Added distribution hints to the DDL for redshift and netezza
This commit is contained in:
clairblacketer
parent
8a90a0733d
commit
2680b2ca47
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@ -0,0 +1,39 @@
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# Copyright 2017 Observational Health Data Sciences and Informatics
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#
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# This file is part of DDLGeneratr
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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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#' Write primary key script
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#'
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#' @param targetdialect The dialect of the target database. Choices are "oracle", "postgresql", "pdw", "redshift", "impala", "netezza", "bigquery", "sql server"
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#'
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#' @export
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writePrimaryKeys <- function(targetdialect) {
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if(!dir.exists("output")){
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dir.create("output")
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}
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if(!dir.exists(paste0("output/",targetdialect))){
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dir.create(paste0("output/",targetdialect))
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}
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sql <- SqlRender::loadRenderTranslateSql(sqlFilename = "OMOP CDM Primary Keys.sql",
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packageName = "DDLGeneratr",
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dbms = targetdialect,
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targetdialect = targetdialect)
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SqlRender::writeSql(sql = sql,
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targetFile = paste0("output/",targetdialect,"/OMOP CDM ",targetdialect," primary keys.txt"))
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}
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@ -27,14 +27,18 @@ writeIndex("postgresql")
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writeIndex("pdw")
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writeIndex("sql server")
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# Step 4: Run the following code to create foreign key constraints for Oracle, Postgres, PDW and Sql Server
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# Step 4: Run the following code to create primary key constraints for Netezza
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writePrimaryKeys("netezza")
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# Step 5: Run the following code to create foreign key constraints for Oracle, Postgres, PDW and Sql Server
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writeConstraints("oracle")
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writeConstraints("postgresql")
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writeConstraints("pdw")
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writeConstraints("sql server")
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# step 5: Run the following code to create the pdf documentation. It will be written to the reports folder.
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# step 6: Run the following code to create the pdf documentation. It will be written to the reports folder.
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rmarkdown::render("reports/OMOP_CDM_PDF.Rmd",
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output_format = "pdf_document",
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@ -0,0 +1,174 @@
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/*********************************************************************************
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# Copyright 2014 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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@targetdialect script to create the required indexes within OMOP common data model, version 5.3
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last revised: 14-November-2017
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author: Patrick Ryan, Clair Blacketer
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description: These primary keys and indices are considered a minimal requirement to ensure adequate performance of analyses.
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*************************/
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/************************
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*************************
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*************************
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*************************
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Primary key constraints
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*************************
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*************************
