
|
|
|
|
Standardized health economics
|
|
|
|
|
|
|
|
************************/
|
|
|
|
|
|
|
|
|
|
CREATE TABLE payer_plan_period
|
|
(
|
|
|
|
payer_plan_period_id INTEGER,
|
|
|
|
person_id INTEGER,
|
|
|
|
payer_plan_period_start_date TIMESTAMP,
|
|
|
|
payer_plan_period_end_date TIMESTAMP,
|
|
|
|
payer_concept_id INTEGER,
|
|
|
|
payer_source_value VARCHAR(50),
|
|
|
|
payer_source_concept_id INTEGER,
|
|
|
|
plan_concept_id INTEGER,
|
|
|
|
plan_source_value VARCHAR(50),
|
|
|
|
plan_source_concept_id INTEGER,
|
|
|
|
sponsor_concept_id INTEGER,
|
|
|
|
sponsor_source_value VARCHAR(50),
|
|
|
|
sponsor_source_concept_id INTEGER,
|
|
|
|
family_source_value VARCHAR(50),
|
|
|
|
stop_reason_concept_id INTEGER,
|
|
|
|
stop_reason_source_value VARCHAR(50),
|
|
|
|
stop_reason_source_concept_id INTEGER
|
|
)
|
|
|
|
;
|
|
|
|
|
|
|
|
|
|
CREATE TABLE cost
|
|
(
|
|
|
|
cost_id INTEGER,
|
|
|
|
cost_event_id INTEGER,
|
|
|
|
cost_domain_id VARCHAR(20),
|
|
|
|
cost_type_concept_id INTEGER,
|
|
|
|
currency_concept_id INTEGER,
|
|
|
|
total_charge FLOAT,
|
|
|
|
total_cost FLOAT,
|
|
|
|
total_paid FLOAT,
|
|
|
|
paid_by_payer FLOAT,
|
|
|
|
paid_by_patient FLOAT,
|
|
|
|
paid_patient_copay FLOAT,
|
|
|
|
paid_patient_coinsurance FLOAT,
|
|
|
|
paid_patient_deductible FLOAT,
|
|
|
|
paid_by_primary FLOAT,
|
|
|
|
paid_ingredient_cost FLOAT,
|
|
|
|
paid_dispensing_fee FLOAT,
|
|
|
|
payer_plan_period_id INTEGER,
|
|
|
|
amount_allowed FLOAT,
|
|
|
|
revenue_code_concept_id INTEGER,
|
|
|
|
revenue_code_source_value VARCHAR(50),
|
|
|
|
drg_concept_id INTEGER,
|
|
|
|
drg_source_value VARCHAR(3)
|
|
|
|
)
|
|
|
|
;
|
|
|
|
|
|
|
|
/************************
|
|
|
|
|
|
|
|
Standardized derived elements
|
|
|
|
|
|
|
|
************************/
|
|
|
|
|
|
|
|
CREATE TABLE cohort
|
|
(
|
|
|
|
cohort_definition_id INTEGER,
|
|
|
|
subject_id INTEGER,
|
|
|
|
cohort_start_date TIMESTAMP,
|
|
|
|
cohort_end_date TIMESTAMP
|
|
|
|
)
|
|
|
|
;
|
|
|
|
|
|
|
|
|
|
CREATE TABLE cohort_attribute
|
|
(
|
|
|
|
cohort_definition_id INTEGER,
|
|
|
|
cohort_start_date TIMESTAMP,
|
|
|
|
cohort_end_date TIMESTAMP,
|
|
|
|
subject_id INTEGER,
|
|
|
|
attribute_definition_id INTEGER,
|
|
|
|
value_as_number FLOAT,
|
|
|
|
value_as_concept_id INTEGER
|
|
|
|
)
|
|
|
|
;
|
|
|
|
|
|
|
|
|
|
CREATE TABLE drug_era
|
|
(
|
|
|
|
drug_era_id INTEGER,
|
|
|
|
person_id INTEGER,
|
|
|
|
drug_concept_id INTEGER,
|
|
|
|
drug_era_start_date TIMESTAMP,
|
|
|
|
drug_era_end_date TIMESTAMP,
|
|
|
|
drug_exposure_count INTEGER,
|
|
|
|
gap_days INTEGER
|
|
|
|
)
|
|
|
|
;
|
|
|
|
|
|
|
|
|
|
CREATE TABLE dose_era
|
|
(
|
|
|
|
dose_era_id INTEGER,
|
|
|
|
person_id INTEGER,
|
|
|
|
drug_concept_id INTEGER,
|
|
|
|
unit_concept_id INTEGER,
|
|
|
|
dose_value FLOAT,
|
|
|
|
dose_era_start_date TIMESTAMP,
|
|
|
|
dose_era_end_date TIMESTAMP
|
|
|
|
)
|
|
|
|
;
|
|
|
|
|
|
CREATE TABLE condition_era
|
|
(
|
|
|
|
condition_era_id INTEGER,
|
|
|
|
person_id INTEGER,
|
|
|
|
condition_concept_id INTEGER,
|
|
|
|
condition_era_start_date TIMESTAMP,
|
|
|
|
condition_era_end_date TIMESTAMP,
|
|
|
|
condition_occurrence_count INTEGER
|
|
)
|
|
;
|