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*************************
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************************/
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/************************
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Standardized vocabulary
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************************/
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ALTER TABLE concept ADD CONSTRAINT xpk_concept PRIMARY KEY NONCLUSTERED (concept_id);
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ALTER TABLE vocabulary ADD CONSTRAINT xpk_vocabulary PRIMARY KEY NONCLUSTERED (vocabulary_id);
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ALTER TABLE domain ADD CONSTRAINT xpk_domain PRIMARY KEY NONCLUSTERED (domain_id);
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ALTER TABLE concept_class ADD CONSTRAINT xpk_concept_class PRIMARY KEY NONCLUSTERED (concept_class_id);
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ALTER TABLE concept_relationship ADD CONSTRAINT xpk_concept_relationship PRIMARY KEY NONCLUSTERED (concept_id_1,concept_id_2,relationship_id);
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ALTER TABLE relationship ADD CONSTRAINT xpk_relationship PRIMARY KEY NONCLUSTERED (relationship_id);
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ALTER TABLE concept_ancestor ADD CONSTRAINT xpk_concept_ancestor PRIMARY KEY NONCLUSTERED (ancestor_concept_id,descendant_concept_id);
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ALTER TABLE source_to_concept_map ADD CONSTRAINT xpk_source_to_concept_map PRIMARY KEY NONCLUSTERED (source_vocabulary_id,target_concept_id,source_code,valid_end_date);
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ALTER TABLE drug_strength ADD CONSTRAINT xpk_drug_strength PRIMARY KEY NONCLUSTERED (drug_concept_id, ingredient_concept_id);
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ALTER TABLE cohort_definition ADD CONSTRAINT xpk_cohort_definition PRIMARY KEY NONCLUSTERED (cohort_definition_id);
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ALTER TABLE attribute_definition ADD CONSTRAINT xpk_attribute_definition PRIMARY KEY NONCLUSTERED (attribute_definition_id);
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/**************************
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Standardized meta-data
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***************************/
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/************************
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Standardized clinical data
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************************/
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/**PRIMARY KEY NONCLUSTERED constraints**/
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ALTER TABLE person ADD CONSTRAINT xpk_person PRIMARY KEY NONCLUSTERED ( person_id ) ;
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ALTER TABLE observation_period ADD CONSTRAINT xpk_observation_period PRIMARY KEY NONCLUSTERED ( observation_period_id ) ;
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ALTER TABLE specimen ADD CONSTRAINT xpk_specimen PRIMARY KEY NONCLUSTERED ( specimen_id ) ;
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ALTER TABLE death ADD CONSTRAINT xpk_death PRIMARY KEY NONCLUSTERED ( person_id ) ;
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ALTER TABLE visit_occurrence ADD CONSTRAINT xpk_visit_occurrence PRIMARY KEY NONCLUSTERED ( visit_occurrence_id ) ;
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ALTER TABLE visit_detail ADD CONSTRAINT xpk_visit_detail PRIMARY KEY NONCLUSTERED ( visit_detail_id ) ;
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ALTER TABLE procedure_occurrence ADD CONSTRAINT xpk_procedure_occurrence PRIMARY KEY NONCLUSTERED ( procedure_occurrence_id ) ;
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ALTER TABLE drug_exposure ADD CONSTRAINT xpk_drug_exposure PRIMARY KEY NONCLUSTERED ( drug_exposure_id ) ;
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ALTER TABLE device_exposure ADD CONSTRAINT xpk_device_exposure PRIMARY KEY NONCLUSTERED ( device_exposure_id ) ;
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ALTER TABLE condition_occurrence ADD CONSTRAINT xpk_condition_occurrence PRIMARY KEY NONCLUSTERED ( condition_occurrence_id ) ;
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ALTER TABLE measurement ADD CONSTRAINT xpk_measurement PRIMARY KEY NONCLUSTERED ( measurement_id ) ;
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ALTER TABLE note ADD CONSTRAINT xpk_note PRIMARY KEY NONCLUSTERED ( note_id ) ;
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ALTER TABLE note_nlp ADD CONSTRAINT xpk_note_nlp PRIMARY KEY NONCLUSTERED ( note_nlp_id ) ;
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ALTER TABLE observation ADD CONSTRAINT xpk_observation PRIMARY KEY NONCLUSTERED ( observation_id ) ;
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/************************
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Standardized health system data
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************************/
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ALTER TABLE location ADD CONSTRAINT xpk_location PRIMARY KEY NONCLUSTERED ( location_id ) ;
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ALTER TABLE care_site ADD CONSTRAINT xpk_care_site PRIMARY KEY NONCLUSTERED ( care_site_id ) ;
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ALTER TABLE provider ADD CONSTRAINT xpk_provider PRIMARY KEY NONCLUSTERED ( provider_id ) ;
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/************************
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Standardized health economics
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************************/
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ALTER TABLE payer_plan_period ADD CONSTRAINT xpk_payer_plan_period PRIMARY KEY NONCLUSTERED ( payer_plan_period_id ) ;
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ALTER TABLE cost ADD CONSTRAINT xpk_visit_cost PRIMARY KEY NONCLUSTERED ( cost_id ) ;
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/************************
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Standardized derived elements
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************************/
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ALTER TABLE cohort ADD CONSTRAINT xpk_cohort PRIMARY KEY NONCLUSTERED ( cohort_definition_id, subject_id, cohort_start_date, cohort_end_date ) ;
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ALTER TABLE cohort_attribute ADD CONSTRAINT xpk_cohort_attribute PRIMARY KEY NONCLUSTERED ( cohort_definition_id, subject_id, cohort_start_date, cohort_end_date, attribute_definition_id ) ;
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ALTER TABLE drug_era ADD CONSTRAINT xpk_drug_era PRIMARY KEY NONCLUSTERED ( drug_era_id ) ;
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ALTER TABLE dose_era ADD CONSTRAINT xpk_dose_era PRIMARY KEY NONCLUSTERED ( dose_era_id ) ;
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ALTER TABLE condition_era ADD CONSTRAINT xpk_condition_era PRIMARY KEY NONCLUSTERED ( condition_era_id ) ;
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@ -221,7 +221,7 @@ Standardized clinical data
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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 INTEGER NOT NULL ,
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@ -246,6 +246,7 @@ CREATE TABLE person
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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 INTEGER NOT NULL ,
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@ -257,6 +258,7 @@ CREATE TABLE observation_period
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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 INTEGER NOT NULL ,
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@ -278,7 +280,7 @@ CREATE TABLE specimen
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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 INTEGER NOT NULL ,
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@ -292,6 +294,7 @@ CREATE TABLE death
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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 INTEGER NOT NULL ,
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@ -315,6 +318,7 @@ CREATE TABLE visit_occurrence
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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 INTEGER NOT NULL ,
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@ -340,6 +344,7 @@ CREATE TABLE visit_detail
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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 INTEGER NOT NULL ,
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@ -360,6 +365,7 @@ CREATE TABLE procedure_occurrence
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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 INTEGER NOT NULL ,
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@ -389,6 +395,7 @@ CREATE TABLE drug_exposure
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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 INTEGER NOT NULL ,
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@ -410,6 +417,7 @@ CREATE TABLE device_exposure
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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 INTEGER NOT NULL ,
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@ -432,6 +440,7 @@ CREATE TABLE condition_occurrence
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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 INTEGER NOT NULL ,
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@ -458,7 +467,7 @@ CREATE TABLE measurement
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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 INTEGER NOT NULL ,
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@ -500,7 +509,7 @@ CREATE TABLE note_nlp
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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 INTEGER NOT NULL ,
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@ -525,7 +534,6 @@ CREATE TABLE observation
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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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@ -538,7 +546,6 @@ CREATE TABLE fact_relationship
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/************************
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Standardized health system data
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@ -546,7 +553,6 @@ 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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@ -561,7 +567,6 @@ CREATE TABLE location
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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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@ -574,7 +579,6 @@ CREATE TABLE care_site
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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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@ -594,8 +598,6 @@ CREATE TABLE provider
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;
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/************************
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Standardized health economics
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@ -603,6 +605,7 @@ Standardized health economics
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************************/
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--HINT DISTRIBUTE_ON_KEY(person_id)
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CREATE TABLE payer_plan_period
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(
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payer_plan_period_id INTEGER NOT NULL ,
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@ -654,15 +657,14 @@ CREATE TABLE cost
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;
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/************************
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Standardized derived elements
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************************/
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--HINT DISTRIBUTE_ON_KEY(subject_id)
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CREATE TABLE cohort
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(
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cohort_definition_id INTEGER NOT NULL ,
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@ -673,6 +675,7 @@ CREATE TABLE cohort
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;
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--HINT DISTRIBUTE_ON_KEY(subject_id)
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CREATE TABLE cohort_attribute
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(
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cohort_definition_id INTEGER NOT NULL ,
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@ -686,8 +689,7 @@ CREATE TABLE cohort_attribute
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;
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--HINT DISTRIBUTE_ON_KEY(person_id)
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CREATE TABLE drug_era
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(
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drug_era_id INTEGER NOT NULL ,
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@ -701,6 +703,7 @@ CREATE TABLE drug_era
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;
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--HINT DISTRIBUTE_ON_KEY(person_id)
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CREATE TABLE dose_era
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(
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dose_era_id INTEGER NOT NULL ,
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@ -714,8 +717,7 @@ CREATE TABLE dose_era
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;
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--HINT DISTRIBUTE_ON_KEY(person_id)
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CREATE TABLE condition_era
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(
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condition_era_id INTEGER NOT NULL ,
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@ -726,10 +728,3 @@ CREATE TABLE condition_era
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condition_occurrence_count INTEGER NULL
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)
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;
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|
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@ -1,207 +0,0 @@
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---
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title: "OMOP Common Data Model Specifications"
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author: "Christian Reich, Patrick Ryan, Rimma Belenkaya, Karthik Natarajan and Clair Blacketer"
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date: "`r Sys.Date()`"
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output:
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pdf_document:
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number_sections: yes
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toc: yes
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linkcolor: blue
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---
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# License
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||||
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```{r child = '@mdFilesLocation/License.md'}
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```
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# Background
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```{r child = '@mdFilesLocation/Background/Background.md'}
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```
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## The Role of the Common Data Model
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```{r child = '@mdFilesLocation/Background/The-Role-of-the-Common-Data-Model.md'}
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```
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## Design Principles
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||||
```{r child = '@mdFilesLocation/Background/Design-Principles.md'}
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||||
```
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||||
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## Data Model Conventions
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```{r child = '@mdFilesLocation/Background/Data-Model-Conventions.md'}
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```
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||||
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# Glossary of Terms
|
||||
```{r child = '@mdFilesLocation/Glossary-of-Terms.md'}
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||||
```
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||||
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# Standardized Vocabularies
|
||||
```{r child = '@mdFilesLocation/StandardizedVocabularies/Standardized-Vocabularies.md'}
|
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```
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||||
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||||
## CONCEPT
|
||||
```{r child = '@mdFilesLocation/StandardizedVocabularies/CONCEPT.md'}
|
||||
```
|
||||
|
||||
## VOCABULARY
|
||||
```{r child = '@mdFilesLocation/StandardizedVocabularies/VOCABULARY.md'}
|
||||
```
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||||
|
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## DOMAIN
|
||||
```{r child = '@mdFilesLocation/StandardizedVocabularies/DOMAIN.md'}
|
||||
```
|
||||
|
||||
## CONCEPT_CLASS
|
||||
```{r child = '@mdFilesLocation/StandardizedVocabularies/CONCEPT_CLASS.md'}
|
||||
```
|
||||
|
||||
## CONCEPT_RELATIONSHIP
|
||||
```{r child = '@mdFilesLocation/StandardizedVocabularies/CONCEPT_RELATIONSHIP.md'}
|
||||
```
|
||||
|
||||
## RELATIONSHIP
|
||||
```{r child = '@mdFilesLocation/StandardizedVocabularies/RELATIONSHIP.md'}
|
||||
```
|
||||
|
||||
## CONCEPT_SYNONYM
|
||||
```{r child = '@mdFilesLocation/StandardizedVocabularies/CONCEPT_SYNONYM.md'}
|
||||
```
|
||||
|
||||
## CONCEPT_ANCESTOR
|
||||
```{r child = '@mdFilesLocation/StandardizedVocabularies/CONCEPT_ANCESTOR.md'}
|
||||
```
|
||||
|
||||
## SOURCE_TO_CONCEPT_MAP
|
||||
```{r child = '@mdFilesLocation/StandardizedVocabularies/SOURCE_TO_CONCEPT_MAP.md'}
|
||||
```
|
||||
|
||||
## DRUG_STRENGTH
|
||||
```{r child = '@mdFilesLocation/StandardizedVocabularies/DRUG_STRENGTH.md'}
|
||||
```
|
||||
|
||||
## COHORT_DEFINITION
|
||||
```{r child = '@mdFilesLocation/StandardizedVocabularies/COHORT_DEFINITION.md'}
|
||||
```
|
||||
|
||||
## ATTRIBUTE_DEFINITION
|
||||
```{r child = '@mdFilesLocation/StandardizedVocabularies/ATTRIBUTE_DEFINITION.md'}
|
||||
```
|
||||
|
||||
# Standardized Metadata
|
||||
```{r child = '@mdFilesLocation/StandardizedMetadata/Standardized-Metadata.md'}
|
||||
```
|
||||
|
||||
## CDM_SOURCE
|
||||
```{r child = '@mdFilesLocation/StandardizedMetadata/CDM_SOURCE.md'}
|
||||
```
|
||||
|
||||
# Standardized Clinical Data Tables
|
||||
```{r child = '@mdFilesLocation/StandardizedclinicalDataTables/Standardized-clinical-Data-Tables.md'}
|
||||
```
|
||||
|
||||
## PERSON
|
||||
```{r child = '@mdFilesLocation/StandardizedclinicalDataTables/PERSON.md'}
|
||||
```
|
||||
|
||||
## OBSERVATION_PERIOD
|
||||
```{r child = '@mdFilesLocation/StandardizedclinicalDataTables/OBSERVATION_PERIOD.md'}
|
||||
```
|
||||
|
||||
## SPECIMEN
|
||||
```{r child = '@mdFilesLocation/StandardizedclinicalDataTables/SPECIMEN.md'}
|
||||
```
|
||||
|
||||
## DEATH
|
||||
```{r child = '@mdFilesLocation/StandardizedclinicalDataTables/DEATH.md'}
|
||||
```
|
||||
|
||||
## VISIT_OCCURRENCE
|
||||
```{r child = '@mdFilesLocation/StandardizedclinicalDataTables/VISIT_OCCURRENCE.md'}
|
||||
```
|
||||
|
||||
## PROCEDURE_OCCURRENCE
|
||||
```{r child = '@mdFilesLocation/StandardizedclinicalDataTables/PROCEDURE_OCCURRENCE.md'}
|
||||
```
|
||||
|
||||
## DRUG_EXPOSURE
|
||||
```{r child = '@mdFilesLocation/StandardizedclinicalDataTables/DRUG_EXPOSURE.md'}
|
||||
```
|
||||
|
||||
## DEVICE_EXPOSURE
|
||||
```{r child = '@mdFilesLocation/StandardizedclinicalDataTables/DEVICE_EXPOSURE.md'}
|
||||
```
|
||||
|
||||
## CONDITION_OCCURRENCE
|
||||
```{r child = '@mdFilesLocation/StandardizedclinicalDataTables/CONDITION_OCCURRENCE.md'}
|
||||
```
|
||||
|
||||
## MEASUREMENT
|
||||
```{r child = '@mdFilesLocation/StandardizedclinicalDataTables/MEASUREMENT.md'}
|
||||
```
|
||||
|
||||
## NOTE
|
||||
```{r child = '@mdFilesLocation/StandardizedclinicalDataTables/NOTE.md'}
|
||||
```
|
||||
|
||||
## NOTE_NLP
|
||||
```{r child = '@mdFilesLocation/StandardizedclinicalDataTables/NOTE_NLP.md'}
|
||||
```
|
||||
|
||||
## OBSERVATION
|
||||
```{r child = '@mdFilesLocation/StandardizedclinicalDataTables/OBSERVATION.md'}
|
||||
```
|
||||
|
||||
## FACT_RELATIONSHIP
|
||||
```{r child = '@mdFilesLocation/StandardizedclinicalDataTables/FACT_RELATIONSHIP.md'}
|
||||
```
|
||||
|
||||
# Standardized Health System Data Tables
|
||||
```{r child = '@mdFilesLocation/StandardizedHealthSystemDataTables/Standardized-Health-System-Data-Tables.md'}
|
||||
```
|
||||
|
||||
## LOCATION
|
||||
```{r child = '@mdFilesLocation/StandardizedHealthSystemDataTables/LOCATION.md'}
|
||||
```
|
||||
|
||||
## CARE_SITE
|
||||
```{r child = '@mdFilesLocation/StandardizedHealthSystemDataTables/CARE_SITE.md'}
|
||||
```
|
||||
|
||||
## PROVIDER
|
||||
```{r child = '@mdFilesLocation/StandardizedHealthSystemDataTables/PROVIDER.md'}
|
||||
```
|
||||
|
||||
# Standardized Health Economics Data Tables
|
||||
```{r child = '@mdFilesLocation/StandardizedHealthEconomicsDataTables/Standardized-Health-Economics-Data-Tables.md'}
|
||||
```
|
||||
|
||||
## PAYER_PLAN_PERIOD
|
||||
```{r child = '@mdFilesLocation/StandardizedHealthEconomicsDataTables/PAYER_PLAN_PERIOD.md'}
|
||||
```
|
||||
|
||||
## COST
|
||||
```{r child = '@mdFilesLocation/StandardizedHealthEconomicsDataTables/COST.md'}
|
||||
```
|
||||
|
||||
# Standardized Derived Elements
|
||||
```{r child = '@mdFilesLocation/StandardizedDerivedElements/Standardized-Derived-Elements.md'}
|
||||
```
|
||||
|
||||
## COHORT
|
||||
```{r child = '@mdFilesLocation/StandardizedDerivedElements/COHORT.md'}
|
||||
```
|
||||
|
||||
## COHORT_ATTRIBUTE
|
||||
```{r child = '@mdFilesLocation/StandardizedDerivedElements/COHORT_ATTRIBUTE.md'}
|
||||
```
|
||||
|
||||
## DRUG_ERA
|
||||
```{r child = '@mdFilesLocation/StandardizedDerivedElements/DRUG_ERA.md'}
|
||||
```
|
||||
|
||||
## DOSE_ERA
|
||||
```{r child = '@mdFilesLocation/StandardizedDerivedElements/DOSE_ERA.md'}
|
||||
```
|
||||
|
||||
## CONDITION_ERA
|
||||
```{r child = '@mdFilesLocation/StandardizedDerivedElements/CONDITION_ERA.md'}
|
||||
```
|
||||
|
|
@ -221,7 +221,7 @@ Standardized clinical data
|
|||
|
||||
************************/
|
||||
|
||||
|
||||
--HINT DISTRIBUTE_ON_KEY(person_id)
|
||||
CREATE TABLE person
|
||||
(
|
||||
person_id INTEGER NOT NULL ,
|
||||
|
|
@ -246,6 +246,7 @@ CREATE TABLE person
|
|||
;
|
||||
|
||||
|
||||
--HINT DISTRIBUTE_ON_KEY(person_id)
|
||||
CREATE TABLE observation_period
|
||||
(
|
||||
observation_period_id INTEGER NOT NULL ,
|
||||
|
|
@ -257,6 +258,7 @@ CREATE TABLE observation_period
|
|||
;
|
||||
|
||||
|
||||
--HINT DISTRIBUTE_ON_KEY(person_id)
|
||||
CREATE TABLE specimen
|
||||
(
|
||||
specimen_id INTEGER NOT NULL ,
|
||||
|
|
@ -278,7 +280,7 @@ CREATE TABLE specimen
|
|||
;
|
||||
|
||||
|
||||
|
||||
--HINT DISTRIBUTE_ON_KEY(person_id)
|
||||
CREATE TABLE death
|
||||
(
|
||||
person_id INTEGER NOT NULL ,
|
||||
|
|
@ -292,6 +294,7 @@ CREATE TABLE death
|
|||
;
|
||||
|
||||
|
||||
--HINT DISTRIBUTE_ON_KEY(person_id)
|
||||
CREATE TABLE visit_occurrence
|
||||
(
|
||||
visit_occurrence_id INTEGER NOT NULL ,
|
||||
|
|
@ -315,6 +318,7 @@ CREATE TABLE visit_occurrence
|
|||
;
|
||||
|
||||
|
||||
--HINT DISTRIBUTE_ON_KEY(person_id)
|
||||
CREATE TABLE visit_detail
|
||||
(
|
||||
visit_detail_id INTEGER NOT NULL ,
|
||||
|
|
@ -340,6 +344,7 @@ CREATE TABLE visit_detail
|
|||
;
|
||||
|
||||
|
||||
--HINT DISTRIBUTE_ON_KEY(person_id)
|
||||
CREATE TABLE procedure_occurrence
|
||||
(
|
||||
procedure_occurrence_id INTEGER NOT NULL ,
|
||||
|
|
@ -360,6 +365,7 @@ CREATE TABLE procedure_occurrence
|
|||
;
|
||||
|
||||
|
||||
--HINT DISTRIBUTE_ON_KEY(person_id)
|
||||
CREATE TABLE drug_exposure
|
||||
(
|
||||
drug_exposure_id INTEGER NOT NULL ,
|
||||
|
|
@ -389,6 +395,7 @@ CREATE TABLE drug_exposure
|
|||
;
|
||||
|
||||
|
||||
--HINT DISTRIBUTE_ON_KEY(person_id)
|
||||
CREATE TABLE device_exposure
|
||||
(
|
||||
device_exposure_id INTEGER NOT NULL ,
|
||||
|
|
@ -410,6 +417,7 @@ CREATE TABLE device_exposure
|
|||
;
|
||||
|
||||
|
||||
--HINT DISTRIBUTE_ON_KEY(person_id)
|
||||
CREATE TABLE condition_occurrence
|
||||
(
|
||||
condition_occurrence_id INTEGER NOT NULL ,
|
||||
|
|
@ -432,6 +440,7 @@ CREATE TABLE condition_occurrence
|
|||
;
|
||||
|
||||
|
||||
--HINT DISTRIBUTE_ON_KEY(person_id)
|
||||
CREATE TABLE measurement
|
||||
(
|
||||
measurement_id INTEGER NOT NULL ,
|
||||
|
|
@ -458,7 +467,7 @@ CREATE TABLE measurement
|
|||
;
|
||||
|
||||
|
||||
|
||||
--HINT DISTRIBUTE_ON_KEY(person_id)
|
||||
CREATE TABLE note
|
||||
(
|
||||
note_id INTEGER NOT NULL ,
|
||||
|
|
@ -500,7 +509,7 @@ CREATE TABLE note_nlp
|
|||
;
|
||||
|
||||
|
||||
|
||||
--HINT DISTRIBUTE_ON_KEY(person_id)
|
||||
CREATE TABLE observation
|
||||
(
|
||||
observation_id INTEGER NOT NULL ,
|
||||
|
|
@ -525,7 +534,6 @@ CREATE TABLE observation
|
|||
;
|
||||
|
||||
|
||||
|
||||
CREATE TABLE fact_relationship
|
||||
(
|
||||
domain_concept_id_1 INTEGER NOT NULL ,
|
||||
|
|
@ -538,7 +546,6 @@ CREATE TABLE fact_relationship
|
|||
|
||||
|
||||
|
||||
|
||||
/************************
|
||||
|
||||
Standardized health system data
|
||||
|
|
@ -546,7 +553,6 @@ Standardized health system data
|
|||
************************/
|
||||
|
||||
|
||||
|
||||
CREATE TABLE location
|
||||
(
|
||||
location_id INTEGER NOT NULL ,
|
||||
|
|
@ -561,7 +567,6 @@ CREATE TABLE location
|
|||
;
|
||||
|
||||
|
||||
|
||||
CREATE TABLE care_site
|
||||
(
|
||||
care_site_id INTEGER NOT NULL ,
|
||||
|
|
@ -574,7 +579,6 @@ CREATE TABLE care_site
|
|||
;
|
||||
|
||||
|
||||
|
||||
CREATE TABLE provider
|
||||
(
|
||||
provider_id INTEGER NOT NULL ,
|
||||
|
|
@ -594,8 +598,6 @@ CREATE TABLE provider
|
|||
;
|
||||
|
||||
|
||||
|
||||
|
||||
/************************
|
||||
|
||||
Standardized health economics
|
||||
|
|
@ -603,6 +605,7 @@ Standardized health economics
|
|||
************************/
|
||||
|
||||
|
||||
--HINT DISTRIBUTE_ON_KEY(person_id)
|
||||
CREATE TABLE payer_plan_period
|
||||
(
|
||||
payer_plan_period_id INTEGER NOT NULL ,
|
||||
|
|
@ -654,15 +657,14 @@ CREATE TABLE cost
|
|||
;
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
/************************
|
||||
|
||||
Standardized derived elements
|
||||
|
||||
************************/
|
||||
|
||||
|
||||
--HINT DISTRIBUTE_ON_KEY(subject_id)
|
||||
CREATE TABLE cohort
|
||||
(
|
||||
cohort_definition_id INTEGER NOT NULL ,
|
||||
|
|
@ -673,12 +675,13 @@ CREATE TABLE cohort
|
|||
;
|
||||
|
||||
|
||||
--HINT DISTRIBUTE_ON_KEY(subject_id)
|
||||
CREATE TABLE cohort_attribute
|
||||
(
|
||||
cohort_definition_id INTEGER NOT NULL ,
|
||||
subject_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 NUMERIC NULL ,
|
||||
value_as_concept_id INTEGER NULL
|
||||
|
|
@ -686,8 +689,7 @@ CREATE TABLE cohort_attribute
|
|||
;
|
||||
|
||||
|
||||
|
||||
|
||||
--HINT DISTRIBUTE_ON_KEY(person_id)
|
||||
CREATE TABLE drug_era
|
||||
(
|
||||
drug_era_id INTEGER NOT NULL ,
|
||||
|
|
@ -701,6 +703,7 @@ CREATE TABLE drug_era
|
|||
;
|
||||
|
||||
|
||||
--HINT DISTRIBUTE_ON_KEY(person_id)
|
||||
CREATE TABLE dose_era
|
||||
(
|
||||
dose_era_id INTEGER NOT NULL ,
|
||||
|
|
@ -714,8 +717,7 @@ CREATE TABLE dose_era
|
|||
;
|
||||
|
||||
|
||||
|
||||
|
||||
--HINT DISTRIBUTE_ON_KEY(person_id)
|
||||
CREATE TABLE condition_era
|
||||
(
|
||||
condition_era_id INTEGER NOT NULL ,
|
||||
|
|
@ -726,10 +728,3 @@ CREATE TABLE condition_era
|
|||
condition_occurrence_count INTEGER NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
|
|
|||
|
|
@ -207,9 +207,9 @@ Standardized clinical data
|
|||
|
||||
************************/
|
||||
|
||||
|
||||
--HINT DISTRIBUTE_ON_KEY(person_id)
|
||||
CREATE TABLE person
|
||||
( person_id INTEGER NOT NULL ,
|
||||
(person_id INTEGER NOT NULL ,
|
||||
gender_concept_id INTEGER NOT NULL ,
|
||||
year_of_birth INTEGER NOT NULL ,
|
||||
month_of_birth INTEGER NULL,
|
||||
|
|
@ -231,9 +231,10 @@ CREATE TABLE person
|
|||
DISTKEY(person_id);
|
||||
|
||||
|
||||
--HINT DISTRIBUTE_ON_KEY(person_id)
|
||||
CREATE TABLE observation_period
|
||||
(observation_period_id INTEGER NOT NULL ,
|
||||
person_id INTEGER NOT NULL ,
|
||||
person_id INTEGER NOT NULL ,
|
||||
observation_period_start_date DATE NOT NULL ,
|
||||
observation_period_end_date DATE NOT NULL ,
|
||||
period_type_concept_id INTEGER NOT NULL
|
||||
|
|
@ -241,9 +242,10 @@ CREATE TABLE observation_period
|
|||
DISTKEY(person_id);
|
||||
|
||||
|
||||
--HINT DISTRIBUTE_ON_KEY(person_id)
|
||||
CREATE TABLE specimen
|
||||
(specimen_id INTEGER NOT NULL ,
|
||||
person_id INTEGER NOT NULL ,
|
||||
person_id INTEGER NOT NULL ,
|
||||
specimen_concept_id INTEGER NOT NULL ,
|
||||
specimen_type_concept_id INTEGER NOT NULL ,
|
||||
specimen_date DATE NOT NULL ,
|
||||
|
|
@ -261,9 +263,9 @@ CREATE TABLE specimen
|
|||
DISTKEY(person_id);
|
||||
|
||||
|
||||
|
||||
--HINT DISTRIBUTE_ON_KEY(person_id)
|
||||
CREATE TABLE death
|
||||
( person_id INTEGER NOT NULL ,
|
||||
(person_id INTEGER NOT NULL ,
|
||||
death_date DATE NOT NULL ,
|
||||
death_datetime TIMESTAMP NULL ,
|
||||
death_type_concept_id INTEGER NOT NULL ,
|
||||
|
|
@ -274,9 +276,10 @@ CREATE TABLE death
|
|||
DISTKEY(person_id);
|
||||
|
||||
|
||||
--HINT DISTRIBUTE_ON_KEY(person_id)
|
||||
CREATE TABLE visit_occurrence
|
||||
(visit_occurrence_id INTEGER NOT NULL ,
|
||||
person_id INTEGER NOT NULL ,
|
||||
person_id INTEGER NOT NULL ,
|
||||
visit_concept_id INTEGER NOT NULL ,
|
||||
visit_start_date DATE NOT NULL ,
|
||||
visit_start_datetime TIMESTAMP NULL ,
|
||||
|
|
@ -296,9 +299,10 @@ CREATE TABLE visit_occurrence
|
|||
DISTKEY(person_id);
|
||||
|
||||
|
||||
--HINT DISTRIBUTE_ON_KEY(person_id)
|
||||
CREATE TABLE visit_detail
|
||||
(visit_detail_id INTEGER NOT NULL ,
|
||||
person_id INTEGER NOT NULL ,
|
||||
person_id INTEGER NOT NULL ,
|
||||
visit_detail_concept_id INTEGER NOT NULL ,
|
||||
visit_start_date DATE NOT NULL ,
|
||||
visit_start_datetime TIMESTAMP NULL ,
|
||||
|
|
@ -320,9 +324,10 @@ CREATE TABLE visit_detail
|
|||
DISTKEY(person_id);
|
||||
|
||||
|
||||
--HINT DISTRIBUTE_ON_KEY(person_id)
|
||||
CREATE TABLE procedure_occurrence
|
||||
(procedure_occurrence_id INTEGER NOT NULL ,
|
||||
person_id INTEGER NOT NULL ,
|
||||
person_id INTEGER NOT NULL ,
|
||||
procedure_concept_id INTEGER NOT NULL ,
|
||||
procedure_date DATE NOT NULL ,
|
||||
procedure_datetime TIMESTAMP NULL ,
|
||||
|
|
@ -339,9 +344,10 @@ CREATE TABLE procedure_occurrence
|
|||
DISTKEY(person_id);
|
||||
|
||||
|
||||
--HINT DISTRIBUTE_ON_KEY(person_id)
|
||||
CREATE TABLE drug_exposure
|
||||
(drug_exposure_id INTEGER NOT NULL ,
|
||||
person_id INTEGER NOT NULL ,
|
||||
person_id INTEGER NOT NULL ,
|
||||
drug_concept_id INTEGER NOT NULL ,
|
||||
drug_exposure_start_date DATE NOT NULL ,
|
||||
drug_exposure_start_datetime TIMESTAMP NULL ,
|
||||
|
|
@ -367,9 +373,10 @@ CREATE TABLE drug_exposure
|
|||
DISTKEY(person_id);
|
||||
|
||||
|
||||
--HINT DISTRIBUTE_ON_KEY(person_id)
|
||||
CREATE TABLE device_exposure
|
||||
(device_exposure_id INTEGER NOT NULL ,
|
||||
person_id INTEGER NOT NULL ,
|
||||
person_id INTEGER NOT NULL ,
|
||||
device_concept_id INTEGER NOT NULL ,
|
||||
device_exposure_start_date DATE NOT NULL ,
|
||||
device_exposure_start_datetime TIMESTAMP NULL ,
|
||||
|
|
@ -387,9 +394,10 @@ CREATE TABLE device_exposure
|
|||
DISTKEY(person_id);
|
||||
|
||||
|
||||
--HINT DISTRIBUTE_ON_KEY(person_id)
|
||||
CREATE TABLE condition_occurrence
|
||||
(condition_occurrence_id INTEGER NOT NULL ,
|
||||
person_id INTEGER NOT NULL ,
|
||||
person_id INTEGER NOT NULL ,
|
||||
condition_concept_id INTEGER NOT NULL ,
|
||||
condition_start_date DATE NOT NULL ,
|
||||
condition_start_datetime TIMESTAMP NULL ,
|
||||
|
|
@ -408,9 +416,10 @@ CREATE TABLE condition_occurrence
|
|||
DISTKEY(person_id);
|
||||
|
||||
|
||||
--HINT DISTRIBUTE_ON_KEY(person_id)
|
||||
CREATE TABLE measurement
|
||||
(measurement_id INTEGER NOT NULL ,
|
||||
person_id INTEGER NOT NULL ,
|
||||
person_id INTEGER NOT NULL ,
|
||||
measurement_concept_id INTEGER NOT NULL ,
|
||||
measurement_date DATE NOT NULL ,
|
||||
measurement_time VARCHAR(10) NULL ,
|
||||
|
|
@ -433,10 +442,10 @@ CREATE TABLE measurement
|
|||
DISTKEY(person_id);
|
||||
|
||||
|
||||
|
||||
--HINT DISTRIBUTE_ON_KEY(person_id)
|
||||
CREATE TABLE note
|
||||
(note_id INTEGER NOT NULL ,
|
||||
person_id INTEGER NOT NULL ,
|
||||
person_id INTEGER NOT NULL ,
|
||||
note_date DATE NOT NULL ,
|
||||
note_datetime TIMESTAMP NULL ,
|
||||
note_type_concept_id INTEGER NOT NULL ,
|
||||
|
|
@ -473,10 +482,10 @@ CREATE TABLE note_nlp
|
|||
DISTSTYLE ALL;
|
||||
|
||||
|
||||
|
||||
--HINT DISTRIBUTE_ON_KEY(person_id)
|
||||
CREATE TABLE observation
|
||||
(observation_id INTEGER NOT NULL ,
|
||||
person_id INTEGER NOT NULL ,
|
||||
person_id INTEGER NOT NULL ,
|
||||
observation_concept_id INTEGER NOT NULL ,
|
||||
observation_date DATE NOT NULL ,
|
||||
observation_datetime TIMESTAMP NULL ,
|
||||
|
|
@ -497,7 +506,6 @@ CREATE TABLE observation
|
|||
DISTKEY(person_id);
|
||||
|
||||
|
||||
|
||||
CREATE TABLE fact_relationship
|
||||
(domain_concept_id_1 INTEGER NOT NULL ,
|
||||
fact_id_1 INTEGER NOT NULL ,
|
||||
|
|
@ -509,7 +517,6 @@ DISTSTYLE ALL;
|
|||
|
||||
|
||||
|
||||
|
||||
/************************
|
||||
|
||||
Standardized health system data
|
||||
|
|
@ -517,7 +524,6 @@ Standardized health system data
|
|||
************************/
|
||||
|
||||
|
||||
|
||||
CREATE TABLE location
|
||||
(location_id INTEGER NOT NULL ,
|
||||
address_1 VARCHAR(50) NULL ,
|
||||
|
|
@ -531,7 +537,6 @@ CREATE TABLE location
|
|||
DISTSTYLE ALL;
|
||||
|
||||
|
||||
|
||||
CREATE TABLE care_site
|
||||
(care_site_id INTEGER NOT NULL ,
|
||||
care_site_name VARCHAR(255) NULL ,
|
||||
|
|
@ -543,7 +548,6 @@ CREATE TABLE care_site
|
|||
DISTSTYLE ALL;
|
||||
|
||||
|
||||
|
||||
CREATE TABLE provider
|
||||
(provider_id INTEGER NOT NULL ,
|
||||
provider_name VARCHAR(255) NULL ,
|
||||
|
|
@ -562,8 +566,6 @@ CREATE TABLE provider
|
|||
DISTSTYLE ALL;
|
||||
|
||||
|
||||
|
||||
|
||||
/************************
|
||||
|
||||
Standardized health economics
|
||||
|
|
@ -571,9 +573,10 @@ Standardized health economics
|
|||
************************/
|
||||
|
||||
|
||||
--HINT DISTRIBUTE_ON_KEY(person_id)
|
||||
CREATE TABLE payer_plan_period
|
||||
(payer_plan_period_id INTEGER NOT NULL ,
|
||||
person_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 ,
|
||||
|
|
@ -620,29 +623,29 @@ CREATE TABLE cost
|
|||
DISTSTYLE ALL;
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
/************************
|
||||
|
||||
Standardized derived elements
|
||||
|
||||
************************/
|
||||
|
||||
|
||||
--HINT DISTRIBUTE_ON_KEY(subject_id)
|
||||
CREATE TABLE cohort
|
||||
(cohort_definition_id INTEGER NOT NULL ,
|
||||
subject_id INTEGER NOT NULL ,
|
||||
subject_id INTEGER NOT NULL ,
|
||||
cohort_start_date DATE NOT NULL ,
|
||||
cohort_end_date DATE NOT NULL
|
||||
)
|
||||
DISTKEY(subject_id);
|
||||
|
||||
|
||||
--HINT DISTRIBUTE_ON_KEY(subject_id)
|
||||
CREATE TABLE cohort_attribute
|
||||
(cohort_definition_id INTEGER NOT NULL ,
|
||||
subject_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
|
||||
|
|
@ -650,11 +653,10 @@ CREATE TABLE cohort_attribute
|
|||
DISTKEY(subject_id);
|
||||
|
||||
|
||||
|
||||
|
||||
--HINT DISTRIBUTE_ON_KEY(person_id)
|
||||
CREATE TABLE drug_era
|
||||
(drug_era_id INTEGER NOT NULL ,
|
||||
person_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 ,
|
||||
|
|
@ -664,9 +666,10 @@ CREATE TABLE drug_era
|
|||
DISTKEY(person_id);
|
||||
|
||||
|
||||
--HINT DISTRIBUTE_ON_KEY(person_id)
|
||||
CREATE TABLE dose_era
|
||||
(dose_era_id INTEGER NOT NULL ,
|
||||
person_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 ,
|
||||
|
|
@ -676,21 +679,13 @@ CREATE TABLE dose_era
|
|||
DISTKEY(person_id);
|
||||
|
||||
|
||||
|
||||
|
||||
--HINT DISTRIBUTE_ON_KEY(person_id)
|
||||
CREATE TABLE condition_era
|
||||
(condition_era_id INTEGER NOT NULL ,
|
||||
person_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
|
||||
)
|
||||
DISTKEY(person_id);
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue