Added SQL files
This commit is contained in:
pbr6cornell
parent
af6937a7c8
commit
c6978ca953
|
|
@ -0,0 +1,544 @@
|
||||||
|
/*********************************************************************************
|
||||||
|
# Copyright 2014 Observational Health Data Sciences and Informatics
|
||||||
|
#
|
||||||
|
#
|
||||||
|
# Licensed under the Apache License, Version 2.0 (the "License");
|
||||||
|
# you may not use this file except in compliance with the License.
|
||||||
|
# You may obtain a copy of the License at
|
||||||
|
#
|
||||||
|
# http://www.apache.org/licenses/LICENSE-2.0
|
||||||
|
#
|
||||||
|
# Unless required by applicable law or agreed to in writing, software
|
||||||
|
# distributed under the License is distributed on an "AS IS" BASIS,
|
||||||
|
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
|
||||||
|
# See the License for the specific language governing permissions and
|
||||||
|
# limitations under the License.
|
||||||
|
********************************************************************************/
|
||||||
|
|
||||||
|
/************************
|
||||||
|
|
||||||
|
####### # # ####### ###### ##### ###### # # ####### #####
|
||||||
|
# # ## ## # # # # # # # # ## ## # # # # # #### # # #### ##### ##### ## # # # ##### ####
|
||||||
|
# # # # # # # # # # # # # # # # # # # # # # # ## # # # # # # # # ## # # #
|
||||||
|
# # # # # # # ###### # # # # # # # # ###### # # # # # # #### # # # # # # # # # # ####
|
||||||
|
# # # # # # # # # # # # # # # # # # # # # # # ##### ###### # # # # # #
|
||||||
|
# # # # # # # # # # # # # # # # # # # # # # ## # # # # # # # # # ## # # #
|
||||||
|
####### # # ####### # ##### ###### # # ## ##### ##### #### # # #### # # # # # # # # # ####
|
||||||
|
|
||||||
|
|
||||||
|
script to create constraints within OMOP common data model, version 5.0 for Oracle database
|
||||||
|
|
||||||
|
last revised: 12 Oct 2014
|
||||||
|
|
||||||
|
author: Patrick Ryan
|
||||||
|
|
||||||
|
*************************/
|
||||||
|
|
||||||
|
|
||||||
|
/************************
|
||||||
|
*************************
|
||||||
|
*************************
|
||||||
|
*************************
|
||||||
|
|
||||||
|
Primary key constraints
|
||||||
|
|
||||||
|
*************************
|
||||||
|
*************************
|
||||||
|
*************************
|
||||||
|
************************/
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/************************
|
||||||
|
|
||||||
|
Standardized vocabulary
|
||||||
|
|
||||||
|
************************/
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
ALTER TABLE concept ADD CONSTRAINT xpk_concept PRIMARY KEY (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE vocabulary ADD CONSTRAINT xpk_vocabulary PRIMARY KEY (vocabulary_id);
|
||||||
|
|
||||||
|
ALTER TABLE domain ADD CONSTRAINT xpk_domain PRIMARY KEY (domain_id);
|
||||||
|
|
||||||
|
ALTER TABLE concept_class ADD CONSTRAINT xpk_concept_class PRIMARY KEY (concept_class_id);
|
||||||
|
|
||||||
|
ALTER TABLE concept_relationship ADD CONSTRAINT xpk_concept_relationship PRIMARY KEY (concept_id_1,concept_id_2,relationship_id);
|
||||||
|
|
||||||
|
ALTER TABLE relationship ADD CONSTRAINT xpk_relationship PRIMARY KEY (relationship_id);
|
||||||
|
|
||||||
|
ALTER TABLE concept_ancestor ADD CONSTRAINT xpk_concept_ancestor PRIMARY KEY (ancestor_concept_id,descendant_concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE source_to_concept_map ADD CONSTRAINT xpk_source_to_concept_map PRIMARY KEY (source_vocabulary_id,target_concept_id,source_code,valid_end_date);
|
||||||
|
|
||||||
|
ALTER TABLE drug_strength ADD CONSTRAINT xpk_drug_strength PRIMARY KEY (drug_concept_id, ingredient_concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE cohort_definition ADD CONSTRAINT xpk_cohort_definition PRIMARY KEY (cohort_definition_id);
|
||||||
|
|
||||||
|
ALTER TABLE attribute_definition ADD CONSTRAINT xpk_attribute_definition PRIMARY KEY (attribute_definition_id);
|
||||||
|
|
||||||
|
|
||||||
|
/**************************
|
||||||
|
|
||||||
|
Standardized meta-data
|
||||||
|
|
||||||
|
***************************/
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/************************
|
||||||
|
|
||||||
|
Standardized clinical data
|
||||||
|
|
||||||
|
************************/
|
||||||
|
|
||||||
|
|
||||||
|
/**PRIMARY KEY NONCLUSTERED constraints**/
|
||||||
|
|
||||||
|
ALTER TABLE person ADD CONSTRAINT xpk_person PRIMARY KEY ( person_id ) ;
|
||||||
|
|
||||||
|
ALTER TABLE observation_period ADD CONSTRAINT xpk_observation_period PRIMARY KEY ( observation_period_id ) ;
|
||||||
|
|
||||||
|
ALTER TABLE specimen ADD CONSTRAINT xpk_specimen PRIMARY KEY ( specimen_id ) ;
|
||||||
|
|
||||||
|
ALTER TABLE death ADD CONSTRAINT xpk_death PRIMARY KEY ( person_id ) ;
|
||||||
|
|
||||||
|
ALTER TABLE visit_occurrence ADD CONSTRAINT xpk_visit_occurrence PRIMARY KEY ( visit_occurrence_id ) ;
|
||||||
|
|
||||||
|
ALTER TABLE procedure_occurrence ADD CONSTRAINT xpk_procedure_occurrence PRIMARY KEY ( procedure_occurrence_id ) ;
|
||||||
|
|
||||||
|
ALTER TABLE drug_exposure ADD CONSTRAINT xpk_drug_exposure PRIMARY KEY ( drug_exposure_id ) ;
|
||||||
|
|
||||||
|
ALTER TABLE device_exposure ADD CONSTRAINT xpk_device_exposure PRIMARY KEY ( device_exposure_id ) ;
|
||||||
|
|
||||||
|
ALTER TABLE condition_occurrence ADD CONSTRAINT xpk_condition_occurrence PRIMARY KEY ( condition_occurrence_id ) ;
|
||||||
|
|
||||||
|
ALTER TABLE measurement ADD CONSTRAINT xpk_measurement PRIMARY KEY ( measurement_id ) ;
|
||||||
|
|
||||||
|
ALTER TABLE note ADD CONSTRAINT xpk_note PRIMARY KEY ( note_id ) ;
|
||||||
|
|
||||||
|
ALTER TABLE observation ADD CONSTRAINT xpk_observation PRIMARY KEY ( observation_id ) ;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/************************
|
||||||
|
|
||||||
|
Standardized health system data
|
||||||
|
|
||||||
|
************************/
|
||||||
|
|
||||||
|
|
||||||
|
ALTER TABLE location ADD CONSTRAINT xpk_location PRIMARY KEY ( location_id ) ;
|
||||||
|
|
||||||
|
ALTER TABLE care_site ADD CONSTRAINT xpk_care_site PRIMARY KEY ( care_site_id ) ;
|
||||||
|
|
||||||
|
ALTER TABLE provider ADD CONSTRAINT xpk_provider PRIMARY KEY ( provider_id ) ;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/************************
|
||||||
|
|
||||||
|
Standardized health economics
|
||||||
|
|
||||||
|
************************/
|
||||||
|
|
||||||
|
|
||||||
|
ALTER TABLE payer_plan_period ADD CONSTRAINT xpk_payer_plan_period PRIMARY KEY ( payer_plan_period_id ) ;
|
||||||
|
|
||||||
|
ALTER TABLE visit_cost ADD CONSTRAINT xpk_visit_cost PRIMARY KEY ( visit_cost_id ) ;
|
||||||
|
|
||||||
|
ALTER TABLE procedure_cost ADD CONSTRAINT xpk_procedure_cost PRIMARY KEY ( procedure_cost_id ) ;
|
||||||
|
|
||||||
|
ALTER TABLE drug_cost ADD CONSTRAINT xpk_drug_cost PRIMARY KEY ( drug_cost_id ) ;
|
||||||
|
|
||||||
|
ALTER TABLE device_cost ADD CONSTRAINT xpk_device_cost PRIMARY KEY ( device_cost_id ) ;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/************************
|
||||||
|
|
||||||
|
Standardized derived elements
|
||||||
|
|
||||||
|
************************/
|
||||||
|
|
||||||
|
ALTER TABLE cohort ADD CONSTRAINT xpk_cohort PRIMARY KEY ( cohort_definition_id, subject_id, cohort_start_date, cohort_end_date ) ;
|
||||||
|
|
||||||
|
ALTER TABLE cohort_attribute ADD CONSTRAINT xpk_cohort_attribute PRIMARY KEY ( cohort_definition_id, subject_id, cohort_start_date, cohort_end_date, attribute_definition_id ) ;
|
||||||
|
|
||||||
|
ALTER TABLE drug_era ADD CONSTRAINT xpk_drug_era PRIMARY KEY ( drug_era_id ) ;
|
||||||
|
|
||||||
|
ALTER TABLE dose_era ADD CONSTRAINT xpk_dose_era PRIMARY KEY ( dose_era_id ) ;
|
||||||
|
|
||||||
|
ALTER TABLE condition_era ADD CONSTRAINT xpk_condition_era PRIMARY KEY ( condition_era_id ) ;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/************************
|
||||||
|
*************************
|
||||||
|
*************************
|
||||||
|
*************************
|
||||||
|
|
||||||
|
Foreign key constraints
|
||||||
|
|
||||||
|
*************************
|
||||||
|
*************************
|
||||||
|
*************************
|
||||||
|
************************/
|
||||||
|
|
||||||
|
|
||||||
|
/************************
|
||||||
|
|
||||||
|
Standardized vocabulary
|
||||||
|
|
||||||
|
************************/
|
||||||
|
|
||||||
|
|
||||||
|
ALTER TABLE concept ADD CONSTRAINT fpk_concept_domain FOREIGN KEY (domain_id) REFERENCES domain (domain_id);
|
||||||
|
|
||||||
|
ALTER TABLE concept ADD CONSTRAINT fpk_concept_class FOREIGN KEY (concept_class_id) REFERENCES concept_class (concept_class_id);
|
||||||
|
|
||||||
|
ALTER TABLE concept ADD CONSTRAINT fpk_concept_vocabulary FOREIGN KEY (vocabulary_id) REFERENCES vocabulary (vocabulary_id);
|
||||||
|
|
||||||
|
ALTER TABLE vocabulary ADD CONSTRAINT fpk_vocabulary_concept FOREIGN KEY (vocabulary_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE domain ADD CONSTRAINT fpk_domain_concept FOREIGN KEY (domain_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE concept_class ADD CONSTRAINT fpk_concept_class_concept FOREIGN KEY (concept_class_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE concept_relationship ADD CONSTRAINT fpk_concept_relationship_c_1 FOREIGN KEY (concept_id_1) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE concept_relationship ADD CONSTRAINT fpk_concept_relationship_c_2 FOREIGN KEY (concept_id_2) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE concept_relationship ADD CONSTRAINT fpk_concept_relationship_id FOREIGN KEY (relationship_id) REFERENCES relationship (relationship_id);
|
||||||
|
|
||||||
|
ALTER TABLE relationship ADD CONSTRAINT fpk_relationship_concept FOREIGN KEY (relationship_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE relationship ADD CONSTRAINT fpk_relationship_reverse FOREIGN KEY (reverse_relationship_id) REFERENCES relationship (relationship_id);
|
||||||
|
|
||||||
|
ALTER TABLE concept_synonym ADD CONSTRAINT fpk_concept_synonym_concept FOREIGN KEY (concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE concept_ancestor ADD CONSTRAINT fpk_concept_ancestor_concept_1 FOREIGN KEY (ancestor_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE concept_ancestor ADD CONSTRAINT fpk_concept_ancestor_concept_2 FOREIGN KEY (descendant_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE source_to_concept_map ADD CONSTRAINT fpk_source_to_concept_map_v_1 FOREIGN KEY (source_vocabulary_id) REFERENCES vocabulary (vocabulary_id);
|
||||||
|
|
||||||
|
ALTER TABLE source_to_concept_map ADD CONSTRAINT fpk_source_to_concept_map_v_2 FOREIGN KEY (target_vocabulary_id) REFERENCES vocabulary (vocabulary_id);
|
||||||
|
|
||||||
|
ALTER TABLE source_to_concept_map ADD CONSTRAINT fpk_source_to_concept_map_c_1 FOREIGN KEY (target_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE drug_strength ADD CONSTRAINT fpk_drug_strength_concept_1 FOREIGN KEY (drug_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE drug_strength ADD CONSTRAINT fpk_drug_strength_concept_2 FOREIGN KEY (ingredient_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE drug_strength ADD CONSTRAINT fpk_drug_strength_unit_1 FOREIGN KEY (amount_unit_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE drug_strength ADD CONSTRAINT fpk_drug_strength_unit_2 FOREIGN KEY (numerator_unit_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE drug_strength ADD CONSTRAINT fpk_drug_strength_unit_3 FOREIGN KEY (denominator_unit_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE cohort_definition ADD CONSTRAINT fpk_cohort_definition_concept FOREIGN KEY (definition_type_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
|
||||||
|
/**************************
|
||||||
|
|
||||||
|
Standardized meta-data
|
||||||
|
|
||||||
|
***************************/
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/************************
|
||||||
|
|
||||||
|
Standardized clinical data
|
||||||
|
|
||||||
|
************************/
|
||||||
|
|
||||||
|
ALTER TABLE person ADD CONSTRAINT fpk_person_gender_concept FOREIGN KEY (gender_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE person ADD CONSTRAINT fpk_person_race_concept FOREIGN KEY (race_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE person ADD CONSTRAINT fpk_person_ethnicity_concept FOREIGN KEY (ethnicity_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE person ADD CONSTRAINT fpk_person_gender_concept_s FOREIGN KEY (gender_source_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE person ADD CONSTRAINT fpk_person_race_concept_s FOREIGN KEY (race_source_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE person ADD CONSTRAINT fpk_person_ethnicity_concept_s FOREIGN KEY (ethnicity_source_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE person ADD CONSTRAINT fpk_person_location FOREIGN KEY (location_id) REFERENCES location (location_id);
|
||||||
|
|
||||||
|
ALTER TABLE person ADD CONSTRAINT fpk_person_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
|
||||||
|
|
||||||
|
ALTER TABLE person ADD CONSTRAINT fpk_person_care_site FOREIGN KEY (care_site_id) REFERENCES care_site (care_site_id);
|
||||||
|
|
||||||
|
|
||||||
|
ALTER TABLE observation_period ADD CONSTRAINT fpk_observation_period_person FOREIGN KEY (person_id) REFERENCES person (person_id);
|
||||||
|
|
||||||
|
ALTER TABLE observation_period ADD CONSTRAINT fpk_observation_period_concept FOREIGN KEY (period_type_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
|
||||||
|
ALTER TABLE specimen ADD CONSTRAINT fpk_specimen_person FOREIGN KEY (person_id) REFERENCES person (person_id);
|
||||||
|
|
||||||
|
ALTER TABLE specimen ADD CONSTRAINT fpk_specimen_concept FOREIGN KEY (specimen_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE specimen ADD CONSTRAINT fpk_specimen_type_concept FOREIGN KEY (specimen_type_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE specimen ADD CONSTRAINT fpk_specimen_unit_concept FOREIGN KEY (unit_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE specimen ADD CONSTRAINT fpk_specimen_site_concept FOREIGN KEY (anatomic_site_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE specimen ADD CONSTRAINT fpk_specimen_status_concept FOREIGN KEY (disease_status_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
|
||||||
|
ALTER TABLE death ADD CONSTRAINT fpk_death_person FOREIGN KEY (person_id) REFERENCES person (person_id);
|
||||||
|
|
||||||
|
ALTER TABLE death ADD CONSTRAINT fpk_death_type_concept FOREIGN KEY (death_type_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE death ADD CONSTRAINT fpk_death_cause_concept FOREIGN KEY (cause_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE death ADD CONSTRAINT fpk_death_cause_concept_s FOREIGN KEY (cause_source_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
|
||||||
|
ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_person FOREIGN KEY (person_id) REFERENCES person (person_id);
|
||||||
|
|
||||||
|
ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_concept FOREIGN KEY (visit_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_type_concept FOREIGN KEY (visit_type_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
|
||||||
|
|
||||||
|
ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_care_site FOREIGN KEY (care_site_id) REFERENCES care_site (care_site_id);
|
||||||
|
|
||||||
|
ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_concept_s FOREIGN KEY (visit_source_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
|
||||||
|
ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_person FOREIGN KEY (person_id) REFERENCES person (person_id);
|
||||||
|
|
||||||
|
ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_concept FOREIGN KEY (procedure_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_type_concept FOREIGN KEY (procedure_type_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_modifier FOREIGN KEY (modifier_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
|
||||||
|
|
||||||
|
ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id);
|
||||||
|
|
||||||
|
ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_concept_s FOREIGN KEY (procedure_source_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
|
||||||
|
ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_person FOREIGN KEY (person_id) REFERENCES person (person_id);
|
||||||
|
|
||||||
|
ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_concept FOREIGN KEY (drug_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_type_concept FOREIGN KEY (drug_type_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_route_concept FOREIGN KEY (route_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_dose_unit_concept FOREIGN KEY (dose_unit_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
|
||||||
|
|
||||||
|
ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id);
|
||||||
|
|
||||||
|
ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_concept_s FOREIGN KEY (drug_source_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
|
||||||
|
ALTER TABLE device_exposure ADD CONSTRAINT fpk_device_person FOREIGN KEY (person_id) REFERENCES person (person_id);
|
||||||
|
|
||||||
|
ALTER TABLE device_exposure ADD CONSTRAINT fpk_device_concept FOREIGN KEY (device_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE device_exposure ADD CONSTRAINT fpk_device_type_concept FOREIGN KEY (device_type_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE device_exposure ADD CONSTRAINT fpk_device_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
|
||||||
|
|
||||||
|
ALTER TABLE device_exposure ADD CONSTRAINT fpk_device_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id);
|
||||||
|
|
||||||
|
ALTER TABLE device_exposure ADD CONSTRAINT fpk_device_concept_s FOREIGN KEY (device_source_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
|
||||||
|
ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_person FOREIGN KEY (person_id) REFERENCES person (person_id);
|
||||||
|
|
||||||
|
ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_concept FOREIGN KEY (condition_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_type_concept FOREIGN KEY (condition_type_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
|
||||||
|
|
||||||
|
ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id);
|
||||||
|
|
||||||
|
ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_concept_s FOREIGN KEY (condition_source_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
|
||||||
|
ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_person FOREIGN KEY (person_id) REFERENCES person (person_id);
|
||||||
|
|
||||||
|
ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_concept FOREIGN KEY (measurement_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_type_concept FOREIGN KEY (measurement_type_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_operator FOREIGN KEY (operator_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_value FOREIGN KEY (value_as_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_unit FOREIGN KEY (unit_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
|
||||||
|
|
||||||
|
ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id);
|
||||||
|
|
||||||
|
ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_concept_s FOREIGN KEY (measurement_source_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
|
||||||
|
ALTER TABLE note ADD CONSTRAINT fpk_note_person FOREIGN KEY (person_id) REFERENCES person (person_id);
|
||||||
|
|
||||||
|
ALTER TABLE note ADD CONSTRAINT fpk_note_type_concept FOREIGN KEY (note_type_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE note ADD CONSTRAINT fpk_note_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
|
||||||
|
|
||||||
|
ALTER TABLE note ADD CONSTRAINT fpk_note_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id);
|
||||||
|
|
||||||
|
|
||||||
|
ALTER TABLE observation ADD CONSTRAINT fpk_observation_person FOREIGN KEY (person_id) REFERENCES person (person_id);
|
||||||
|
|
||||||
|
ALTER TABLE observation ADD CONSTRAINT fpk_observation_concept FOREIGN KEY (observation_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE observation ADD CONSTRAINT fpk_observation_type_concept FOREIGN KEY (observation_type_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE observation ADD CONSTRAINT fpk_observation_value FOREIGN KEY (value_as_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE observation ADD CONSTRAINT fpk_observation_qualifier FOREIGN KEY (qualifier_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE observation ADD CONSTRAINT fpk_observation_unit FOREIGN KEY (unit_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE observation ADD CONSTRAINT fpk_observation_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
|
||||||
|
|
||||||
|
ALTER TABLE observation ADD CONSTRAINT fpk_observation_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id);
|
||||||
|
|
||||||
|
ALTER TABLE observation ADD CONSTRAINT fpk_observation_concept_s FOREIGN KEY (observation_source_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
|
||||||
|
ALTER TABLE fact_relationship ADD CONSTRAINT fpk_fact_domain_1 FOREIGN KEY (domain_concept_id_1) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE fact_relationship ADD CONSTRAINT fpk_fact_domain_2 FOREIGN KEY (domain_concept_id_2) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE fact_relationship ADD CONSTRAINT fpk_fact_relationship FOREIGN KEY (relationship_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/************************
|
||||||
|
|
||||||
|
Standardized health system data
|
||||||
|
|
||||||
|
************************/
|
||||||
|
|
||||||
|
ALTER TABLE care_site ADD CONSTRAINT fpk_care_site_location FOREIGN KEY (location_id) REFERENCES location (location_id);
|
||||||
|
|
||||||
|
ALTER TABLE care_site ADD CONSTRAINT fpk_care_site_place FOREIGN KEY (place_of_service_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
|
||||||
|
ALTER TABLE provider ADD CONSTRAINT fpk_provider_specialty FOREIGN KEY (specialty_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE provider ADD CONSTRAINT fpk_provider_care_site FOREIGN KEY (care_site_id) REFERENCES care_site (care_site_id);
|
||||||
|
|
||||||
|
ALTER TABLE provider ADD CONSTRAINT fpk_provider_gender FOREIGN KEY (gender_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE provider ADD CONSTRAINT fpk_provider_specialty_s FOREIGN KEY (specialty_source_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE provider ADD CONSTRAINT fpk_provider_gender_s FOREIGN KEY (gender_source_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/************************
|
||||||
|
|
||||||
|
Standardized health economics
|
||||||
|
|
||||||
|
************************/
|
||||||
|
|
||||||
|
ALTER TABLE payer_plan_period ADD CONSTRAINT fpk_payer_plan_period FOREIGN KEY (person_id) REFERENCES person (person_id);
|
||||||
|
|
||||||
|
|
||||||
|
ALTER TABLE visit_cost ADD CONSTRAINT fpk_visit_cost_id FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id);
|
||||||
|
|
||||||
|
ALTER TABLE visit_cost ADD CONSTRAINT fpk_visit_cost_currency FOREIGN KEY (currency_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE visit_cost ADD CONSTRAINT fpk_visit_cost_period FOREIGN KEY (payer_plan_period_id) REFERENCES payer_plan_period (payer_plan_period_id);
|
||||||
|
|
||||||
|
|
||||||
|
ALTER TABLE procedure_cost ADD CONSTRAINT fpk_procedure_cost_id FOREIGN KEY (procedure_occurrence_id) REFERENCES procedure_occurrence (procedure_occurrence_id);
|
||||||
|
|
||||||
|
ALTER TABLE procedure_cost ADD CONSTRAINT fpk_procedure_cost_currency FOREIGN KEY (currency_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE procedure_cost ADD CONSTRAINT fpk_procedure_cost_period FOREIGN KEY (payer_plan_period_id) REFERENCES payer_plan_period (payer_plan_period_id);
|
||||||
|
|
||||||
|
ALTER TABLE procedure_cost ADD CONSTRAINT fpk_procedure_cost_revenue FOREIGN KEY (revenue_code_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
|
||||||
|
ALTER TABLE drug_cost ADD CONSTRAINT fpk_drug_cost_id FOREIGN KEY (drug_exposure_id) REFERENCES drug_exposure (drug_exposure_id);
|
||||||
|
|
||||||
|
ALTER TABLE drug_cost ADD CONSTRAINT fpk_drug_cost_currency FOREIGN KEY (currency_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE drug_cost ADD CONSTRAINT fpk_drug_cost_period FOREIGN KEY (payer_plan_period_id) REFERENCES payer_plan_period (payer_plan_period_id);
|
||||||
|
|
||||||
|
|
||||||
|
ALTER TABLE device_cost ADD CONSTRAINT fpk_device_cost_id FOREIGN KEY (device_exposure_id) REFERENCES device_exposure (device_exposure_id);
|
||||||
|
|
||||||
|
ALTER TABLE device_cost ADD CONSTRAINT fpk_device_cost_currency FOREIGN KEY (currency_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE device_cost ADD CONSTRAINT fpk_device_cost_period FOREIGN KEY (payer_plan_period_id) REFERENCES payer_plan_period (payer_plan_period_id);
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/************************
|
||||||
|
|
||||||
|
Standardized derived elements
|
||||||
|
|
||||||
|
************************/
|
||||||
|
|
||||||
|
|
||||||
|
ALTER TABLE cohort ADD CONSTRAINT fpk_cohort_definition FOREIGN KEY (cohort_definition_id) REFERENCES cohort_definition (cohort_definition_id);
|
||||||
|
|
||||||
|
|
||||||
|
ALTER TABLE cohort_attribute ADD CONSTRAINT fpk_ca_cohort_definition FOREIGN KEY (cohort_definition_id) REFERENCES cohort_definition (cohort_definition_id);
|
||||||
|
|
||||||
|
ALTER TABLE cohort_attribute ADD CONSTRAINT fpk_ca_attribute_definition FOREIGN KEY (attribute_definition_id) REFERENCES attribute_definition (attribute_definition_id);
|
||||||
|
|
||||||
|
ALTER TABLE cohort_attribute ADD CONSTRAINT fpk_ca_value FOREIGN KEY (value_as_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
|
||||||
|
ALTER TABLE drug_era ADD CONSTRAINT fpk_drug_era_person FOREIGN KEY (person_id) REFERENCES person (person_id);
|
||||||
|
|
||||||
|
ALTER TABLE drug_era ADD CONSTRAINT fpk_drug_era_concept FOREIGN KEY (drug_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
|
||||||
|
ALTER TABLE dose_era ADD CONSTRAINT fpk_dose_era_person FOREIGN KEY (person_id) REFERENCES person (person_id);
|
||||||
|
|
||||||
|
ALTER TABLE dose_era ADD CONSTRAINT fpk_dose_era_concept FOREIGN KEY (drug_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE dose_era ADD CONSTRAINT fpk_dose_era_unit_concept FOREIGN KEY (unit_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
|
||||||
|
ALTER TABLE condition_era ADD CONSTRAINT fpk_condition_era_person FOREIGN KEY (person_id) REFERENCES person (person_id);
|
||||||
|
|
||||||
|
ALTER TABLE condition_era ADD CONSTRAINT fpk_condition_era_concept FOREIGN KEY (condition_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
|
@ -0,0 +1,709 @@
|
||||||
|
/*********************************************************************************
|
||||||
|
# Copyright 2014 Observational Health Data Sciences and Informatics
|
||||||
|
#
|
||||||
|
#
|
||||||
|
# Licensed under the Apache License, Version 2.0 (the "License");
|
||||||
|
# you may not use this file except in compliance with the License.
|
||||||
|
# You may obtain a copy of the License at
|
||||||
|
#
|
||||||
|
# http://www.apache.org/licenses/LICENSE-2.0
|
||||||
|
#
|
||||||
|
# Unless required by applicable law or agreed to in writing, software
|
||||||
|
# distributed under the License is distributed on an "AS IS" BASIS,
|
||||||
|
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
|
||||||
|
# See the License for the specific language governing permissions and
|
||||||
|
# limitations under the License.
|
||||||
|
********************************************************************************/
|
||||||
|
|
||||||
|
/************************
|
||||||
|
|
||||||
|
####### # # ####### ###### ##### ###### # # #######
|
||||||
|
# # ## ## # # # # # # # # ## ## # # #
|
||||||
|
# # # # # # # # # # # # # # # # # # # #
|
||||||
|
# # # # # # # ###### # # # # # # # # ######
|
||||||
|
# # # # # # # # # # # # # # #
|
||||||
|
# # # # # # # # # # # # # # # # #
|
||||||
|
####### # # ####### # ##### ###### # # ## #####
|
||||||
|
|
||||||
|
|
||||||
|
script to create OMOP common data model, version 5.0 for Oracle database
|
||||||
|
|
||||||
|
last revised: 12 Oct 2014
|
||||||
|
|
||||||
|
author: Patrick Ryan
|
||||||
|
|
||||||
|
|
||||||
|
*************************/
|
||||||
|
|
||||||
|
|
||||||
|
/************************
|
||||||
|
|
||||||
|
Standardized vocabulary
|
||||||
|
|
||||||
|
************************/
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE concept (
|
||||||
|
concept_id INTEGER NOT NULL,
|
||||||
|
concept_name VARCHAR(255) NOT NULL,
|
||||||
|
domain_id VARCHAR(20) NOT NULL,
|
||||||
|
vocabulary_id VARCHAR(20) NOT NULL,
|
||||||
|
concept_class_id VARCHAR(20) NOT NULL,
|
||||||
|
standard_concept VARCHAR(1) NULL,
|
||||||
|
concept_code VARCHAR(50) NOT NULL,
|
||||||
|
valid_start_date DATE NOT NULL,
|
||||||
|
valid_end_date DATE NOT NULL,
|
||||||
|
invalid_reason VARCHAR(1) NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE vocabulary (
|
||||||
|
vocabulary_id VARCHAR(20) NOT NULL,
|
||||||
|
vocabulary_name VARCHAR(255) NOT NULL,
|
||||||
|
vocabulary_reference VARCHAR(255) NULL,
|
||||||
|
vocabulary_version VARCHAR(255) NULL,
|
||||||
|
vocabulary_concept_id INTEGER NOT NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE domain (
|
||||||
|
domain_id VARCHAR(20) NOT NULL,
|
||||||
|
domain_name VARCHAR(255) NOT NULL,
|
||||||
|
domain_concept_id INTEGER NOT NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE concept_class (
|
||||||
|
concept_class_id VARCHAR(20) NOT NULL,
|
||||||
|
concept_class_name VARCHAR(255) NOT NULL,
|
||||||
|
concept_class_concept_id INTEGER NOT NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE concept_relationship (
|
||||||
|
concept_id_1 INTEGER NOT NULL,
|
||||||
|
concept_id_2 INTEGER NOT NULL,
|
||||||
|
relationship_id VARCHAR(20) NOT NULL,
|
||||||
|
valid_start_date DATE NOT NULL,
|
||||||
|
valid_end_date DATE NOT NULL,
|
||||||
|
invalid_reason VARCHAR(1) NULL)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE relationship (
|
||||||
|
relationship_id VARCHAR(20) NOT NULL,
|
||||||
|
relationship_name VARCHAR(255) NOT NULL,
|
||||||
|
is_hierarchical VARCHAR(1) NOT NULL,
|
||||||
|
defines_ancestry VARCHAR(1) NOT NULL,
|
||||||
|
reverse_relationship_id VARCHAR(20) NOT NULL,
|
||||||
|
relationship_concept_id INTEGER NOT NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE concept_synonym (
|
||||||
|
concept_id INTEGER NOT NULL,
|
||||||
|
concept_synonym_name VARCHAR(1000) NOT NULL,
|
||||||
|
language_concept_id INTEGER NOT NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE concept_ancestor (
|
||||||
|
ancestor_concept_id INTEGER NOT NULL,
|
||||||
|
descendant_concept_id INTEGER NOT NULL,
|
||||||
|
min_levels_of_separation INTEGER NOT NULL,
|
||||||
|
max_levels_of_separation INTEGER NOT NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE source_to_concept_map (
|
||||||
|
source_code VARCHAR(50) NOT NULL,
|
||||||
|
source_concept_id INTEGER NOT NULL,
|
||||||
|
source_vocabulary_id VARCHAR(20) NOT NULL,
|
||||||
|
source_code_description VARCHAR(255) NULL,
|
||||||
|
target_concept_id INTEGER NOT NULL,
|
||||||
|
target_vocabulary_id VARCHAR(20) NOT NULL,
|
||||||
|
valid_start_date DATE NOT NULL,
|
||||||
|
valid_end_date DATE NOT NULL,
|
||||||
|
invalid_reason VARCHAR(1) NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE drug_strength (
|
||||||
|
drug_concept_id INTEGER NOT NULL,
|
||||||
|
ingredient_concept_id INTEGER NOT NULL,
|
||||||
|
amount_value FLOAT NULL,
|
||||||
|
amount_unit_concept_id INTEGER NULL,
|
||||||
|
numerator_value FLOAT NULL,
|
||||||
|
numerator_unit_concept_id INTEGER NULL,
|
||||||
|
denominator_unit_concept_id INTEGER NULL,
|
||||||
|
valid_start_date DATE NOT NULL,
|
||||||
|
valid_end_date DATE NOT NULL,
|
||||||
|
invalid_reason VARCHAR(1) NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE cohort_definition (
|
||||||
|
cohort_definition_id INTEGER NOT NULL,
|
||||||
|
cohort_definition_name VARCHAR(255) NOT NULL,
|
||||||
|
cohort_definition_description CLOB NULL,
|
||||||
|
definition_type_concept_id INTEGER NOT NULL,
|
||||||
|
cohort_definition_syntax CLOB NULL,
|
||||||
|
subject_concept_id INTEGER NOT NULL,
|
||||||
|
cohort_initiation_date DATE NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE attribute_definition (
|
||||||
|
attribute_definition_id INTEGER NOT NULL,
|
||||||
|
attribute_name VARCHAR(255) NOT NULL,
|
||||||
|
attribute_description CLOB NULL,
|
||||||
|
attribute_type_concept_id INTEGER NOT NULL,
|
||||||
|
attribute_syntax CLOB NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
/**************************
|
||||||
|
|
||||||
|
Standardized meta-data
|
||||||
|
|
||||||
|
***************************/
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE cdm_source
|
||||||
|
(
|
||||||
|
cdm_source_name VARCHAR(255) NOT NULL,
|
||||||
|
cdm_source_abbreviation VARCHAR(25) NULL,
|
||||||
|
cdm_holder VARCHAR(255) NULL,
|
||||||
|
source_description CLOB NULL,
|
||||||
|
source_documentation_reference VARCHAR(255) NULL,
|
||||||
|
cdm_etl_reference VARCHAR(255) NULL,
|
||||||
|
source_release_date DATE NULL,
|
||||||
|
cdm_release_date DATE NULL,
|
||||||
|
cdm_version VARCHAR(10) NULL,
|
||||||
|
vocabulary_version VARCHAR(20) NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/************************
|
||||||
|
|
||||||
|
Standardized clinical data
|
||||||
|
|
||||||
|
************************/
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE person
|
||||||
|
(
|
||||||
|
person_id INTEGER NOT NULL ,
|
||||||
|
gender_concept_id INTEGER NOT NULL ,
|
||||||
|
year_of_birth INTEGER NOT NULL ,
|
||||||
|
month_of_birth INTEGER NULL,
|
||||||
|
day_of_birth INTEGER NULL,
|
||||||
|
time_of_birth VARCHAR(10) NULL,
|
||||||
|
race_concept_id INTEGER NOT NULL,
|
||||||
|
ethnicity_concept_id INTEGER NOT NULL,
|
||||||
|
location_id INTEGER NULL,
|
||||||
|
provider_id INTEGER NULL,
|
||||||
|
care_site_id INTEGER NULL,
|
||||||
|
person_source_value VARCHAR(50) NULL,
|
||||||
|
gender_source_value VARCHAR(50) NULL,
|
||||||
|
gender_source_concept_id INTEGER NULL,
|
||||||
|
race_source_value VARCHAR(50) NULL,
|
||||||
|
race_source_concept_id INTEGER NULL,
|
||||||
|
ethnicity_source_value VARCHAR(50) NULL,
|
||||||
|
ethnicity_source_concept_id INTEGER NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE observation_period
|
||||||
|
(
|
||||||
|
observation_period_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
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE specimen
|
||||||
|
(
|
||||||
|
specimen_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 ,
|
||||||
|
specimen_time VARCHAR(10) NULL ,
|
||||||
|
quantity FLOAT NULL ,
|
||||||
|
unit_concept_id INTEGER NULL ,
|
||||||
|
anatomic_site_concept_id INTEGER NULL ,
|
||||||
|
disease_status_concept_id INTEGER NULL ,
|
||||||
|
specimen_source_id VARCHAR(50) NULL ,
|
||||||
|
specimen_source_value VARCHAR(50) NULL ,
|
||||||
|
unit_source_value VARCHAR(50) NULL ,
|
||||||
|
anatomic_site_source_value VARCHAR(50) NULL ,
|
||||||
|
disease_status_source_value VARCHAR(50) NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE death
|
||||||
|
(
|
||||||
|
person_id INTEGER NOT NULL ,
|
||||||
|
death_date DATE NOT NULL ,
|
||||||
|
death_type_concept_id INTEGER NOT NULL ,
|
||||||
|
cause_concept_id INTEGER NULL ,
|
||||||
|
cause_source_value VARCHAR(50) NULL,
|
||||||
|
cause_source_concept_id INTEGER NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE visit_occurrence
|
||||||
|
(
|
||||||
|
visit_occurrence_id INTEGER NOT NULL ,
|
||||||
|
person_id INTEGER NOT NULL ,
|
||||||
|
visit_concept_id INTEGER NOT NULL ,
|
||||||
|
visit_start_date DATE NOT NULL ,
|
||||||
|
visit_start_time VARCHAR(10) NULL ,
|
||||||
|
visit_end_date DATE NOT NULL ,
|
||||||
|
visit_end_time VARCHAR(10) NULL ,
|
||||||
|
visit_type_concept_id INTEGER NOT NULL ,
|
||||||
|
provider_id INTEGER NULL,
|
||||||
|
care_site_id INTEGER NULL,
|
||||||
|
visit_source_value VARCHAR(50) NULL,
|
||||||
|
visit_source_concept_id INTEGER NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE procedure_occurrence
|
||||||
|
(
|
||||||
|
procedure_occurrence_id INTEGER NOT NULL ,
|
||||||
|
person_id INTEGER NOT NULL ,
|
||||||
|
procedure_concept_id INTEGER NOT NULL ,
|
||||||
|
procedure_date DATE NOT NULL ,
|
||||||
|
procedure_type_concept_id INTEGER NOT NULL ,
|
||||||
|
modifier_concept_id INTEGER NULL ,
|
||||||
|
quantity INTEGER NULL ,
|
||||||
|
provider_id INTEGER NULL ,
|
||||||
|
visit_occurrence_id INTEGER NULL ,
|
||||||
|
procedure_source_value VARCHAR(50) NULL ,
|
||||||
|
procedure_source_concept_id INTEGER NULL ,
|
||||||
|
qualifier_source_value VARCHAR(50) NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE drug_exposure
|
||||||
|
(
|
||||||
|
drug_exposure_id INTEGER NOT NULL ,
|
||||||
|
person_id INTEGER NOT NULL ,
|
||||||
|
drug_concept_id INTEGER NOT NULL ,
|
||||||
|
drug_exposure_start_date DATE NOT NULL ,
|
||||||
|
drug_exposure_end_date DATE NULL ,
|
||||||
|
drug_type_concept_id INTEGER NOT NULL ,
|
||||||
|
stop_reason VARCHAR(20) NULL ,
|
||||||
|
refills INTEGER NULL ,
|
||||||
|
quantity FLOAT NULL ,
|
||||||
|
days_supply INTEGER NULL ,
|
||||||
|
sig CLOB NULL ,
|
||||||
|
route_concept_id INTEGER NULL ,
|
||||||
|
effective_drug_dose FLOAT NULL ,
|
||||||
|
dose_unit_concept_id INTEGER NULL ,
|
||||||
|
lot_number VARCHAR(50) NULL ,
|
||||||
|
provider_id INTEGER NULL ,
|
||||||
|
visit_occurrence_id INTEGER NULL ,
|
||||||
|
drug_source_value VARCHAR(50) NULL ,
|
||||||
|
drug_source_concept_id INTEGER NULL ,
|
||||||
|
route_source_value VARCHAR(50) NULL ,
|
||||||
|
dose_unit_source_value VARCHAR(50) NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE device_exposure
|
||||||
|
(
|
||||||
|
device_exposure_id INTEGER NOT NULL ,
|
||||||
|
person_id INTEGER NOT NULL ,
|
||||||
|
device_concept_id INTEGER NOT NULL ,
|
||||||
|
device_exposure_start_date DATE NOT NULL ,
|
||||||
|
device_exposure_end_date DATE NULL ,
|
||||||
|
device_type_concept_id INTEGER NOT NULL ,
|
||||||
|
unique_device_id VARCHAR(50) NULL ,
|
||||||
|
quantity INTEGER NULL ,
|
||||||
|
provider_id INTEGER NULL ,
|
||||||
|
visit_occurrence_id INTEGER NULL ,
|
||||||
|
device_source_value VARCHAR(100) NULL ,
|
||||||
|
device_source_concept_id INTEGER NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE condition_occurrence
|
||||||
|
(
|
||||||
|
condition_occurrence_id INTEGER NOT NULL ,
|
||||||
|
person_id INTEGER NOT NULL ,
|
||||||
|
condition_concept_id INTEGER NOT NULL ,
|
||||||
|
condition_start_date DATE NOT NULL ,
|
||||||
|
condition_end_date DATE NULL ,
|
||||||
|
condition_type_concept_id INTEGER NOT NULL ,
|
||||||
|
stop_reason VARCHAR(20) NULL ,
|
||||||
|
provider_id INTEGER NULL ,
|
||||||
|
visit_occurrence_id INTEGER NULL ,
|
||||||
|
condition_source_value VARCHAR(50) NULL ,
|
||||||
|
condition_source_concept_id INTEGER NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE measurement
|
||||||
|
(
|
||||||
|
measurement_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 ,
|
||||||
|
measurement_type_concept_id INTEGER NOT NULL ,
|
||||||
|
operator_concept_id INTEGER NULL ,
|
||||||
|
value_as_number FLOAT NULL ,
|
||||||
|
value_as_concept_id INTEGER NULL ,
|
||||||
|
unit_concept_id INTEGER NULL ,
|
||||||
|
range_low FLOAT NULL ,
|
||||||
|
range_high FLOAT NULL ,
|
||||||
|
provider_id INTEGER NULL ,
|
||||||
|
visit_occurrence_id INTEGER NULL ,
|
||||||
|
measurement_source_value VARCHAR(50) NULL ,
|
||||||
|
measurement_source_concept_id INTEGER NULL ,
|
||||||
|
unit_source_value VARCHAR(50) NULL ,
|
||||||
|
value_source_value VARCHAR(50) NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE note
|
||||||
|
(
|
||||||
|
note_id INTEGER NOT NULL ,
|
||||||
|
person_id INTEGER NOT NULL ,
|
||||||
|
note_date DATE NOT NULL ,
|
||||||
|
note_time VARCHAR(10) NULL ,
|
||||||
|
note_type_concept_id INTEGER NOT NULL ,
|
||||||
|
note_text CLOB NOT NULL ,
|
||||||
|
provider_id INTEGER NULL ,
|
||||||
|
visit_occurrence_id INTEGER NULL ,
|
||||||
|
note_source_value VARCHAR(50) NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE observation
|
||||||
|
(
|
||||||
|
observation_id INTEGER NOT NULL ,
|
||||||
|
person_id INTEGER NOT NULL ,
|
||||||
|
observation_concept_id INTEGER NOT NULL ,
|
||||||
|
observation_date DATE NOT NULL ,
|
||||||
|
observation_time VARCHAR(10) NULL ,
|
||||||
|
observation_type_concept_id INTEGER NOT NULL ,
|
||||||
|
value_as_number FLOAT NULL ,
|
||||||
|
value_as_string VARCHAR(60) NULL ,
|
||||||
|
value_as_concept_id INTEGER NULL ,
|
||||||
|
qualifier_concept_id INTEGER NULL ,
|
||||||
|
unit_concept_id INTEGER NULL ,
|
||||||
|
provider_id INTEGER NULL ,
|
||||||
|
visit_occurrence_id INTEGER NULL ,
|
||||||
|
observation_source_value VARCHAR(50) NULL ,
|
||||||
|
observation_source_concept_id INTEGER NULL ,
|
||||||
|
unit_source_value VARCHAR(50) NULL ,
|
||||||
|
qualifier_source_value VARCHAR(50) NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE fact_relationship
|
||||||
|
(
|
||||||
|
domain_concept_id_1 INTEGER NOT NULL ,
|
||||||
|
fact_id_1 INTEGER NOT NULL ,
|
||||||
|
domain_concept_id_2 INTEGER NOT NULL ,
|
||||||
|
fact_id_2 INTEGER NOT NULL ,
|
||||||
|
relationship_concept_id INTEGER NOT NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/************************
|
||||||
|
|
||||||
|
Standardized health system data
|
||||||
|
|
||||||
|
************************/
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE location
|
||||||
|
(
|
||||||
|
location_id INTEGER NOT NULL ,
|
||||||
|
address_1 VARCHAR(50) NULL ,
|
||||||
|
address_2 VARCHAR(50) NULL ,
|
||||||
|
city VARCHAR(50) NULL ,
|
||||||
|
state VARCHAR(2) NULL ,
|
||||||
|
zip VARCHAR(9) NULL ,
|
||||||
|
county VARCHAR(20) NULL ,
|
||||||
|
location_source_value VARCHAR(50) NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE care_site
|
||||||
|
(
|
||||||
|
care_site_id INTEGER NOT NULL ,
|
||||||
|
care_site_name VARCHAR(255) NULL ,
|
||||||
|
place_of_service_concept_id INTEGER NULL ,
|
||||||
|
location_id INTEGER NULL ,
|
||||||
|
care_site_source_value VARCHAR(50) NULL ,
|
||||||
|
place_of_service_source_value VARCHAR(50) NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE provider
|
||||||
|
(
|
||||||
|
provider_id INTEGER NOT NULL ,
|
||||||
|
provider_name VARCHAR(255) NULL ,
|
||||||
|
NPI VARCHAR(20) NULL ,
|
||||||
|
DEA VARCHAR(20) NULL ,
|
||||||
|
specialty_concept_id INTEGER NULL ,
|
||||||
|
care_site_id INTEGER NULL ,
|
||||||
|
year_of_birth INTEGER NULL ,
|
||||||
|
gender_concept_id INTEGER NULL ,
|
||||||
|
provider_source_value VARCHAR(50) NULL ,
|
||||||
|
specialty_source_value VARCHAR(50) NULL ,
|
||||||
|
specialty_source_concept_id INTEGER NULL ,
|
||||||
|
gender_source_value VARCHAR(50) NULL ,
|
||||||
|
gender_source_concept_id INTEGER NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/************************
|
||||||
|
|
||||||
|
Standardized health economics
|
||||||
|
|
||||||
|
************************/
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE payer_plan_period
|
||||||
|
(
|
||||||
|
payer_plan_period_id INTEGER NOT NULL ,
|
||||||
|
person_id INTEGER NOT NULL ,
|
||||||
|
payer_plan_period_start_date DATE NOT NULL ,
|
||||||
|
payer_plan_period_end_date DATE NOT NULL ,
|
||||||
|
payer_source_value VARCHAR (50) NULL ,
|
||||||
|
plan_source_value VARCHAR (50) NULL ,
|
||||||
|
family_source_value VARCHAR (50) NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE visit_cost
|
||||||
|
(
|
||||||
|
visit_cost_id INTEGER NOT NULL ,
|
||||||
|
visit_occurrence_id INTEGER NOT NULL ,
|
||||||
|
currency_concept_id INTEGER NULL ,
|
||||||
|
paid_copay FLOAT NULL ,
|
||||||
|
paid_coinsurance FLOAT NULL ,
|
||||||
|
paid_toward_deductible FLOAT NULL ,
|
||||||
|
paid_by_payer FLOAT NULL ,
|
||||||
|
paid_by_coordination_benefits FLOAT NULL ,
|
||||||
|
total_out_of_pocket FLOAT NULL ,
|
||||||
|
total_paid FLOAT NULL ,
|
||||||
|
payer_plan_period_id INTEGER NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE procedure_cost
|
||||||
|
(
|
||||||
|
procedure_cost_id INTEGER NOT NULL ,
|
||||||
|
procedure_occurrence_id INTEGER NOT NULL ,
|
||||||
|
currency_concept_id INTEGER NULL ,
|
||||||
|
paid_copay FLOAT NULL ,
|
||||||
|
paid_coinsurance FLOAT NULL ,
|
||||||
|
paid_toward_deductible FLOAT NULL ,
|
||||||
|
paid_by_payer FLOAT NULL ,
|
||||||
|
paid_by_coordination_benefits FLOAT NULL ,
|
||||||
|
total_out_of_pocket FLOAT NULL ,
|
||||||
|
total_paid FLOAT NULL ,
|
||||||
|
revenue_code_concept_id INTEGER NULL ,
|
||||||
|
payer_plan_period_id INTEGER NULL ,
|
||||||
|
revenue_code_source_value VARCHAR(50) NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE drug_cost
|
||||||
|
(
|
||||||
|
drug_cost_id INTEGER NOT NULL ,
|
||||||
|
drug_exposure_id INTEGER NOT NULL ,
|
||||||
|
currency_concept_id INTEGER NULL ,
|
||||||
|
paid_copay FLOAT NULL ,
|
||||||
|
paid_coinsurance FLOAT NULL ,
|
||||||
|
paid_toward_deductible FLOAT NULL ,
|
||||||
|
paid_by_payer FLOAT NULL ,
|
||||||
|
paid_by_coordination_benefits FLOAT NULL ,
|
||||||
|
total_out_of_pocket FLOAT NULL ,
|
||||||
|
total_paid FLOAT NULL ,
|
||||||
|
ingredient_cost FLOAT NULL ,
|
||||||
|
dispensing_fee FLOAT NULL ,
|
||||||
|
average_wholesale_price FLOAT NULL ,
|
||||||
|
payer_plan_period_id INTEGER NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE device_cost
|
||||||
|
(
|
||||||
|
device_cost_id INTEGER NOT NULL ,
|
||||||
|
device_exposure_id INTEGER NOT NULL ,
|
||||||
|
currency_concept_id INTEGER NULL ,
|
||||||
|
paid_copay FLOAT NULL ,
|
||||||
|
paid_coinsurance FLOAT NULL ,
|
||||||
|
paid_toward_deductible FLOAT NULL ,
|
||||||
|
paid_by_payer FLOAT NULL ,
|
||||||
|
paid_by_coordination_benefits FLOAT NULL ,
|
||||||
|
total_out_of_pocket FLOAT NULL ,
|
||||||
|
total_paid FLOAT NULL ,
|
||||||
|
payer_plan_period_id INTEGER NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/************************
|
||||||
|
|
||||||
|
Standardized derived elements
|
||||||
|
|
||||||
|
************************/
|
||||||
|
|
||||||
|
CREATE TABLE cohort
|
||||||
|
(
|
||||||
|
cohort_definition_id INTEGER NOT NULL ,
|
||||||
|
subject_id INTEGER NOT NULL ,
|
||||||
|
cohort_start_date DATE NOT NULL ,
|
||||||
|
cohort_end_date DATE NOT NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE cohort_attribute
|
||||||
|
(
|
||||||
|
cohort_definition_id INTEGER NOT NULL ,
|
||||||
|
cohort_start_date DATE NOT NULL ,
|
||||||
|
cohort_end_date DATE NOT NULL ,
|
||||||
|
subject_id INTEGER NOT NULL ,
|
||||||
|
attribute_definition_id INTEGER NOT NULL ,
|
||||||
|
value_as_number FLOAT NULL ,
|
||||||
|
value_as_concept_id INTEGER NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE drug_era
|
||||||
|
(
|
||||||
|
drug_era_id INTEGER NOT NULL ,
|
||||||
|
person_id INTEGER NOT NULL ,
|
||||||
|
drug_concept_id INTEGER NOT NULL ,
|
||||||
|
drug_era_start_date DATE NOT NULL ,
|
||||||
|
drug_era_end_date DATE NOT NULL ,
|
||||||
|
drug_exposure_count INTEGER NULL ,
|
||||||
|
gap_days INTEGER NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE dose_era
|
||||||
|
(
|
||||||
|
dose_era_id INTEGER NOT NULL ,
|
||||||
|
person_id INTEGER NOT NULL ,
|
||||||
|
drug_concept_id INTEGER NOT NULL ,
|
||||||
|
unit_concept_id INTEGER NOT NULL ,
|
||||||
|
dose_value FLOAT NOT NULL ,
|
||||||
|
dose_era_start_date DATE NOT NULL ,
|
||||||
|
dose_era_end_date DATE NOT NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE condition_era
|
||||||
|
(
|
||||||
|
condition_era_id INTEGER NOT NULL ,
|
||||||
|
person_id INTEGER NOT NULL ,
|
||||||
|
condition_concept_id INTEGER NOT NULL ,
|
||||||
|
condition_era_start_date DATE NOT NULL ,
|
||||||
|
condition_era_end_date DATE NOT NULL ,
|
||||||
|
condition_occurrence_count INTEGER NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
@ -0,0 +1,168 @@
|
||||||
|
/*********************************************************************************
|
||||||
|
# Copyright 2014 Observational Health Data Sciences and Informatics
|
||||||
|
#
|
||||||
|
#
|
||||||
|
# Licensed under the Apache License, Version 2.0 (the "License");
|
||||||
|
# you may not use this file except in compliance with the License.
|
||||||
|
# You may obtain a copy of the License at
|
||||||
|
#
|
||||||
|
# http://www.apache.org/licenses/LICENSE-2.0
|
||||||
|
#
|
||||||
|
# Unless required by applicable law or agreed to in writing, software
|
||||||
|
# distributed under the License is distributed on an "AS IS" BASIS,
|
||||||
|
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
|
||||||
|
# See the License for the specific language governing permissions and
|
||||||
|
# limitations under the License.
|
||||||
|
********************************************************************************/
|
||||||
|
|
||||||
|
/************************
|
||||||
|
|
||||||
|
####### # # ####### ###### ##### ###### # # ####### ###
|
||||||
|
# # ## ## # # # # # # # # ## ## # # # # # # ##### ###### # # ###### ####
|
||||||
|
# # # # # # # # # # # # # # # # # # # # # ## # # # # # # # #
|
||||||
|
# # # # # # # ###### # # # # # # # # ###### # # # # # # ##### ## ##### ####
|
||||||
|
# # # # # # # # # # # # # # # # # # # # # # ## # #
|
||||||
|
# # # # # # # # # # # # # # # # # # # ## # # # # # # # #
|
||||||
|
####### # # ####### # ##### ###### # # ## ##### ### # # ##### ###### # # ###### ####
|
||||||
|
|
||||||
|
|
||||||
|
script to create the required indexes within OMOP common data model, version 5.0 for Oracle database
|
||||||
|
|
||||||
|
last revised: 12 Oct 2014
|
||||||
|
|
||||||
|
author: Patrick Ryan
|
||||||
|
|
||||||
|
description: These indices are considered a minimal requirement to ensure adequate performance of analyses.
|
||||||
|
|
||||||
|
*************************/
|
||||||
|
|
||||||
|
|
||||||
|
/************************
|
||||||
|
|
||||||
|
Standardized vocabulary
|
||||||
|
|
||||||
|
************************/
|
||||||
|
|
||||||
|
CREATE INDEX idx_concept_code ON concept (concept_code ASC);
|
||||||
|
CREATE INDEX idx_concept_vocabluary_id ON concept (vocabulary_id ASC);
|
||||||
|
CREATE INDEX idx_concept_domain_id ON concept (domain_id ASC);
|
||||||
|
CREATE INDEX idx_concept_class_id ON concept (concept_class_id ASC);
|
||||||
|
|
||||||
|
CREATE INDEX idx_concept_relationship_id_1 ON concept_relationship (concept_id_1 ASC);
|
||||||
|
CREATE INDEX idx_concept_relationship_id_2 ON concept_relationship (concept_id_2 ASC);
|
||||||
|
CREATE INDEX idx_concept_relationship_id_3 ON concept_relationship (relationship_id ASC);
|
||||||
|
|
||||||
|
CREATE INDEX idx_concept_synonym_id ON concept_synonym (concept_id ASC);
|
||||||
|
|
||||||
|
CREATE INDEX idx_concept_ancestor_id_1 ON concept_ancestor (ancestor_concept_id ASC);
|
||||||
|
CREATE INDEX idx_concept_ancestor_id_2 ON concept_ancestor (descendant_concept_id ASC);
|
||||||
|
|
||||||
|
CREATE INDEX idx_source_to_concept_map_id_3 ON source_to_concept_map (target_concept_id ASC);
|
||||||
|
CREATE INDEX idx_source_to_concept_map_id_1 ON source_to_concept_map (source_vocabulary_id ASC);
|
||||||
|
CREATE INDEX idx_source_to_concept_map_id_2 ON source_to_concept_map (target_vocabulary_id ASC);
|
||||||
|
CREATE INDEX idx_source_to_concept_map_code ON source_to_concept_map (source_code ASC);
|
||||||
|
|
||||||
|
CREATE INDEX idx_drug_strength_id_1 ON drug_strength (drug_concept_id ASC);
|
||||||
|
CREATE INDEX idx_drug_strength_id_2 ON drug_strength (ingredient_concept_id ASC);
|
||||||
|
|
||||||
|
/**************************
|
||||||
|
|
||||||
|
Standardized meta-data
|
||||||
|
|
||||||
|
***************************/
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/************************
|
||||||
|
|
||||||
|
Standardized clinical data
|
||||||
|
|
||||||
|
************************/
|
||||||
|
|
||||||
|
CREATE INDEX idx_observation_period_id ON observation_period (person_id ASC);
|
||||||
|
|
||||||
|
CREATE INDEX idx_specimen_person_id ON specimen (person_id ASC);
|
||||||
|
CREATE INDEX idx_specimen_concept_id ON specimen (specimen_concept_id ASC);
|
||||||
|
|
||||||
|
CREATE INDEX idx_visit_person_id ON visit_occurrence (person_id ASC);
|
||||||
|
CREATE INDEX idx_visit_concept_id ON visit_occurrence (visit_concept_id ASC);
|
||||||
|
|
||||||
|
CREATE INDEX idx_procedure_person_id ON procedure_occurrence (person_id ASC);
|
||||||
|
CREATE INDEX idx_procedure_concept_id ON procedure_occurrence (procedure_concept_id ASC);
|
||||||
|
CREATE INDEX idx_procedure_visit_id ON procedure_occurrence (visit_occurrence_id ASC);
|
||||||
|
|
||||||
|
CREATE INDEX idx_drug_person_id ON drug_exposure (person_id ASC);
|
||||||
|
CREATE INDEX idx_drug_concept_id ON drug_exposure (drug_concept_id ASC);
|
||||||
|
CREATE INDEX idx_drug_visit_id ON drug_exposure (visit_occurrence_id ASC);
|
||||||
|
|
||||||
|
CREATE INDEX idx_device_person_id ON device_exposure (person_id ASC);
|
||||||
|
CREATE INDEX idx_device_concept_id ON device_exposure (device_concept_id ASC);
|
||||||
|
CREATE INDEX idx_device_visit_id ON device_exposure (visit_occurrence_id ASC);
|
||||||
|
|
||||||
|
CREATE INDEX idx_condition_person_id ON condition_occurrence (person_id ASC);
|
||||||
|
CREATE INDEX idx_condition_concept_id ON condition_occurrence (condition_concept_id ASC);
|
||||||
|
CREATE INDEX idx_condition_visit_id ON condition_occurrence (visit_occurrence_id ASC);
|
||||||
|
|
||||||
|
CREATE INDEX idx_measurement_person_id ON measurement (person_id ASC);
|
||||||
|
CREATE INDEX idx_measurement_concept_id ON measurement (measurement_concept_id ASC);
|
||||||
|
CREATE INDEX idx_measurement_visit_id ON measurement (visit_occurrence_id ASC);
|
||||||
|
|
||||||
|
CREATE INDEX idx_note_person_id ON note (person_id ASC);
|
||||||
|
CREATE INDEX idx_note_concept_id ON note (note_type_concept_id ASC);
|
||||||
|
CREATE INDEX idx_note_visit_id ON note (visit_occurrence_id ASC);
|
||||||
|
|
||||||
|
CREATE INDEX idx_observation_person_id ON observation (person_id ASC);
|
||||||
|
CREATE INDEX idx_observation_concept_id ON observation (observation_concept_id ASC);
|
||||||
|
CREATE INDEX idx_observation_visit_id ON observation (visit_occurrence_id ASC);
|
||||||
|
|
||||||
|
CREATE INDEX idx_fact_relationship_id_1 ON fact_relationship (domain_concept_id_1 ASC);
|
||||||
|
CREATE INDEX idx_fact_relationship_id_2 ON fact_relationship (domain_concept_id_2 ASC);
|
||||||
|
CREATE INDEX idx_fact_relationship_id_3 ON fact_relationship (relationship_concept_id ASC);
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/************************
|
||||||
|
|
||||||
|
Standardized health system data
|
||||||
|
|
||||||
|
************************/
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/************************
|
||||||
|
|
||||||
|
Standardized health economics
|
||||||
|
|
||||||
|
************************/
|
||||||
|
|
||||||
|
CREATE INDEX idx_period_person_id ON payer_plan_period (person_id ASC);
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/************************
|
||||||
|
|
||||||
|
Standardized derived elements
|
||||||
|
|
||||||
|
************************/
|
||||||
|
|
||||||
|
CREATE INDEX idx_cohort_subject_id ON cohort (subject_id ASC);
|
||||||
|
CREATE INDEX idx_cohort_c_definition_id ON cohort (cohort_definition_id ASC);
|
||||||
|
|
||||||
|
CREATE INDEX idx_ca_subject_id ON cohort_attribute (subject_id ASC);
|
||||||
|
CREATE INDEX idx_ca_definition_id ON cohort_attribute (cohort_definition_id ASC);
|
||||||
|
|
||||||
|
CREATE INDEX idx_drug_era_person_id ON drug_era (person_id ASC);
|
||||||
|
CREATE INDEX idx_drug_era_concept_id ON drug_era (drug_concept_id ASC);
|
||||||
|
|
||||||
|
CREATE INDEX idx_dose_era_person_id ON dose_era (person_id ASC);
|
||||||
|
CREATE INDEX idx_dose_era_concept_id ON dose_era (drug_concept_id ASC);
|
||||||
|
|
||||||
|
CREATE INDEX idx_condition_era_person_id ON condition_era (person_id ASC);
|
||||||
|
CREATE INDEX idx_condition_era_concept_id ON condition_era (condition_concept_id ASC);
|
||||||
|
|
||||||
|
|
@ -0,0 +1,188 @@
|
||||||
|
/*********************************************************************************
|
||||||
|
# Copyright 2014 Observational Health Data Sciences and Informatics
|
||||||
|
#
|
||||||
|
#
|
||||||
|
# Licensed under the Apache License, Version 2.0 (the "License");
|
||||||
|
# you may not use this file except in compliance with the License.
|
||||||
|
# You may obtain a copy of the License at
|
||||||
|
#
|
||||||
|
# http://www.apache.org/licenses/LICENSE-2.0
|
||||||
|
#
|
||||||
|
# Unless required by applicable law or agreed to in writing, software
|
||||||
|
# distributed under the License is distributed on an "AS IS" BASIS,
|
||||||
|
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
|
||||||
|
# See the License for the specific language governing permissions and
|
||||||
|
# limitations under the License.
|
||||||
|
********************************************************************************/
|
||||||
|
|
||||||
|
/************************
|
||||||
|
|
||||||
|
####### # # ####### ###### ##### ###### # # ####### ###
|
||||||
|
# # ## ## # # # # # # # # ## ## # # # # # # ##### ###### # # ###### ####
|
||||||
|
# # # # # # # # # # # # # # # # # # # # # ## # # # # # # # #
|
||||||
|
# # # # # # # ###### # # # # # # # # ###### # # # # # # ##### ## ##### ####
|
||||||
|
# # # # # # # # # # # # # # # # # # # # # # ## # #
|
||||||
|
# # # # # # # # # # # # # # # # # # # ## # # # # # # # #
|
||||||
|
####### # # ####### # ##### ###### # # ## ##### ### # # ##### ###### # # ###### ####
|
||||||
|
|
||||||
|
|
||||||
|
script to create the required indexes within OMOP common data model, version 5.0 for Oracle database
|
||||||
|
|
||||||
|
last revised: 12 Oct 2014
|
||||||
|
|
||||||
|
author: Patrick Ryan
|
||||||
|
|
||||||
|
description: These indices are considered a minimal requirement to ensure adequate performance of analyses.
|
||||||
|
|
||||||
|
*************************/
|
||||||
|
|
||||||
|
|
||||||
|
/************************
|
||||||
|
|
||||||
|
Standardized vocabulary
|
||||||
|
|
||||||
|
************************/
|
||||||
|
|
||||||
|
CREATE UNIQUE INDEX idx_concept_concept_id ON concept (concept_id ASC);
|
||||||
|
|
||||||
|
CREATE INDEX idx_concept_code ON concept (concept_code ASC);
|
||||||
|
CREATE INDEX idx_concept_vocabluary_id ON concept (vocabulary_id ASC);
|
||||||
|
CREATE INDEX idx_concept_domain_id ON concept (domain_id ASC);
|
||||||
|
CREATE INDEX idx_concept_class_id ON concept (concept_class_id ASC);
|
||||||
|
|
||||||
|
CREATE UNIQUE INDEX idx_vocabulary_vocabulary_id ON vocabulary (vocabulary_id ASC);
|
||||||
|
|
||||||
|
CREATE UNIQUE INDEX idx_domain_domain_id ON domain (domain_id ASC);
|
||||||
|
|
||||||
|
CREATE UNIQUE INDEX idx_concept_class_class_id ON concept_class (concept_class_id ASC);
|
||||||
|
|
||||||
|
CREATE INDEX idx_concept_relationship_id_1 ON concept_relationship (concept_id_1 ASC);
|
||||||
|
CREATE INDEX idx_concept_relationship_id_2 ON concept_relationship (concept_id_2 ASC);
|
||||||
|
CREATE INDEX idx_concept_relationship_id_3 ON concept_relationship (relationship_id ASC);
|
||||||
|
|
||||||
|
CREATE UNIQUE INDEX idx_relationship_rel_id ON relationship (relationship_id ASC);
|
||||||
|
|
||||||
|
CREATE INDEX idx_concept_synonym_id ON concept_synonym (concept_id ASC);
|
||||||
|
|
||||||
|
CREATE INDEX idx_concept_ancestor_id_1 ON concept_ancestor (ancestor_concept_id ASC);
|
||||||
|
CREATE INDEX idx_concept_ancestor_id_2 ON concept_ancestor (descendant_concept_id ASC);
|
||||||
|
|
||||||
|
CREATE INDEX idx_source_to_concept_map_id_3 ON source_to_concept_map (target_concept_id ASC);
|
||||||
|
CREATE INDEX idx_source_to_concept_map_id_1 ON source_to_concept_map (source_vocabulary_id ASC);
|
||||||
|
CREATE INDEX idx_source_to_concept_map_id_2 ON source_to_concept_map (target_vocabulary_id ASC);
|
||||||
|
CREATE INDEX idx_source_to_concept_map_code ON source_to_concept_map (source_code ASC);
|
||||||
|
|
||||||
|
CREATE INDEX idx_drug_strength_id_1 ON drug_strength (drug_concept_id ASC);
|
||||||
|
CREATE INDEX idx_drug_strength_id_2 ON drug_strength (ingredient_concept_id ASC);
|
||||||
|
|
||||||
|
CREATE INDEX idx_cohort_definition_id ON cohort_definition (cohort_definition_id ASC);
|
||||||
|
|
||||||
|
CREATE INDEX idx_attribute_definition_id ON attribute_definition (attribute_definition_id ASC);
|
||||||
|
|
||||||
|
|
||||||
|
/**************************
|
||||||
|
|
||||||
|
Standardized meta-data
|
||||||
|
|
||||||
|
***************************/
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/************************
|
||||||
|
|
||||||
|
Standardized clinical data
|
||||||
|
|
||||||
|
************************/
|
||||||
|
|
||||||
|
CREATE UNIQUE INDEX idx_person_id ON person (person_id ASC);
|
||||||
|
|
||||||
|
CREATE INDEX idx_observation_period_id ON observation_period (person_id ASC);
|
||||||
|
|
||||||
|
CREATE INDEX idx_specimen_person_id ON specimen (person_id ASC);
|
||||||
|
CREATE INDEX idx_specimen_concept_id ON specimen (specimen_concept_id ASC);
|
||||||
|
|
||||||
|
CREATE INDEX idx_death_person_id ON death (person_id ASC);
|
||||||
|
|
||||||
|
CREATE INDEX idx_visit_person_id ON visit_occurrence (person_id ASC);
|
||||||
|
CREATE INDEX idx_visit_concept_id ON visit_occurrence (visit_concept_id ASC);
|
||||||
|
|
||||||
|
CREATE INDEX idx_procedure_person_id ON procedure_occurrence (person_id ASC);
|
||||||
|
CREATE INDEX idx_procedure_concept_id ON procedure_occurrence (procedure_concept_id ASC);
|
||||||
|
CREATE INDEX idx_procedure_visit_id ON procedure_occurrence (visit_occurrence_id ASC);
|
||||||
|
|
||||||
|
CREATE INDEX idx_drug_person_id ON drug_exposure (person_id ASC);
|
||||||
|
CREATE INDEX idx_drug_concept_id ON drug_exposure (drug_concept_id ASC);
|
||||||
|
CREATE INDEX idx_drug_visit_id ON drug_exposure (visit_occurrence_id ASC);
|
||||||
|
|
||||||
|
CREATE INDEX idx_device_person_id ON device_exposure (person_id ASC);
|
||||||
|
CREATE INDEX idx_device_concept_id ON device_exposure (device_concept_id ASC);
|
||||||
|
CREATE INDEX idx_device_visit_id ON device_exposure (visit_occurrence_id ASC);
|
||||||
|
|
||||||
|
CREATE INDEX idx_condition_person_id ON condition_occurrence (person_id ASC);
|
||||||
|
CREATE INDEX idx_condition_concept_id ON condition_occurrence (condition_concept_id ASC);
|
||||||
|
CREATE INDEX idx_condition_visit_id ON condition_occurrence (visit_occurrence_id ASC);
|
||||||
|
|
||||||
|
CREATE INDEX idx_measurement_person_id ON measurement (person_id ASC);
|
||||||
|
CREATE INDEX idx_measurement_concept_id ON measurement (measurement_concept_id ASC);
|
||||||
|
CREATE INDEX idx_measurement_visit_id ON measurement (visit_occurrence_id ASC);
|
||||||
|
|
||||||
|
CREATE INDEX idx_note_person_id ON note (person_id ASC);
|
||||||
|
CREATE INDEX idx_note_concept_id ON note (note_type_concept_id ASC);
|
||||||
|
CREATE INDEX idx_note_visit_id ON note (visit_occurrence_id ASC);
|
||||||
|
|
||||||
|
CREATE INDEX idx_observation_person_id ON observation (person_id ASC);
|
||||||
|
CREATE INDEX idx_observation_concept_id ON observation (observation_concept_id ASC);
|
||||||
|
CREATE INDEX idx_observation_visit_id ON observation (visit_occurrence_id ASC);
|
||||||
|
|
||||||
|
CREATE INDEX idx_fact_relationship_id_1 ON fact_relationship (domain_concept_id_1 ASC);
|
||||||
|
CREATE INDEX idx_fact_relationship_id_2 ON fact_relationship (domain_concept_id_2 ASC);
|
||||||
|
CREATE INDEX idx_fact_relationship_id_3 ON fact_relationship (relationship_concept_id ASC);
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/************************
|
||||||
|
|
||||||
|
Standardized health system data
|
||||||
|
|
||||||
|
************************/
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/************************
|
||||||
|
|
||||||
|
Standardized health economics
|
||||||
|
|
||||||
|
************************/
|
||||||
|
|
||||||
|
CREATE INDEX idx_period_person_id ON payer_plan_period (person_id ASC);
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/************************
|
||||||
|
|
||||||
|
Standardized derived elements
|
||||||
|
|
||||||
|
************************/
|
||||||
|
|
||||||
|
|
||||||
|
CREATE INDEX idx_cohort_subject_id ON cohort (subject_id ASC);
|
||||||
|
CREATE INDEX idx_cohort_c_definition_id ON cohort (cohort_definition_id ASC);
|
||||||
|
|
||||||
|
CREATE INDEX idx_ca_subject_id ON cohort_attribute (subject_id ASC);
|
||||||
|
CREATE INDEX idx_ca_definition_id ON cohort_attribute (cohort_definition_id ASC);
|
||||||
|
|
||||||
|
CREATE INDEX idx_drug_era_person_id ON drug_era (person_id ASC);
|
||||||
|
CREATE INDEX idx_drug_era_concept_id ON drug_era (drug_concept_id ASC);
|
||||||
|
|
||||||
|
CREATE INDEX idx_dose_era_person_id ON dose_era (person_id ASC);
|
||||||
|
CREATE INDEX idx_dose_era_concept_id ON dose_era (drug_concept_id ASC);
|
||||||
|
|
||||||
|
CREATE INDEX idx_condition_era_person_id ON condition_era (person_id ASC);
|
||||||
|
CREATE INDEX idx_condition_era_concept_id ON condition_era (condition_concept_id ASC);
|
||||||
|
|
||||||
|
|
@ -0,0 +1,545 @@
|
||||||
|
/*********************************************************************************
|
||||||
|
# Copyright 2014 Observational Health Data Sciences and Informatics
|
||||||
|
#
|
||||||
|
#
|
||||||
|
# Licensed under the Apache License, Version 2.0 (the "License");
|
||||||
|
# you may not use this file except in compliance with the License.
|
||||||
|
# You may obtain a copy of the License at
|
||||||
|
#
|
||||||
|
# http://www.apache.org/licenses/LICENSE-2.0
|
||||||
|
#
|
||||||
|
# Unless required by applicable law or agreed to in writing, software
|
||||||
|
# distributed under the License is distributed on an "AS IS" BASIS,
|
||||||
|
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
|
||||||
|
# See the License for the specific language governing permissions and
|
||||||
|
# limitations under the License.
|
||||||
|
********************************************************************************/
|
||||||
|
|
||||||
|
/************************
|
||||||
|
|
||||||
|
####### # # ####### ###### ##### ###### # # ####### #####
|
||||||
|
# # ## ## # # # # # # # # ## ## # # # # # #### # # #### ##### ##### ## # # # ##### ####
|
||||||
|
# # # # # # # # # # # # # # # # # # # # # # # ## # # # # # # # # ## # # #
|
||||||
|
# # # # # # # ###### # # # # # # # # ###### # # # # # # #### # # # # # # # # # # ####
|
||||||
|
# # # # # # # # # # # # # # # # # # # # # # # ##### ###### # # # # # #
|
||||||
|
# # # # # # # # # # # # # # # # # # # # # # ## # # # # # # # # # ## # # #
|
||||||
|
####### # # ####### # ##### ###### # # ## ##### ##### #### # # #### # # # # # # # # # ####
|
||||||
|
|
||||||
|
|
||||||
|
script to create constraints within OMOP common data model, version 5.0 for PostgreSQL database
|
||||||
|
|
||||||
|
last revised: 12 Oct 2014
|
||||||
|
|
||||||
|
author: Patrick Ryan
|
||||||
|
|
||||||
|
|
||||||
|
*************************/
|
||||||
|
|
||||||
|
|
||||||
|
/************************
|
||||||
|
*************************
|
||||||
|
*************************
|
||||||
|
*************************
|
||||||
|
|
||||||
|
Primary key constraints
|
||||||
|
|
||||||
|
*************************
|
||||||
|
*************************
|
||||||
|
*************************
|
||||||
|
************************/
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/************************
|
||||||
|
|
||||||
|
Standardized vocabulary
|
||||||
|
|
||||||
|
************************/
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
ALTER TABLE concept ADD CONSTRAINT xpk_concept PRIMARY KEY (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE vocabulary ADD CONSTRAINT xpk_vocabulary PRIMARY KEY (vocabulary_id);
|
||||||
|
|
||||||
|
ALTER TABLE domain ADD CONSTRAINT xpk_domain PRIMARY KEY (domain_id);
|
||||||
|
|
||||||
|
ALTER TABLE concept_class ADD CONSTRAINT xpk_concept_class PRIMARY KEY (concept_class_id);
|
||||||
|
|
||||||
|
ALTER TABLE concept_relationship ADD CONSTRAINT xpk_concept_relationship PRIMARY KEY (concept_id_1,concept_id_2,relationship_id);
|
||||||
|
|
||||||
|
ALTER TABLE relationship ADD CONSTRAINT xpk_relationship PRIMARY KEY (relationship_id);
|
||||||
|
|
||||||
|
ALTER TABLE concept_ancestor ADD CONSTRAINT xpk_concept_ancestor PRIMARY KEY (ancestor_concept_id,descendant_concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE source_to_concept_map ADD CONSTRAINT xpk_source_to_concept_map PRIMARY KEY (source_vocabulary_id,target_concept_id,source_code,valid_end_date);
|
||||||
|
|
||||||
|
ALTER TABLE drug_strength ADD CONSTRAINT xpk_drug_strength PRIMARY KEY (drug_concept_id, ingredient_concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE cohort_definition ADD CONSTRAINT xpk_cohort_definition PRIMARY KEY (cohort_definition_id);
|
||||||
|
|
||||||
|
ALTER TABLE attribute_definition ADD CONSTRAINT xpk_attribute_definition PRIMARY KEY (attribute_definition_id);
|
||||||
|
|
||||||
|
|
||||||
|
/**************************
|
||||||
|
|
||||||
|
Standardized meta-data
|
||||||
|
|
||||||
|
***************************/
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/************************
|
||||||
|
|
||||||
|
Standardized clinical data
|
||||||
|
|
||||||
|
************************/
|
||||||
|
|
||||||
|
|
||||||
|
/**PRIMARY KEY NONCLUSTERED constraints**/
|
||||||
|
|
||||||
|
ALTER TABLE person ADD CONSTRAINT xpk_person PRIMARY KEY ( person_id ) ;
|
||||||
|
|
||||||
|
ALTER TABLE observation_period ADD CONSTRAINT xpk_observation_period PRIMARY KEY ( observation_period_id ) ;
|
||||||
|
|
||||||
|
ALTER TABLE specimen ADD CONSTRAINT xpk_specimen PRIMARY KEY ( specimen_id ) ;
|
||||||
|
|
||||||
|
ALTER TABLE death ADD CONSTRAINT xpk_death PRIMARY KEY ( person_id ) ;
|
||||||
|
|
||||||
|
ALTER TABLE visit_occurrence ADD CONSTRAINT xpk_visit_occurrence PRIMARY KEY ( visit_occurrence_id ) ;
|
||||||
|
|
||||||
|
ALTER TABLE procedure_occurrence ADD CONSTRAINT xpk_procedure_occurrence PRIMARY KEY ( procedure_occurrence_id ) ;
|
||||||
|
|
||||||
|
ALTER TABLE drug_exposure ADD CONSTRAINT xpk_drug_exposure PRIMARY KEY ( drug_exposure_id ) ;
|
||||||
|
|
||||||
|
ALTER TABLE device_exposure ADD CONSTRAINT xpk_device_exposure PRIMARY KEY ( device_exposure_id ) ;
|
||||||
|
|
||||||
|
ALTER TABLE condition_occurrence ADD CONSTRAINT xpk_condition_occurrence PRIMARY KEY ( condition_occurrence_id ) ;
|
||||||
|
|
||||||
|
ALTER TABLE measurement ADD CONSTRAINT xpk_measurement PRIMARY KEY ( measurement_id ) ;
|
||||||
|
|
||||||
|
ALTER TABLE note ADD CONSTRAINT xpk_note PRIMARY KEY ( note_id ) ;
|
||||||
|
|
||||||
|
ALTER TABLE observation ADD CONSTRAINT xpk_observation PRIMARY KEY ( observation_id ) ;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/************************
|
||||||
|
|
||||||
|
Standardized health system data
|
||||||
|
|
||||||
|
************************/
|
||||||
|
|
||||||
|
|
||||||
|
ALTER TABLE location ADD CONSTRAINT xpk_location PRIMARY KEY ( location_id ) ;
|
||||||
|
|
||||||
|
ALTER TABLE care_site ADD CONSTRAINT xpk_care_site PRIMARY KEY ( care_site_id ) ;
|
||||||
|
|
||||||
|
ALTER TABLE provider ADD CONSTRAINT xpk_provider PRIMARY KEY ( provider_id ) ;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/************************
|
||||||
|
|
||||||
|
Standardized health economics
|
||||||
|
|
||||||
|
************************/
|
||||||
|
|
||||||
|
|
||||||
|
ALTER TABLE payer_plan_period ADD CONSTRAINT xpk_payer_plan_period PRIMARY KEY ( payer_plan_period_id ) ;
|
||||||
|
|
||||||
|
ALTER TABLE visit_cost ADD CONSTRAINT xpk_visit_cost PRIMARY KEY ( visit_cost_id ) ;
|
||||||
|
|
||||||
|
ALTER TABLE procedure_cost ADD CONSTRAINT xpk_procedure_cost PRIMARY KEY ( procedure_cost_id ) ;
|
||||||
|
|
||||||
|
ALTER TABLE drug_cost ADD CONSTRAINT xpk_drug_cost PRIMARY KEY ( drug_cost_id ) ;
|
||||||
|
|
||||||
|
ALTER TABLE device_cost ADD CONSTRAINT xpk_device_cost PRIMARY KEY ( device_cost_id ) ;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/************************
|
||||||
|
|
||||||
|
Standardized derived elements
|
||||||
|
|
||||||
|
************************/
|
||||||
|
|
||||||
|
ALTER TABLE cohort ADD CONSTRAINT xpk_cohort PRIMARY KEY ( cohort_definition_id, subject_id, cohort_start_date, cohort_end_date ) ;
|
||||||
|
|
||||||
|
ALTER TABLE cohort_attribute ADD CONSTRAINT xpk_cohort_attribute PRIMARY KEY ( cohort_definition_id, subject_id, cohort_start_date, cohort_end_date, attribute_definition_id ) ;
|
||||||
|
|
||||||
|
ALTER TABLE drug_era ADD CONSTRAINT xpk_drug_era PRIMARY KEY ( drug_era_id ) ;
|
||||||
|
|
||||||
|
ALTER TABLE dose_era ADD CONSTRAINT xpk_dose_era PRIMARY KEY ( dose_era_id ) ;
|
||||||
|
|
||||||
|
ALTER TABLE condition_era ADD CONSTRAINT xpk_condition_era PRIMARY KEY ( condition_era_id ) ;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/************************
|
||||||
|
*************************
|
||||||
|
*************************
|
||||||
|
*************************
|
||||||
|
|
||||||
|
Foreign key constraints
|
||||||
|
|
||||||
|
*************************
|
||||||
|
*************************
|
||||||
|
*************************
|
||||||
|
************************/
|
||||||
|
|
||||||
|
|
||||||
|
/************************
|
||||||
|
|
||||||
|
Standardized vocabulary
|
||||||
|
|
||||||
|
************************/
|
||||||
|
|
||||||
|
|
||||||
|
ALTER TABLE concept ADD CONSTRAINT fpk_concept_domain FOREIGN KEY (domain_id) REFERENCES domain (domain_id);
|
||||||
|
|
||||||
|
ALTER TABLE concept ADD CONSTRAINT fpk_concept_class FOREIGN KEY (concept_class_id) REFERENCES concept_class (concept_class_id);
|
||||||
|
|
||||||
|
ALTER TABLE concept ADD CONSTRAINT fpk_concept_vocabulary FOREIGN KEY (vocabulary_id) REFERENCES vocabulary (vocabulary_id);
|
||||||
|
|
||||||
|
ALTER TABLE vocabulary ADD CONSTRAINT fpk_vocabulary_concept FOREIGN KEY (vocabulary_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE domain ADD CONSTRAINT fpk_domain_concept FOREIGN KEY (domain_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE concept_class ADD CONSTRAINT fpk_concept_class_concept FOREIGN KEY (concept_class_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE concept_relationship ADD CONSTRAINT fpk_concept_relationship_c_1 FOREIGN KEY (concept_id_1) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE concept_relationship ADD CONSTRAINT fpk_concept_relationship_c_2 FOREIGN KEY (concept_id_2) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE concept_relationship ADD CONSTRAINT fpk_concept_relationship_id FOREIGN KEY (relationship_id) REFERENCES relationship (relationship_id);
|
||||||
|
|
||||||
|
ALTER TABLE relationship ADD CONSTRAINT fpk_relationship_concept FOREIGN KEY (relationship_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE relationship ADD CONSTRAINT fpk_relationship_reverse FOREIGN KEY (reverse_relationship_id) REFERENCES relationship (relationship_id);
|
||||||
|
|
||||||
|
ALTER TABLE concept_synonym ADD CONSTRAINT fpk_concept_synonym_concept FOREIGN KEY (concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE concept_ancestor ADD CONSTRAINT fpk_concept_ancestor_concept_1 FOREIGN KEY (ancestor_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE concept_ancestor ADD CONSTRAINT fpk_concept_ancestor_concept_2 FOREIGN KEY (descendant_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE source_to_concept_map ADD CONSTRAINT fpk_source_to_concept_map_v_1 FOREIGN KEY (source_vocabulary_id) REFERENCES vocabulary (vocabulary_id);
|
||||||
|
|
||||||
|
ALTER TABLE source_to_concept_map ADD CONSTRAINT fpk_source_to_concept_map_v_2 FOREIGN KEY (target_vocabulary_id) REFERENCES vocabulary (vocabulary_id);
|
||||||
|
|
||||||
|
ALTER TABLE source_to_concept_map ADD CONSTRAINT fpk_source_to_concept_map_c_1 FOREIGN KEY (target_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE drug_strength ADD CONSTRAINT fpk_drug_strength_concept_1 FOREIGN KEY (drug_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE drug_strength ADD CONSTRAINT fpk_drug_strength_concept_2 FOREIGN KEY (ingredient_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE drug_strength ADD CONSTRAINT fpk_drug_strength_unit_1 FOREIGN KEY (amount_unit_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE drug_strength ADD CONSTRAINT fpk_drug_strength_unit_2 FOREIGN KEY (numerator_unit_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE drug_strength ADD CONSTRAINT fpk_drug_strength_unit_3 FOREIGN KEY (denominator_unit_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE cohort_definition ADD CONSTRAINT fpk_cohort_definition_concept FOREIGN KEY (definition_type_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
|
||||||
|
/**************************
|
||||||
|
|
||||||
|
Standardized meta-data
|
||||||
|
|
||||||
|
***************************/
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/************************
|
||||||
|
|
||||||
|
Standardized clinical data
|
||||||
|
|
||||||
|
************************/
|
||||||
|
|
||||||
|
ALTER TABLE person ADD CONSTRAINT fpk_person_gender_concept FOREIGN KEY (gender_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE person ADD CONSTRAINT fpk_person_race_concept FOREIGN KEY (race_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE person ADD CONSTRAINT fpk_person_ethnicity_concept FOREIGN KEY (ethnicity_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE person ADD CONSTRAINT fpk_person_gender_concept_s FOREIGN KEY (gender_source_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE person ADD CONSTRAINT fpk_person_race_concept_s FOREIGN KEY (race_source_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE person ADD CONSTRAINT fpk_person_ethnicity_concept_s FOREIGN KEY (ethnicity_source_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE person ADD CONSTRAINT fpk_person_location FOREIGN KEY (location_id) REFERENCES location (location_id);
|
||||||
|
|
||||||
|
ALTER TABLE person ADD CONSTRAINT fpk_person_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
|
||||||
|
|
||||||
|
ALTER TABLE person ADD CONSTRAINT fpk_person_care_site FOREIGN KEY (care_site_id) REFERENCES care_site (care_site_id);
|
||||||
|
|
||||||
|
|
||||||
|
ALTER TABLE observation_period ADD CONSTRAINT fpk_observation_period_person FOREIGN KEY (person_id) REFERENCES person (person_id);
|
||||||
|
|
||||||
|
ALTER TABLE observation_period ADD CONSTRAINT fpk_observation_period_concept FOREIGN KEY (period_type_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
|
||||||
|
ALTER TABLE specimen ADD CONSTRAINT fpk_specimen_person FOREIGN KEY (person_id) REFERENCES person (person_id);
|
||||||
|
|
||||||
|
ALTER TABLE specimen ADD CONSTRAINT fpk_specimen_concept FOREIGN KEY (specimen_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE specimen ADD CONSTRAINT fpk_specimen_type_concept FOREIGN KEY (specimen_type_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE specimen ADD CONSTRAINT fpk_specimen_unit_concept FOREIGN KEY (unit_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE specimen ADD CONSTRAINT fpk_specimen_site_concept FOREIGN KEY (anatomic_site_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE specimen ADD CONSTRAINT fpk_specimen_status_concept FOREIGN KEY (disease_status_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
|
||||||
|
ALTER TABLE death ADD CONSTRAINT fpk_death_person FOREIGN KEY (person_id) REFERENCES person (person_id);
|
||||||
|
|
||||||
|
ALTER TABLE death ADD CONSTRAINT fpk_death_type_concept FOREIGN KEY (death_type_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE death ADD CONSTRAINT fpk_death_cause_concept FOREIGN KEY (cause_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE death ADD CONSTRAINT fpk_death_cause_concept_s FOREIGN KEY (cause_source_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
|
||||||
|
ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_person FOREIGN KEY (person_id) REFERENCES person (person_id);
|
||||||
|
|
||||||
|
ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_concept FOREIGN KEY (visit_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_type_concept FOREIGN KEY (visit_type_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
|
||||||
|
|
||||||
|
ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_care_site FOREIGN KEY (care_site_id) REFERENCES care_site (care_site_id);
|
||||||
|
|
||||||
|
ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_concept_s FOREIGN KEY (visit_source_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
|
||||||
|
ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_person FOREIGN KEY (person_id) REFERENCES person (person_id);
|
||||||
|
|
||||||
|
ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_concept FOREIGN KEY (procedure_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_type_concept FOREIGN KEY (procedure_type_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_modifier FOREIGN KEY (modifier_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
|
||||||
|
|
||||||
|
ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id);
|
||||||
|
|
||||||
|
ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_concept_s FOREIGN KEY (procedure_source_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
|
||||||
|
ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_person FOREIGN KEY (person_id) REFERENCES person (person_id);
|
||||||
|
|
||||||
|
ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_concept FOREIGN KEY (drug_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_type_concept FOREIGN KEY (drug_type_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_route_concept FOREIGN KEY (route_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_dose_unit_concept FOREIGN KEY (dose_unit_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
|
||||||
|
|
||||||
|
ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id);
|
||||||
|
|
||||||
|
ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_concept_s FOREIGN KEY (drug_source_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
|
||||||
|
ALTER TABLE device_exposure ADD CONSTRAINT fpk_device_person FOREIGN KEY (person_id) REFERENCES person (person_id);
|
||||||
|
|
||||||
|
ALTER TABLE device_exposure ADD CONSTRAINT fpk_device_concept FOREIGN KEY (device_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE device_exposure ADD CONSTRAINT fpk_device_type_concept FOREIGN KEY (device_type_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE device_exposure ADD CONSTRAINT fpk_device_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
|
||||||
|
|
||||||
|
ALTER TABLE device_exposure ADD CONSTRAINT fpk_device_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id);
|
||||||
|
|
||||||
|
ALTER TABLE device_exposure ADD CONSTRAINT fpk_device_concept_s FOREIGN KEY (device_source_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
|
||||||
|
ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_person FOREIGN KEY (person_id) REFERENCES person (person_id);
|
||||||
|
|
||||||
|
ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_concept FOREIGN KEY (condition_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_type_concept FOREIGN KEY (condition_type_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
|
||||||
|
|
||||||
|
ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id);
|
||||||
|
|
||||||
|
ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_concept_s FOREIGN KEY (condition_source_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
|
||||||
|
ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_person FOREIGN KEY (person_id) REFERENCES person (person_id);
|
||||||
|
|
||||||
|
ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_concept FOREIGN KEY (measurement_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_type_concept FOREIGN KEY (measurement_type_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_operator FOREIGN KEY (operator_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_value FOREIGN KEY (value_as_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_unit FOREIGN KEY (unit_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
|
||||||
|
|
||||||
|
ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id);
|
||||||
|
|
||||||
|
ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_concept_s FOREIGN KEY (measurement_source_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
|
||||||
|
ALTER TABLE note ADD CONSTRAINT fpk_note_person FOREIGN KEY (person_id) REFERENCES person (person_id);
|
||||||
|
|
||||||
|
ALTER TABLE note ADD CONSTRAINT fpk_note_type_concept FOREIGN KEY (note_type_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE note ADD CONSTRAINT fpk_note_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
|
||||||
|
|
||||||
|
ALTER TABLE note ADD CONSTRAINT fpk_note_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id);
|
||||||
|
|
||||||
|
|
||||||
|
ALTER TABLE observation ADD CONSTRAINT fpk_observation_person FOREIGN KEY (person_id) REFERENCES person (person_id);
|
||||||
|
|
||||||
|
ALTER TABLE observation ADD CONSTRAINT fpk_observation_concept FOREIGN KEY (observation_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE observation ADD CONSTRAINT fpk_observation_type_concept FOREIGN KEY (observation_type_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE observation ADD CONSTRAINT fpk_observation_value FOREIGN KEY (value_as_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE observation ADD CONSTRAINT fpk_observation_qualifier FOREIGN KEY (qualifier_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE observation ADD CONSTRAINT fpk_observation_unit FOREIGN KEY (unit_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE observation ADD CONSTRAINT fpk_observation_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
|
||||||
|
|
||||||
|
ALTER TABLE observation ADD CONSTRAINT fpk_observation_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id);
|
||||||
|
|
||||||
|
ALTER TABLE observation ADD CONSTRAINT fpk_observation_concept_s FOREIGN KEY (observation_source_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
|
||||||
|
ALTER TABLE fact_relationship ADD CONSTRAINT fpk_fact_domain_1 FOREIGN KEY (domain_concept_id_1) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE fact_relationship ADD CONSTRAINT fpk_fact_domain_2 FOREIGN KEY (domain_concept_id_2) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE fact_relationship ADD CONSTRAINT fpk_fact_relationship FOREIGN KEY (relationship_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/************************
|
||||||
|
|
||||||
|
Standardized health system data
|
||||||
|
|
||||||
|
************************/
|
||||||
|
|
||||||
|
ALTER TABLE care_site ADD CONSTRAINT fpk_care_site_location FOREIGN KEY (location_id) REFERENCES location (location_id);
|
||||||
|
|
||||||
|
ALTER TABLE care_site ADD CONSTRAINT fpk_care_site_place FOREIGN KEY (place_of_service_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
|
||||||
|
ALTER TABLE provider ADD CONSTRAINT fpk_provider_specialty FOREIGN KEY (specialty_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE provider ADD CONSTRAINT fpk_provider_care_site FOREIGN KEY (care_site_id) REFERENCES care_site (care_site_id);
|
||||||
|
|
||||||
|
ALTER TABLE provider ADD CONSTRAINT fpk_provider_gender FOREIGN KEY (gender_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE provider ADD CONSTRAINT fpk_provider_specialty_s FOREIGN KEY (specialty_source_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE provider ADD CONSTRAINT fpk_provider_gender_s FOREIGN KEY (gender_source_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/************************
|
||||||
|
|
||||||
|
Standardized health economics
|
||||||
|
|
||||||
|
************************/
|
||||||
|
|
||||||
|
ALTER TABLE payer_plan_period ADD CONSTRAINT fpk_payer_plan_period FOREIGN KEY (person_id) REFERENCES person (person_id);
|
||||||
|
|
||||||
|
|
||||||
|
ALTER TABLE visit_cost ADD CONSTRAINT fpk_visit_cost_id FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id);
|
||||||
|
|
||||||
|
ALTER TABLE visit_cost ADD CONSTRAINT fpk_visit_cost_currency FOREIGN KEY (currency_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE visit_cost ADD CONSTRAINT fpk_visit_cost_period FOREIGN KEY (payer_plan_period_id) REFERENCES payer_plan_period (payer_plan_period_id);
|
||||||
|
|
||||||
|
|
||||||
|
ALTER TABLE procedure_cost ADD CONSTRAINT fpk_procedure_cost_id FOREIGN KEY (procedure_occurrence_id) REFERENCES procedure_occurrence (procedure_occurrence_id);
|
||||||
|
|
||||||
|
ALTER TABLE procedure_cost ADD CONSTRAINT fpk_procedure_cost_currency FOREIGN KEY (currency_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE procedure_cost ADD CONSTRAINT fpk_procedure_cost_period FOREIGN KEY (payer_plan_period_id) REFERENCES payer_plan_period (payer_plan_period_id);
|
||||||
|
|
||||||
|
ALTER TABLE procedure_cost ADD CONSTRAINT fpk_procedure_cost_revenue FOREIGN KEY (revenue_code_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
|
||||||
|
ALTER TABLE drug_cost ADD CONSTRAINT fpk_drug_cost_id FOREIGN KEY (drug_exposure_id) REFERENCES drug_exposure (drug_exposure_id);
|
||||||
|
|
||||||
|
ALTER TABLE drug_cost ADD CONSTRAINT fpk_drug_cost_currency FOREIGN KEY (currency_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE drug_cost ADD CONSTRAINT fpk_drug_cost_period FOREIGN KEY (payer_plan_period_id) REFERENCES payer_plan_period (payer_plan_period_id);
|
||||||
|
|
||||||
|
|
||||||
|
ALTER TABLE device_cost ADD CONSTRAINT fpk_device_cost_id FOREIGN KEY (device_exposure_id) REFERENCES device_exposure (device_exposure_id);
|
||||||
|
|
||||||
|
ALTER TABLE device_cost ADD CONSTRAINT fpk_device_cost_currency FOREIGN KEY (currency_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE device_cost ADD CONSTRAINT fpk_device_cost_period FOREIGN KEY (payer_plan_period_id) REFERENCES payer_plan_period (payer_plan_period_id);
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/************************
|
||||||
|
|
||||||
|
Standardized derived elements
|
||||||
|
|
||||||
|
************************/
|
||||||
|
|
||||||
|
|
||||||
|
ALTER TABLE cohort ADD CONSTRAINT fpk_cohort_definition FOREIGN KEY (cohort_definition_id) REFERENCES cohort_definition (cohort_definition_id);
|
||||||
|
|
||||||
|
|
||||||
|
ALTER TABLE cohort_attribute ADD CONSTRAINT fpk_ca_cohort_definition FOREIGN KEY (cohort_definition_id) REFERENCES cohort_definition (cohort_definition_id);
|
||||||
|
|
||||||
|
ALTER TABLE cohort_attribute ADD CONSTRAINT fpk_ca_attribute_definition FOREIGN KEY (attribute_definition_id) REFERENCES attribute_definition (attribute_definition_id);
|
||||||
|
|
||||||
|
ALTER TABLE cohort_attribute ADD CONSTRAINT fpk_ca_value FOREIGN KEY (value_as_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
|
||||||
|
ALTER TABLE drug_era ADD CONSTRAINT fpk_drug_era_person FOREIGN KEY (person_id) REFERENCES person (person_id);
|
||||||
|
|
||||||
|
ALTER TABLE drug_era ADD CONSTRAINT fpk_drug_era_concept FOREIGN KEY (drug_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
|
||||||
|
ALTER TABLE dose_era ADD CONSTRAINT fpk_dose_era_person FOREIGN KEY (person_id) REFERENCES person (person_id);
|
||||||
|
|
||||||
|
ALTER TABLE dose_era ADD CONSTRAINT fpk_dose_era_concept FOREIGN KEY (drug_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE dose_era ADD CONSTRAINT fpk_dose_era_unit_concept FOREIGN KEY (unit_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
|
||||||
|
ALTER TABLE condition_era ADD CONSTRAINT fpk_condition_era_person FOREIGN KEY (person_id) REFERENCES person (person_id);
|
||||||
|
|
||||||
|
ALTER TABLE condition_era ADD CONSTRAINT fpk_condition_era_concept FOREIGN KEY (condition_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
|
@ -0,0 +1,709 @@
|
||||||
|
/*********************************************************************************
|
||||||
|
# Copyright 2014 Observational Health Data Sciences and Informatics
|
||||||
|
#
|
||||||
|
#
|
||||||
|
# Licensed under the Apache License, Version 2.0 (the "License");
|
||||||
|
# you may not use this file except in compliance with the License.
|
||||||
|
# You may obtain a copy of the License at
|
||||||
|
#
|
||||||
|
# http://www.apache.org/licenses/LICENSE-2.0
|
||||||
|
#
|
||||||
|
# Unless required by applicable law or agreed to in writing, software
|
||||||
|
# distributed under the License is distributed on an "AS IS" BASIS,
|
||||||
|
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
|
||||||
|
# See the License for the specific language governing permissions and
|
||||||
|
# limitations under the License.
|
||||||
|
********************************************************************************/
|
||||||
|
|
||||||
|
/************************
|
||||||
|
|
||||||
|
####### # # ####### ###### ##### ###### # # #######
|
||||||
|
# # ## ## # # # # # # # # ## ## # # #
|
||||||
|
# # # # # # # # # # # # # # # # # # # #
|
||||||
|
# # # # # # # ###### # # # # # # # # ######
|
||||||
|
# # # # # # # # # # # # # # #
|
||||||
|
# # # # # # # # # # # # # # # # #
|
||||||
|
####### # # ####### # ##### ###### # # ## #####
|
||||||
|
|
||||||
|
|
||||||
|
script to create OMOP common data model, version 5.0 for PostgreSQL database
|
||||||
|
|
||||||
|
last revised: 12 Oct 2014
|
||||||
|
|
||||||
|
author: Patrick Ryan
|
||||||
|
|
||||||
|
|
||||||
|
*************************/
|
||||||
|
|
||||||
|
|
||||||
|
/************************
|
||||||
|
|
||||||
|
Standardized vocabulary
|
||||||
|
|
||||||
|
************************/
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE concept (
|
||||||
|
concept_id INTEGER NOT NULL,
|
||||||
|
concept_name VARCHAR(255) NOT NULL,
|
||||||
|
domain_id VARCHAR(20) NOT NULL,
|
||||||
|
vocabulary_id VARCHAR(20) NOT NULL,
|
||||||
|
concept_class_id VARCHAR(20) NOT NULL,
|
||||||
|
standard_concept VARCHAR(1) NULL,
|
||||||
|
concept_code VARCHAR(50) NOT NULL,
|
||||||
|
valid_start_date DATE NOT NULL,
|
||||||
|
valid_end_date DATE NOT NULL,
|
||||||
|
invalid_reason VARCHAR(1) NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE vocabulary (
|
||||||
|
vocabulary_id VARCHAR(20) NOT NULL,
|
||||||
|
vocabulary_name VARCHAR(255) NOT NULL,
|
||||||
|
vocabulary_reference VARCHAR(255) NULL,
|
||||||
|
vocabulary_version VARCHAR(255) NULL,
|
||||||
|
vocabulary_concept_id INTEGER NOT NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE domain (
|
||||||
|
domain_id VARCHAR(20) NOT NULL,
|
||||||
|
domain_name VARCHAR(255) NOT NULL,
|
||||||
|
domain_concept_id INTEGER NOT NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE concept_class (
|
||||||
|
concept_class_id VARCHAR(20) NOT NULL,
|
||||||
|
concept_class_name VARCHAR(255) NOT NULL,
|
||||||
|
concept_class_concept_id INTEGER NOT NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE concept_relationship (
|
||||||
|
concept_id_1 INTEGER NOT NULL,
|
||||||
|
concept_id_2 INTEGER NOT NULL,
|
||||||
|
relationship_id VARCHAR(20) NOT NULL,
|
||||||
|
valid_start_date DATE NOT NULL,
|
||||||
|
valid_end_date DATE NOT NULL,
|
||||||
|
invalid_reason VARCHAR(1) NULL)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE relationship (
|
||||||
|
relationship_id VARCHAR(20) NOT NULL,
|
||||||
|
relationship_name VARCHAR(255) NOT NULL,
|
||||||
|
is_hierarchical VARCHAR(1) NOT NULL,
|
||||||
|
defines_ancestry VARCHAR(1) NOT NULL,
|
||||||
|
reverse_relationship_id VARCHAR(20) NOT NULL,
|
||||||
|
relationship_concept_id INTEGER NOT NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE concept_synonym (
|
||||||
|
concept_id INTEGER NOT NULL,
|
||||||
|
concept_synonym_name VARCHAR(1000) NOT NULL,
|
||||||
|
language_concept_id INTEGER NOT NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE concept_ancestor (
|
||||||
|
ancestor_concept_id INTEGER NOT NULL,
|
||||||
|
descendant_concept_id INTEGER NOT NULL,
|
||||||
|
min_levels_of_separation INTEGER NOT NULL,
|
||||||
|
max_levels_of_separation INTEGER NOT NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE source_to_concept_map (
|
||||||
|
source_code VARCHAR(50) NOT NULL,
|
||||||
|
source_concept_id INTEGER NOT NULL,
|
||||||
|
source_vocabulary_id VARCHAR(20) NOT NULL,
|
||||||
|
source_code_description VARCHAR(255) NULL,
|
||||||
|
target_concept_id INTEGER NOT NULL,
|
||||||
|
target_vocabulary_id VARCHAR(20) NOT NULL,
|
||||||
|
valid_start_date DATE NOT NULL,
|
||||||
|
valid_end_date DATE NOT NULL,
|
||||||
|
invalid_reason VARCHAR(1) NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE drug_strength (
|
||||||
|
drug_concept_id INTEGER NOT NULL,
|
||||||
|
ingredient_concept_id INTEGER NOT NULL,
|
||||||
|
amount_value NUMERIC NULL,
|
||||||
|
amount_unit_concept_id INTEGER NULL,
|
||||||
|
numerator_value NUMERIC NULL,
|
||||||
|
numerator_unit_concept_id INTEGER NULL,
|
||||||
|
denominator_unit_concept_id INTEGER NULL,
|
||||||
|
valid_start_date DATE NOT NULL,
|
||||||
|
valid_end_date DATE NOT NULL,
|
||||||
|
invalid_reason VARCHAR(1) NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE cohort_definition (
|
||||||
|
cohort_definition_id INTEGER NOT NULL,
|
||||||
|
cohort_definition_name VARCHAR(255) NOT NULL,
|
||||||
|
cohort_definition_description TEXT NULL,
|
||||||
|
definition_type_concept_id INTEGER NOT NULL,
|
||||||
|
cohort_definition_syntax TEXT NULL,
|
||||||
|
subject_concept_id INTEGER NOT NULL,
|
||||||
|
cohort_initiation_date DATE NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE attribute_definition (
|
||||||
|
attribute_definition_id INTEGER NOT NULL,
|
||||||
|
attribute_name VARCHAR(255) NOT NULL,
|
||||||
|
attribute_description TEXT NULL,
|
||||||
|
attribute_type_concept_id INTEGER NOT NULL,
|
||||||
|
attribute_syntax TEXT NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
/**************************
|
||||||
|
|
||||||
|
Standardized meta-data
|
||||||
|
|
||||||
|
***************************/
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE cdm_source
|
||||||
|
(
|
||||||
|
cdm_source_name VARCHAR(255) NOT NULL,
|
||||||
|
cdm_source_abbreviation VARCHAR(25) NULL,
|
||||||
|
cdm_holder VARCHAR(255) NULL,
|
||||||
|
source_description TEXT NULL,
|
||||||
|
source_documentation_reference VARCHAR(255) NULL,
|
||||||
|
cdm_etl_reference VARCHAR(255) NULL,
|
||||||
|
source_release_date DATE NULL,
|
||||||
|
cdm_release_date DATE NULL,
|
||||||
|
cdm_version VARCHAR(10) NULL,
|
||||||
|
vocabulary_version VARCHAR(20) NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/************************
|
||||||
|
|
||||||
|
Standardized clinical data
|
||||||
|
|
||||||
|
************************/
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE person
|
||||||
|
(
|
||||||
|
person_id INTEGER NOT NULL ,
|
||||||
|
gender_concept_id INTEGER NOT NULL ,
|
||||||
|
year_of_birth INTEGER NOT NULL ,
|
||||||
|
month_of_birth INTEGER NULL,
|
||||||
|
day_of_birth INTEGER NULL,
|
||||||
|
time_of_birth VARCHAR(10) NULL,
|
||||||
|
race_concept_id INTEGER NOT NULL,
|
||||||
|
ethnicity_concept_id INTEGER NOT NULL,
|
||||||
|
location_id INTEGER NULL,
|
||||||
|
provider_id INTEGER NULL,
|
||||||
|
care_site_id INTEGER NULL,
|
||||||
|
person_source_value VARCHAR(50) NULL,
|
||||||
|
gender_source_value VARCHAR(50) NULL,
|
||||||
|
gender_source_concept_id INTEGER NULL,
|
||||||
|
race_source_value VARCHAR(50) NULL,
|
||||||
|
race_source_concept_id INTEGER NULL,
|
||||||
|
ethnicity_source_value VARCHAR(50) NULL,
|
||||||
|
ethnicity_source_concept_id INTEGER NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE observation_period
|
||||||
|
(
|
||||||
|
observation_period_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
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE specimen
|
||||||
|
(
|
||||||
|
specimen_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 ,
|
||||||
|
specimen_time VARCHAR(10) NULL ,
|
||||||
|
quantity NUMERIC NULL ,
|
||||||
|
unit_concept_id INTEGER NULL ,
|
||||||
|
anatomic_site_concept_id INTEGER NULL ,
|
||||||
|
disease_status_concept_id INTEGER NULL ,
|
||||||
|
specimen_source_id VARCHAR(50) NULL ,
|
||||||
|
specimen_source_value VARCHAR(50) NULL ,
|
||||||
|
unit_source_value VARCHAR(50) NULL ,
|
||||||
|
anatomic_site_source_value VARCHAR(50) NULL ,
|
||||||
|
disease_status_source_value VARCHAR(50) NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE death
|
||||||
|
(
|
||||||
|
person_id INTEGER NOT NULL ,
|
||||||
|
death_date DATE NOT NULL ,
|
||||||
|
death_type_concept_id INTEGER NOT NULL ,
|
||||||
|
cause_concept_id INTEGER NULL ,
|
||||||
|
cause_source_value VARCHAR(50) NULL,
|
||||||
|
cause_source_concept_id INTEGER NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE visit_occurrence
|
||||||
|
(
|
||||||
|
visit_occurrence_id INTEGER NOT NULL ,
|
||||||
|
person_id INTEGER NOT NULL ,
|
||||||
|
visit_concept_id INTEGER NOT NULL ,
|
||||||
|
visit_start_date DATE NOT NULL ,
|
||||||
|
visit_start_time VARCHAR(10) NULL ,
|
||||||
|
visit_end_date DATE NOT NULL ,
|
||||||
|
visit_end_time VARCHAR(10) NULL ,
|
||||||
|
visit_type_concept_id INTEGER NOT NULL ,
|
||||||
|
provider_id INTEGER NULL,
|
||||||
|
care_site_id INTEGER NULL,
|
||||||
|
visit_source_value VARCHAR(50) NULL,
|
||||||
|
visit_source_concept_id INTEGER NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE procedure_occurrence
|
||||||
|
(
|
||||||
|
procedure_occurrence_id INTEGER NOT NULL ,
|
||||||
|
person_id INTEGER NOT NULL ,
|
||||||
|
procedure_concept_id INTEGER NOT NULL ,
|
||||||
|
procedure_date DATE NOT NULL ,
|
||||||
|
procedure_type_concept_id INTEGER NOT NULL ,
|
||||||
|
modifier_concept_id INTEGER NULL ,
|
||||||
|
quantity INTEGER NULL ,
|
||||||
|
provider_id INTEGER NULL ,
|
||||||
|
visit_occurrence_id INTEGER NULL ,
|
||||||
|
procedure_source_value VARCHAR(50) NULL ,
|
||||||
|
procedure_source_concept_id INTEGER NULL ,
|
||||||
|
qualifier_source_value VARCHAR(50) NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE drug_exposure
|
||||||
|
(
|
||||||
|
drug_exposure_id INTEGER NOT NULL ,
|
||||||
|
person_id INTEGER NOT NULL ,
|
||||||
|
drug_concept_id INTEGER NOT NULL ,
|
||||||
|
drug_exposure_start_date DATE NOT NULL ,
|
||||||
|
drug_exposure_end_date DATE NULL ,
|
||||||
|
drug_type_concept_id INTEGER NOT NULL ,
|
||||||
|
stop_reason VARCHAR(20) NULL ,
|
||||||
|
refills INTEGER NULL ,
|
||||||
|
quantity NUMERIC NULL ,
|
||||||
|
days_supply INTEGER NULL ,
|
||||||
|
sig TEXT NULL ,
|
||||||
|
route_concept_id INTEGER NULL ,
|
||||||
|
effective_drug_dose NUMERIC NULL ,
|
||||||
|
dose_unit_concept_id INTEGER NULL ,
|
||||||
|
lot_number VARCHAR(50) NULL ,
|
||||||
|
provider_id INTEGER NULL ,
|
||||||
|
visit_occurrence_id INTEGER NULL ,
|
||||||
|
drug_source_value VARCHAR(50) NULL ,
|
||||||
|
drug_source_concept_id INTEGER NULL ,
|
||||||
|
route_source_value VARCHAR(50) NULL ,
|
||||||
|
dose_unit_source_value VARCHAR(50) NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE device_exposure
|
||||||
|
(
|
||||||
|
device_exposure_id INTEGER NOT NULL ,
|
||||||
|
person_id INTEGER NOT NULL ,
|
||||||
|
device_concept_id INTEGER NOT NULL ,
|
||||||
|
device_exposure_start_date DATE NOT NULL ,
|
||||||
|
device_exposure_end_date DATE NULL ,
|
||||||
|
device_type_concept_id INTEGER NOT NULL ,
|
||||||
|
unique_device_id VARCHAR(50) NULL ,
|
||||||
|
quantity INTEGER NULL ,
|
||||||
|
provider_id INTEGER NULL ,
|
||||||
|
visit_occurrence_id INTEGER NULL ,
|
||||||
|
device_source_value VARCHAR(100) NULL ,
|
||||||
|
device_source_concept_id INTEGER NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE condition_occurrence
|
||||||
|
(
|
||||||
|
condition_occurrence_id INTEGER NOT NULL ,
|
||||||
|
person_id INTEGER NOT NULL ,
|
||||||
|
condition_concept_id INTEGER NOT NULL ,
|
||||||
|
condition_start_date DATE NOT NULL ,
|
||||||
|
condition_end_date DATE NULL ,
|
||||||
|
condition_type_concept_id INTEGER NOT NULL ,
|
||||||
|
stop_reason VARCHAR(20) NULL ,
|
||||||
|
provider_id INTEGER NULL ,
|
||||||
|
visit_occurrence_id INTEGER NULL ,
|
||||||
|
condition_source_value VARCHAR(50) NULL ,
|
||||||
|
condition_source_concept_id INTEGER NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE measurement
|
||||||
|
(
|
||||||
|
measurement_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 ,
|
||||||
|
measurement_type_concept_id INTEGER NOT NULL ,
|
||||||
|
operator_concept_id INTEGER NULL ,
|
||||||
|
value_as_number NUMERIC NULL ,
|
||||||
|
value_as_concept_id INTEGER NULL ,
|
||||||
|
unit_concept_id INTEGER NULL ,
|
||||||
|
range_low NUMERIC NULL ,
|
||||||
|
range_high NUMERIC NULL ,
|
||||||
|
provider_id INTEGER NULL ,
|
||||||
|
visit_occurrence_id INTEGER NULL ,
|
||||||
|
measurement_source_value VARCHAR(50) NULL ,
|
||||||
|
measurement_source_concept_id INTEGER NULL ,
|
||||||
|
unit_source_value VARCHAR(50) NULL ,
|
||||||
|
value_source_value VARCHAR(50) NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE note
|
||||||
|
(
|
||||||
|
note_id INTEGER NOT NULL ,
|
||||||
|
person_id INTEGER NOT NULL ,
|
||||||
|
note_date DATE NOT NULL ,
|
||||||
|
note_time VARCHAR(10) NULL ,
|
||||||
|
note_type_concept_id INTEGER NOT NULL ,
|
||||||
|
note_text TEXT NOT NULL ,
|
||||||
|
provider_id INTEGER NULL ,
|
||||||
|
visit_occurrence_id INTEGER NULL ,
|
||||||
|
note_source_value VARCHAR(50) NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE observation
|
||||||
|
(
|
||||||
|
observation_id INTEGER NOT NULL ,
|
||||||
|
person_id INTEGER NOT NULL ,
|
||||||
|
observation_concept_id INTEGER NOT NULL ,
|
||||||
|
observation_date DATE NOT NULL ,
|
||||||
|
observation_time VARCHAR(10) NULL ,
|
||||||
|
observation_type_concept_id INTEGER NOT NULL ,
|
||||||
|
value_as_number NUMERIC NULL ,
|
||||||
|
value_as_string VARCHAR(60) NULL ,
|
||||||
|
value_as_concept_id INTEGER NULL ,
|
||||||
|
qualifier_concept_id INTEGER NULL ,
|
||||||
|
unit_concept_id INTEGER NULL ,
|
||||||
|
provider_id INTEGER NULL ,
|
||||||
|
visit_occurrence_id INTEGER NULL ,
|
||||||
|
observation_source_value VARCHAR(50) NULL ,
|
||||||
|
observation_source_concept_id INTEGER NULL ,
|
||||||
|
unit_source_value VARCHAR(50) NULL ,
|
||||||
|
qualifier_source_value VARCHAR(50) NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE fact_relationship
|
||||||
|
(
|
||||||
|
domain_concept_id_1 INTEGER NOT NULL ,
|
||||||
|
fact_id_1 INTEGER NOT NULL ,
|
||||||
|
domain_concept_id_2 INTEGER NOT NULL ,
|
||||||
|
fact_id_2 INTEGER NOT NULL ,
|
||||||
|
relationship_concept_id INTEGER NOT NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/************************
|
||||||
|
|
||||||
|
Standardized health system data
|
||||||
|
|
||||||
|
************************/
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE location
|
||||||
|
(
|
||||||
|
location_id INTEGER NOT NULL ,
|
||||||
|
address_1 VARCHAR(50) NULL ,
|
||||||
|
address_2 VARCHAR(50) NULL ,
|
||||||
|
city VARCHAR(50) NULL ,
|
||||||
|
state VARCHAR(2) NULL ,
|
||||||
|
zip VARCHAR(9) NULL ,
|
||||||
|
county VARCHAR(20) NULL ,
|
||||||
|
location_source_value VARCHAR(50) NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE care_site
|
||||||
|
(
|
||||||
|
care_site_id INTEGER NOT NULL ,
|
||||||
|
care_site_name VARCHAR(255) NULL ,
|
||||||
|
place_of_service_concept_id INTEGER NULL ,
|
||||||
|
location_id INTEGER NULL ,
|
||||||
|
care_site_source_value VARCHAR(50) NULL ,
|
||||||
|
place_of_service_source_value VARCHAR(50) NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE provider
|
||||||
|
(
|
||||||
|
provider_id INTEGER NOT NULL ,
|
||||||
|
provider_name VARCHAR(255) NULL ,
|
||||||
|
NPI VARCHAR(20) NULL ,
|
||||||
|
DEA VARCHAR(20) NULL ,
|
||||||
|
specialty_concept_id INTEGER NULL ,
|
||||||
|
care_site_id INTEGER NULL ,
|
||||||
|
year_of_birth INTEGER NULL ,
|
||||||
|
gender_concept_id INTEGER NULL ,
|
||||||
|
provider_source_value VARCHAR(50) NULL ,
|
||||||
|
specialty_source_value VARCHAR(50) NULL ,
|
||||||
|
specialty_source_concept_id INTEGER NULL ,
|
||||||
|
gender_source_value VARCHAR(50) NULL ,
|
||||||
|
gender_source_concept_id INTEGER NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/************************
|
||||||
|
|
||||||
|
Standardized health economics
|
||||||
|
|
||||||
|
************************/
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE payer_plan_period
|
||||||
|
(
|
||||||
|
payer_plan_period_id INTEGER NOT NULL ,
|
||||||
|
person_id INTEGER NOT NULL ,
|
||||||
|
payer_plan_period_start_date DATE NOT NULL ,
|
||||||
|
payer_plan_period_end_date DATE NOT NULL ,
|
||||||
|
payer_source_value VARCHAR (50) NULL ,
|
||||||
|
plan_source_value VARCHAR (50) NULL ,
|
||||||
|
family_source_value VARCHAR (50) NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE visit_cost
|
||||||
|
(
|
||||||
|
visit_cost_id INTEGER NOT NULL ,
|
||||||
|
visit_occurrence_id INTEGER NOT NULL ,
|
||||||
|
currency_concept_id INTEGER NULL ,
|
||||||
|
paid_copay NUMERIC NULL ,
|
||||||
|
paid_coinsurance NUMERIC NULL ,
|
||||||
|
paid_toward_deductible NUMERIC NULL ,
|
||||||
|
paid_by_payer NUMERIC NULL ,
|
||||||
|
paid_by_coordination_benefits NUMERIC NULL ,
|
||||||
|
total_out_of_pocket NUMERIC NULL ,
|
||||||
|
total_paid NUMERIC NULL ,
|
||||||
|
payer_plan_period_id INTEGER NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE procedure_cost
|
||||||
|
(
|
||||||
|
procedure_cost_id INTEGER NOT NULL ,
|
||||||
|
procedure_occurrence_id INTEGER NOT NULL ,
|
||||||
|
currency_concept_id INTEGER NULL ,
|
||||||
|
paid_copay NUMERIC NULL ,
|
||||||
|
paid_coinsurance NUMERIC NULL ,
|
||||||
|
paid_toward_deductible NUMERIC NULL ,
|
||||||
|
paid_by_payer NUMERIC NULL ,
|
||||||
|
paid_by_coordination_benefits NUMERIC NULL ,
|
||||||
|
total_out_of_pocket NUMERIC NULL ,
|
||||||
|
total_paid NUMERIC NULL ,
|
||||||
|
revenue_code_concept_id INTEGER NULL ,
|
||||||
|
payer_plan_period_id INTEGER NULL ,
|
||||||
|
revenue_code_source_value VARCHAR(50) NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE drug_cost
|
||||||
|
(
|
||||||
|
drug_cost_id INTEGER NOT NULL ,
|
||||||
|
drug_exposure_id INTEGER NOT NULL ,
|
||||||
|
currency_concept_id INTEGER NULL ,
|
||||||
|
paid_copay NUMERIC NULL ,
|
||||||
|
paid_coinsurance NUMERIC NULL ,
|
||||||
|
paid_toward_deductible NUMERIC NULL ,
|
||||||
|
paid_by_payer NUMERIC NULL ,
|
||||||
|
paid_by_coordination_benefits NUMERIC NULL ,
|
||||||
|
total_out_of_pocket NUMERIC NULL ,
|
||||||
|
total_paid NUMERIC NULL ,
|
||||||
|
ingredient_cost NUMERIC NULL ,
|
||||||
|
dispensing_fee NUMERIC NULL ,
|
||||||
|
average_wholesale_price NUMERIC NULL ,
|
||||||
|
payer_plan_period_id INTEGER NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE device_cost
|
||||||
|
(
|
||||||
|
device_cost_id INTEGER NOT NULL ,
|
||||||
|
device_exposure_id INTEGER NOT NULL ,
|
||||||
|
currency_concept_id INTEGER NULL ,
|
||||||
|
paid_copay NUMERIC NULL ,
|
||||||
|
paid_coinsurance NUMERIC NULL ,
|
||||||
|
paid_toward_deductible NUMERIC NULL ,
|
||||||
|
paid_by_payer NUMERIC NULL ,
|
||||||
|
paid_by_coordination_benefits NUMERIC NULL ,
|
||||||
|
total_out_of_pocket NUMERIC NULL ,
|
||||||
|
total_paid NUMERIC NULL ,
|
||||||
|
payer_plan_period_id INTEGER NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/************************
|
||||||
|
|
||||||
|
Standardized derived elements
|
||||||
|
|
||||||
|
************************/
|
||||||
|
|
||||||
|
CREATE TABLE cohort
|
||||||
|
(
|
||||||
|
cohort_definition_id INTEGER NOT NULL ,
|
||||||
|
subject_id INTEGER NOT NULL ,
|
||||||
|
cohort_start_date DATE NOT NULL ,
|
||||||
|
cohort_end_date DATE NOT NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE cohort_attribute
|
||||||
|
(
|
||||||
|
cohort_definition_id INTEGER NOT NULL ,
|
||||||
|
cohort_start_date DATE NOT NULL ,
|
||||||
|
cohort_end_date DATE NOT NULL ,
|
||||||
|
subject_id INTEGER NOT NULL ,
|
||||||
|
attribute_definition_id INTEGER NOT NULL ,
|
||||||
|
value_as_number NUMERIC NULL ,
|
||||||
|
value_as_concept_id INTEGER NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE drug_era
|
||||||
|
(
|
||||||
|
drug_era_id INTEGER NOT NULL ,
|
||||||
|
person_id INTEGER NOT NULL ,
|
||||||
|
drug_concept_id INTEGER NOT NULL ,
|
||||||
|
drug_era_start_date DATE NOT NULL ,
|
||||||
|
drug_era_end_date DATE NOT NULL ,
|
||||||
|
drug_exposure_count INTEGER NULL ,
|
||||||
|
gap_days INTEGER NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE dose_era
|
||||||
|
(
|
||||||
|
dose_era_id INTEGER NOT NULL ,
|
||||||
|
person_id INTEGER NOT NULL ,
|
||||||
|
drug_concept_id INTEGER NOT NULL ,
|
||||||
|
unit_concept_id INTEGER NOT NULL ,
|
||||||
|
dose_value NUMERIC NOT NULL ,
|
||||||
|
dose_era_start_date DATE NOT NULL ,
|
||||||
|
dose_era_end_date DATE NOT NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE condition_era
|
||||||
|
(
|
||||||
|
condition_era_id INTEGER NOT NULL ,
|
||||||
|
person_id INTEGER NOT NULL ,
|
||||||
|
condition_concept_id INTEGER NOT NULL ,
|
||||||
|
condition_era_start_date DATE NOT NULL ,
|
||||||
|
condition_era_end_date DATE NOT NULL ,
|
||||||
|
condition_occurrence_count INTEGER NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
@ -0,0 +1,214 @@
|
||||||
|
/*********************************************************************************
|
||||||
|
# Copyright 2014 Observational Health Data Sciences and Informatics
|
||||||
|
#
|
||||||
|
#
|
||||||
|
# Licensed under the Apache License, Version 2.0 (the "License");
|
||||||
|
# you may not use this file except in compliance with the License.
|
||||||
|
# You may obtain a copy of the License at
|
||||||
|
#
|
||||||
|
# http://www.apache.org/licenses/LICENSE-2.0
|
||||||
|
#
|
||||||
|
# Unless required by applicable law or agreed to in writing, software
|
||||||
|
# distributed under the License is distributed on an "AS IS" BASIS,
|
||||||
|
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
|
||||||
|
# See the License for the specific language governing permissions and
|
||||||
|
# limitations under the License.
|
||||||
|
********************************************************************************/
|
||||||
|
|
||||||
|
/************************
|
||||||
|
|
||||||
|
####### # # ####### ###### ##### ###### # # ####### ###
|
||||||
|
# # ## ## # # # # # # # # ## ## # # # # # # ##### ###### # # ###### ####
|
||||||
|
# # # # # # # # # # # # # # # # # # # # # ## # # # # # # # #
|
||||||
|
# # # # # # # ###### # # # # # # # # ###### # # # # # # ##### ## ##### ####
|
||||||
|
# # # # # # # # # # # # # # # # # # # # # # ## # #
|
||||||
|
# # # # # # # # # # # # # # # # # # # ## # # # # # # # #
|
||||||
|
####### # # ####### # ##### ###### # # ## ##### ### # # ##### ###### # # ###### ####
|
||||||
|
|
||||||
|
|
||||||
|
script to create the required indexes within OMOP common data model, version 5.0 for PostgreSQL database
|
||||||
|
|
||||||
|
last revised: 12 Oct 2014
|
||||||
|
|
||||||
|
author: Patrick Ryan
|
||||||
|
|
||||||
|
description: These indices are considered a minimal requirement to ensure adequate performance of analyses.
|
||||||
|
|
||||||
|
*************************/
|
||||||
|
|
||||||
|
|
||||||
|
/************************
|
||||||
|
|
||||||
|
Standardized vocabulary
|
||||||
|
|
||||||
|
************************/
|
||||||
|
|
||||||
|
CREATE UNIQUE INDEX idx_concept_concept_id ON concept (concept_id ASC);
|
||||||
|
CLUSTER concept USING idx_concept_concept_id ;
|
||||||
|
CREATE INDEX idx_concept_code ON concept (concept_code ASC);
|
||||||
|
CREATE INDEX idx_concept_vocabluary_id ON concept (vocabulary_id ASC);
|
||||||
|
CREATE INDEX idx_concept_domain_id ON concept (domain_id ASC);
|
||||||
|
CREATE INDEX idx_concept_class_id ON concept (concept_class_id ASC);
|
||||||
|
|
||||||
|
CREATE UNIQUE INDEX idx_vocabulary_vocabulary_id ON vocabulary (vocabulary_id ASC);
|
||||||
|
CLUSTER vocabulary USING idx_vocabulary_vocabulary_id ;
|
||||||
|
|
||||||
|
CREATE UNIQUE INDEX idx_domain_domain_id ON domain (domain_id ASC);
|
||||||
|
CLUSTER domain USING idx_domain_domain_id ;
|
||||||
|
|
||||||
|
CREATE UNIQUE INDEX idx_concept_class_class_id ON concept_class (concept_class_id ASC);
|
||||||
|
CLUSTER concept_class USING idx_concept_class_class_id ;
|
||||||
|
|
||||||
|
CREATE INDEX idx_concept_relationship_id_1 ON concept_relationship (concept_id_1 ASC);
|
||||||
|
CREATE INDEX idx_concept_relationship_id_2 ON concept_relationship (concept_id_2 ASC);
|
||||||
|
CREATE INDEX idx_concept_relationship_id_3 ON concept_relationship (relationship_id ASC);
|
||||||
|
|
||||||
|
CREATE UNIQUE INDEX idx_relationship_rel_id ON relationship (relationship_id ASC);
|
||||||
|
CLUSTER relationship USING idx_relationship_rel_id ;
|
||||||
|
|
||||||
|
CREATE INDEX idx_concept_synonym_id ON concept_synonym (concept_id ASC);
|
||||||
|
CLUSTER concept_synonym USING idx_concept_synonym_id ;
|
||||||
|
|
||||||
|
CREATE INDEX idx_concept_ancestor_id_1 ON concept_ancestor (ancestor_concept_id ASC);
|
||||||
|
CLUSTER concept_ancestor USING idx_concept_ancestor_id_1 ;
|
||||||
|
CREATE INDEX idx_concept_ancestor_id_2 ON concept_ancestor (descendant_concept_id ASC);
|
||||||
|
|
||||||
|
CREATE INDEX idx_source_to_concept_map_id_3 ON source_to_concept_map (target_concept_id ASC);
|
||||||
|
CLUSTER source_to_concept_map USING idx_source_to_concept_map_id_3 ;
|
||||||
|
CREATE INDEX idx_source_to_concept_map_id_1 ON source_to_concept_map (source_vocabulary_id ASC);
|
||||||
|
CREATE INDEX idx_source_to_concept_map_id_2 ON source_to_concept_map (target_vocabulary_id ASC);
|
||||||
|
CREATE INDEX idx_source_to_concept_map_code ON source_to_concept_map (source_code ASC);
|
||||||
|
|
||||||
|
CREATE INDEX idx_drug_strength_id_1 ON drug_strength (drug_concept_id ASC);
|
||||||
|
CLUSTER drug_strength USING idx_drug_strength_id_1 ;
|
||||||
|
CREATE INDEX idx_drug_strength_id_2 ON drug_strength (ingredient_concept_id ASC);
|
||||||
|
|
||||||
|
CREATE INDEX idx_cohort_definition_id ON cohort_definition (cohort_definition_id ASC);
|
||||||
|
CLUSTER cohort_definition USING idx_cohort_definition_id ;
|
||||||
|
|
||||||
|
CREATE INDEX idx_attribute_definition_id ON attribute_definition (attribute_definition_id ASC);
|
||||||
|
CLUSTER attribute_definition USING idx_attribute_definition_id ;
|
||||||
|
|
||||||
|
|
||||||
|
/**************************
|
||||||
|
|
||||||
|
Standardized meta-data
|
||||||
|
|
||||||
|
***************************/
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/************************
|
||||||
|
|
||||||
|
Standardized clinical data
|
||||||
|
|
||||||
|
************************/
|
||||||
|
|
||||||
|
CREATE UNIQUE INDEX idx_person_id ON person (person_id ASC);
|
||||||
|
CLUSTER person USING idx_person_id ;
|
||||||
|
|
||||||
|
CREATE INDEX idx_observation_period_id ON observation_period (person_id ASC);
|
||||||
|
CLUSTER observation_period USING idx_observation_period_id ;
|
||||||
|
|
||||||
|
CREATE INDEX idx_specimen_person_id ON specimen (person_id ASC);
|
||||||
|
CLUSTER specimen USING idx_specimen_person_id ;
|
||||||
|
CREATE INDEX idx_specimen_concept_id ON specimen (specimen_concept_id ASC);
|
||||||
|
|
||||||
|
CREATE INDEX idx_death_person_id ON death (person_id ASC);
|
||||||
|
CLUSTER death USING idx_death_person_id ;
|
||||||
|
|
||||||
|
CREATE INDEX idx_visit_person_id ON visit_occurrence (person_id ASC);
|
||||||
|
CLUSTER visit_occurrence USING idx_visit_person_id ;
|
||||||
|
CREATE INDEX idx_visit_concept_id ON visit_occurrence (visit_concept_id ASC);
|
||||||
|
|
||||||
|
CREATE INDEX idx_procedure_person_id ON procedure_occurrence (person_id ASC);
|
||||||
|
CLUSTER procedure_occurrence USING idx_procedure_person_id ;
|
||||||
|
CREATE INDEX idx_procedure_concept_id ON procedure_occurrence (procedure_concept_id ASC);
|
||||||
|
CREATE INDEX idx_procedure_visit_id ON procedure_occurrence (visit_occurrence_id ASC);
|
||||||
|
|
||||||
|
CREATE INDEX idx_drug_person_id ON drug_exposure (person_id ASC);
|
||||||
|
CLUSTER drug_exposure USING idx_drug_person_id ;
|
||||||
|
CREATE INDEX idx_drug_concept_id ON drug_exposure (drug_concept_id ASC);
|
||||||
|
CREATE INDEX idx_drug_visit_id ON drug_exposure (visit_occurrence_id ASC);
|
||||||
|
|
||||||
|
CREATE INDEX idx_device_person_id ON device_exposure (person_id ASC);
|
||||||
|
CLUSTER device_exposure USING idx_device_person_id ;
|
||||||
|
CREATE INDEX idx_device_concept_id ON device_exposure (device_concept_id ASC);
|
||||||
|
CREATE INDEX idx_device_visit_id ON device_exposure (visit_occurrence_id ASC);
|
||||||
|
|
||||||
|
CREATE INDEX idx_condition_person_id ON condition_occurrence (person_id ASC);
|
||||||
|
CLUSTER condition_occurrence USING idx_condition_person_id ;
|
||||||
|
CREATE INDEX idx_condition_concept_id ON condition_occurrence (condition_concept_id ASC);
|
||||||
|
CREATE INDEX idx_condition_visit_id ON condition_occurrence (visit_occurrence_id ASC);
|
||||||
|
|
||||||
|
CREATE INDEX idx_measurement_person_id ON measurement (person_id ASC);
|
||||||
|
CLUSTER measurement USING idx_measurement_person_id ;
|
||||||
|
CREATE INDEX idx_measurement_concept_id ON measurement (measurement_concept_id ASC);
|
||||||
|
CREATE INDEX idx_measurement_visit_id ON measurement (visit_occurrence_id ASC);
|
||||||
|
|
||||||
|
CREATE INDEX idx_note_person_id ON note (person_id ASC);
|
||||||
|
CLUSTER note USING idx_note_person_id ;
|
||||||
|
CREATE INDEX idx_note_concept_id ON note (note_type_concept_id ASC);
|
||||||
|
CREATE INDEX idx_note_visit_id ON note (visit_occurrence_id ASC);
|
||||||
|
|
||||||
|
CREATE INDEX idx_observation_person_id ON observation (person_id ASC);
|
||||||
|
CLUSTER observation USING idx_observation_person_id ;
|
||||||
|
CREATE INDEX idx_observation_concept_id ON observation (observation_concept_id ASC);
|
||||||
|
CREATE INDEX idx_observation_visit_id ON observation (visit_occurrence_id ASC);
|
||||||
|
|
||||||
|
CREATE INDEX idx_fact_relationship_id_1 ON fact_relationship (domain_concept_id_1 ASC);
|
||||||
|
CREATE INDEX idx_fact_relationship_id_2 ON fact_relationship (domain_concept_id_2 ASC);
|
||||||
|
CREATE INDEX idx_fact_relationship_id_3 ON fact_relationship (relationship_concept_id ASC);
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/************************
|
||||||
|
|
||||||
|
Standardized health system data
|
||||||
|
|
||||||
|
************************/
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/************************
|
||||||
|
|
||||||
|
Standardized health economics
|
||||||
|
|
||||||
|
************************/
|
||||||
|
|
||||||
|
CREATE INDEX idx_period_person_id ON payer_plan_period (person_id ASC);
|
||||||
|
CLUSTER payer_plan_period USING idx_period_person_id ;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/************************
|
||||||
|
|
||||||
|
Standardized derived elements
|
||||||
|
|
||||||
|
************************/
|
||||||
|
|
||||||
|
|
||||||
|
CREATE INDEX idx_cohort_subject_id ON cohort (subject_id ASC);
|
||||||
|
CREATE INDEX idx_cohort_c_definition_id ON cohort (cohort_definition_id ASC);
|
||||||
|
|
||||||
|
CREATE INDEX idx_ca_subject_id ON cohort_attribute (subject_id ASC);
|
||||||
|
CREATE INDEX idx_ca_definition_id ON cohort_attribute (cohort_definition_id ASC);
|
||||||
|
|
||||||
|
CREATE INDEX idx_drug_era_person_id ON drug_era (person_id ASC);
|
||||||
|
CLUSTER drug_era USING idx_drug_era_person_id ;
|
||||||
|
CREATE INDEX idx_drug_era_concept_id ON drug_era (drug_concept_id ASC);
|
||||||
|
|
||||||
|
CREATE INDEX idx_dose_era_person_id ON dose_era (person_id ASC);
|
||||||
|
CLUSTER dose_era USING idx_dose_era_person_id ;
|
||||||
|
CREATE INDEX idx_dose_era_concept_id ON dose_era (drug_concept_id ASC);
|
||||||
|
|
||||||
|
CREATE INDEX idx_condition_era_person_id ON condition_era (person_id ASC);
|
||||||
|
CLUSTER condition_era USING idx_condition_era_person_id ;
|
||||||
|
CREATE INDEX idx_condition_era_concept_id ON condition_era (condition_concept_id ASC);
|
||||||
|
|
||||||
|
|
@ -0,0 +1,545 @@
|
||||||
|
/*********************************************************************************
|
||||||
|
# Copyright 2014 Observational Health Data Sciences and Informatics
|
||||||
|
#
|
||||||
|
#
|
||||||
|
# Licensed under the Apache License, Version 2.0 (the "License");
|
||||||
|
# you may not use this file except in compliance with the License.
|
||||||
|
# You may obtain a copy of the License at
|
||||||
|
#
|
||||||
|
# http://www.apache.org/licenses/LICENSE-2.0
|
||||||
|
#
|
||||||
|
# Unless required by applicable law or agreed to in writing, software
|
||||||
|
# distributed under the License is distributed on an "AS IS" BASIS,
|
||||||
|
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
|
||||||
|
# See the License for the specific language governing permissions and
|
||||||
|
# limitations under the License.
|
||||||
|
********************************************************************************/
|
||||||
|
|
||||||
|
/************************
|
||||||
|
|
||||||
|
####### # # ####### ###### ##### ###### # # ####### #####
|
||||||
|
# # ## ## # # # # # # # # ## ## # # # # # #### # # #### ##### ##### ## # # # ##### ####
|
||||||
|
# # # # # # # # # # # # # # # # # # # # # # # ## # # # # # # # # ## # # #
|
||||||
|
# # # # # # # ###### # # # # # # # # ###### # # # # # # #### # # # # # # # # # # ####
|
||||||
|
# # # # # # # # # # # # # # # # # # # # # # # ##### ###### # # # # # #
|
||||||
|
# # # # # # # # # # # # # # # # # # # # # # ## # # # # # # # # # ## # # #
|
||||||
|
####### # # ####### # ##### ###### # # ## ##### ##### #### # # #### # # # # # # # # # ####
|
||||||
|
|
||||||
|
|
||||||
|
script to create constraints within OMOP common data model, version 5.0 for SQL Server database
|
||||||
|
|
||||||
|
last revised: 12 Oct 2014
|
||||||
|
|
||||||
|
author: Patrick Ryan
|
||||||
|
|
||||||
|
|
||||||
|
*************************/
|
||||||
|
|
||||||
|
|
||||||
|
/************************
|
||||||
|
*************************
|
||||||
|
*************************
|
||||||
|
*************************
|
||||||
|
|
||||||
|
Primary key constraints
|
||||||
|
|
||||||
|
*************************
|
||||||
|
*************************
|
||||||
|
*************************
|
||||||
|
************************/
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/************************
|
||||||
|
|
||||||
|
Standardized vocabulary
|
||||||
|
|
||||||
|
************************/
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
ALTER TABLE concept ADD CONSTRAINT xpk_concept PRIMARY KEY NONCLUSTERED (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE vocabulary ADD CONSTRAINT xpk_vocabulary PRIMARY KEY NONCLUSTERED (vocabulary_id);
|
||||||
|
|
||||||
|
ALTER TABLE domain ADD CONSTRAINT xpk_domain PRIMARY KEY NONCLUSTERED (domain_id);
|
||||||
|
|
||||||
|
ALTER TABLE concept_class ADD CONSTRAINT xpk_concept_class PRIMARY KEY NONCLUSTERED (concept_class_id);
|
||||||
|
|
||||||
|
ALTER TABLE concept_relationship ADD CONSTRAINT xpk_concept_relationship PRIMARY KEY NONCLUSTERED (concept_id_1,concept_id_2,relationship_id);
|
||||||
|
|
||||||
|
ALTER TABLE relationship ADD CONSTRAINT xpk_relationship PRIMARY KEY NONCLUSTERED (relationship_id);
|
||||||
|
|
||||||
|
ALTER TABLE concept_ancestor ADD CONSTRAINT xpk_concept_ancestor PRIMARY KEY NONCLUSTERED (ancestor_concept_id,descendant_concept_id);
|
||||||
|
|
||||||
|
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);
|
||||||
|
|
||||||
|
ALTER TABLE drug_strength ADD CONSTRAINT xpk_drug_strength PRIMARY KEY NONCLUSTERED (drug_concept_id, ingredient_concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE cohort_definition ADD CONSTRAINT xpk_cohort_definition PRIMARY KEY NONCLUSTERED (cohort_definition_id);
|
||||||
|
|
||||||
|
ALTER TABLE attribute_definition ADD CONSTRAINT xpk_attribute_definition PRIMARY KEY NONCLUSTERED (attribute_definition_id);
|
||||||
|
|
||||||
|
|
||||||
|
/**************************
|
||||||
|
|
||||||
|
Standardized meta-data
|
||||||
|
|
||||||
|
***************************/
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/************************
|
||||||
|
|
||||||
|
Standardized clinical data
|
||||||
|
|
||||||
|
************************/
|
||||||
|
|
||||||
|
|
||||||
|
/**PRIMARY KEY NONCLUSTERED constraints**/
|
||||||
|
|
||||||
|
ALTER TABLE person ADD CONSTRAINT xpk_person PRIMARY KEY NONCLUSTERED ( person_id ) ;
|
||||||
|
|
||||||
|
ALTER TABLE observation_period ADD CONSTRAINT xpk_observation_period PRIMARY KEY NONCLUSTERED ( observation_period_id ) ;
|
||||||
|
|
||||||
|
ALTER TABLE specimen ADD CONSTRAINT xpk_specimen PRIMARY KEY NONCLUSTERED ( specimen_id ) ;
|
||||||
|
|
||||||
|
ALTER TABLE death ADD CONSTRAINT xpk_death PRIMARY KEY NONCLUSTERED ( person_id ) ;
|
||||||
|
|
||||||
|
ALTER TABLE visit_occurrence ADD CONSTRAINT xpk_visit_occurrence PRIMARY KEY NONCLUSTERED ( visit_occurrence_id ) ;
|
||||||
|
|
||||||
|
ALTER TABLE procedure_occurrence ADD CONSTRAINT xpk_procedure_occurrence PRIMARY KEY NONCLUSTERED ( procedure_occurrence_id ) ;
|
||||||
|
|
||||||
|
ALTER TABLE drug_exposure ADD CONSTRAINT xpk_drug_exposure PRIMARY KEY NONCLUSTERED ( drug_exposure_id ) ;
|
||||||
|
|
||||||
|
ALTER TABLE device_exposure ADD CONSTRAINT xpk_device_exposure PRIMARY KEY NONCLUSTERED ( device_exposure_id ) ;
|
||||||
|
|
||||||
|
ALTER TABLE condition_occurrence ADD CONSTRAINT xpk_condition_occurrence PRIMARY KEY NONCLUSTERED ( condition_occurrence_id ) ;
|
||||||
|
|
||||||
|
ALTER TABLE measurement ADD CONSTRAINT xpk_measurement PRIMARY KEY NONCLUSTERED ( measurement_id ) ;
|
||||||
|
|
||||||
|
ALTER TABLE note ADD CONSTRAINT xpk_note PRIMARY KEY NONCLUSTERED ( note_id ) ;
|
||||||
|
|
||||||
|
ALTER TABLE observation ADD CONSTRAINT xpk_observation PRIMARY KEY NONCLUSTERED ( observation_id ) ;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/************************
|
||||||
|
|
||||||
|
Standardized health system data
|
||||||
|
|
||||||
|
************************/
|
||||||
|
|
||||||
|
|
||||||
|
ALTER TABLE location ADD CONSTRAINT xpk_location PRIMARY KEY NONCLUSTERED ( location_id ) ;
|
||||||
|
|
||||||
|
ALTER TABLE care_site ADD CONSTRAINT xpk_care_site PRIMARY KEY NONCLUSTERED ( care_site_id ) ;
|
||||||
|
|
||||||
|
ALTER TABLE provider ADD CONSTRAINT xpk_provider PRIMARY KEY NONCLUSTERED ( provider_id ) ;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/************************
|
||||||
|
|
||||||
|
Standardized health economics
|
||||||
|
|
||||||
|
************************/
|
||||||
|
|
||||||
|
|
||||||
|
ALTER TABLE payer_plan_period ADD CONSTRAINT xpk_payer_plan_period PRIMARY KEY NONCLUSTERED ( payer_plan_period_id ) ;
|
||||||
|
|
||||||
|
ALTER TABLE visit_cost ADD CONSTRAINT xpk_visit_cost PRIMARY KEY NONCLUSTERED ( visit_cost_id ) ;
|
||||||
|
|
||||||
|
ALTER TABLE procedure_cost ADD CONSTRAINT xpk_procedure_cost PRIMARY KEY NONCLUSTERED ( procedure_cost_id ) ;
|
||||||
|
|
||||||
|
ALTER TABLE drug_cost ADD CONSTRAINT xpk_drug_cost PRIMARY KEY NONCLUSTERED ( drug_cost_id ) ;
|
||||||
|
|
||||||
|
ALTER TABLE device_cost ADD CONSTRAINT xpk_device_cost PRIMARY KEY NONCLUSTERED ( device_cost_id ) ;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/************************
|
||||||
|
|
||||||
|
Standardized derived elements
|
||||||
|
|
||||||
|
************************/
|
||||||
|
|
||||||
|
ALTER TABLE cohort ADD CONSTRAINT xpk_cohort PRIMARY KEY NONCLUSTERED ( cohort_definition_id, subject_id, cohort_start_date, cohort_end_date ) ;
|
||||||
|
|
||||||
|
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 ) ;
|
||||||
|
|
||||||
|
ALTER TABLE drug_era ADD CONSTRAINT xpk_drug_era PRIMARY KEY NONCLUSTERED ( drug_era_id ) ;
|
||||||
|
|
||||||
|
ALTER TABLE dose_era ADD CONSTRAINT xpk_dose_era PRIMARY KEY NONCLUSTERED ( dose_era_id ) ;
|
||||||
|
|
||||||
|
ALTER TABLE condition_era ADD CONSTRAINT xpk_condition_era PRIMARY KEY NONCLUSTERED ( condition_era_id ) ;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/************************
|
||||||
|
*************************
|
||||||
|
*************************
|
||||||
|
*************************
|
||||||
|
|
||||||
|
Foreign key constraints
|
||||||
|
|
||||||
|
*************************
|
||||||
|
*************************
|
||||||
|
*************************
|
||||||
|
************************/
|
||||||
|
|
||||||
|
|
||||||
|
/************************
|
||||||
|
|
||||||
|
Standardized vocabulary
|
||||||
|
|
||||||
|
************************/
|
||||||
|
|
||||||
|
|
||||||
|
ALTER TABLE concept ADD CONSTRAINT fpk_concept_domain FOREIGN KEY (domain_id) REFERENCES domain (domain_id);
|
||||||
|
|
||||||
|
ALTER TABLE concept ADD CONSTRAINT fpk_concept_class FOREIGN KEY (concept_class_id) REFERENCES concept_class (concept_class_id);
|
||||||
|
|
||||||
|
ALTER TABLE concept ADD CONSTRAINT fpk_concept_vocabulary FOREIGN KEY (vocabulary_id) REFERENCES vocabulary (vocabulary_id);
|
||||||
|
|
||||||
|
ALTER TABLE vocabulary ADD CONSTRAINT fpk_vocabulary_concept FOREIGN KEY (vocabulary_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE domain ADD CONSTRAINT fpk_domain_concept FOREIGN KEY (domain_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE concept_class ADD CONSTRAINT fpk_concept_class_concept FOREIGN KEY (concept_class_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE concept_relationship ADD CONSTRAINT fpk_concept_relationship_c_1 FOREIGN KEY (concept_id_1) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE concept_relationship ADD CONSTRAINT fpk_concept_relationship_c_2 FOREIGN KEY (concept_id_2) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE concept_relationship ADD CONSTRAINT fpk_concept_relationship_id FOREIGN KEY (relationship_id) REFERENCES relationship (relationship_id);
|
||||||
|
|
||||||
|
ALTER TABLE relationship ADD CONSTRAINT fpk_relationship_concept FOREIGN KEY (relationship_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE relationship ADD CONSTRAINT fpk_relationship_reverse FOREIGN KEY (reverse_relationship_id) REFERENCES relationship (relationship_id);
|
||||||
|
|
||||||
|
ALTER TABLE concept_synonym ADD CONSTRAINT fpk_concept_synonym_concept FOREIGN KEY (concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE concept_ancestor ADD CONSTRAINT fpk_concept_ancestor_concept_1 FOREIGN KEY (ancestor_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE concept_ancestor ADD CONSTRAINT fpk_concept_ancestor_concept_2 FOREIGN KEY (descendant_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE source_to_concept_map ADD CONSTRAINT fpk_source_to_concept_map_v_1 FOREIGN KEY (source_vocabulary_id) REFERENCES vocabulary (vocabulary_id);
|
||||||
|
|
||||||
|
ALTER TABLE source_to_concept_map ADD CONSTRAINT fpk_source_to_concept_map_v_2 FOREIGN KEY (target_vocabulary_id) REFERENCES vocabulary (vocabulary_id);
|
||||||
|
|
||||||
|
ALTER TABLE source_to_concept_map ADD CONSTRAINT fpk_source_to_concept_map_c_1 FOREIGN KEY (target_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE drug_strength ADD CONSTRAINT fpk_drug_strength_concept_1 FOREIGN KEY (drug_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE drug_strength ADD CONSTRAINT fpk_drug_strength_concept_2 FOREIGN KEY (ingredient_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE drug_strength ADD CONSTRAINT fpk_drug_strength_unit_1 FOREIGN KEY (amount_unit_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE drug_strength ADD CONSTRAINT fpk_drug_strength_unit_2 FOREIGN KEY (numerator_unit_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE drug_strength ADD CONSTRAINT fpk_drug_strength_unit_3 FOREIGN KEY (denominator_unit_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE cohort_definition ADD CONSTRAINT fpk_cohort_definition_concept FOREIGN KEY (definition_type_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
|
||||||
|
/**************************
|
||||||
|
|
||||||
|
Standardized meta-data
|
||||||
|
|
||||||
|
***************************/
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/************************
|
||||||
|
|
||||||
|
Standardized clinical data
|
||||||
|
|
||||||
|
************************/
|
||||||
|
|
||||||
|
ALTER TABLE person ADD CONSTRAINT fpk_person_gender_concept FOREIGN KEY (gender_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE person ADD CONSTRAINT fpk_person_race_concept FOREIGN KEY (race_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE person ADD CONSTRAINT fpk_person_ethnicity_concept FOREIGN KEY (ethnicity_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE person ADD CONSTRAINT fpk_person_gender_concept_s FOREIGN KEY (gender_source_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE person ADD CONSTRAINT fpk_person_race_concept_s FOREIGN KEY (race_source_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE person ADD CONSTRAINT fpk_person_ethnicity_concept_s FOREIGN KEY (ethnicity_source_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE person ADD CONSTRAINT fpk_person_location FOREIGN KEY (location_id) REFERENCES location (location_id);
|
||||||
|
|
||||||
|
ALTER TABLE person ADD CONSTRAINT fpk_person_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
|
||||||
|
|
||||||
|
ALTER TABLE person ADD CONSTRAINT fpk_person_care_site FOREIGN KEY (care_site_id) REFERENCES care_site (care_site_id);
|
||||||
|
|
||||||
|
|
||||||
|
ALTER TABLE observation_period ADD CONSTRAINT fpk_observation_period_person FOREIGN KEY (person_id) REFERENCES person (person_id);
|
||||||
|
|
||||||
|
ALTER TABLE observation_period ADD CONSTRAINT fpk_observation_period_concept FOREIGN KEY (period_type_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
|
||||||
|
ALTER TABLE specimen ADD CONSTRAINT fpk_specimen_person FOREIGN KEY (person_id) REFERENCES person (person_id);
|
||||||
|
|
||||||
|
ALTER TABLE specimen ADD CONSTRAINT fpk_specimen_concept FOREIGN KEY (specimen_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE specimen ADD CONSTRAINT fpk_specimen_type_concept FOREIGN KEY (specimen_type_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE specimen ADD CONSTRAINT fpk_specimen_unit_concept FOREIGN KEY (unit_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE specimen ADD CONSTRAINT fpk_specimen_site_concept FOREIGN KEY (anatomic_site_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE specimen ADD CONSTRAINT fpk_specimen_status_concept FOREIGN KEY (disease_status_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
|
||||||
|
ALTER TABLE death ADD CONSTRAINT fpk_death_person FOREIGN KEY (person_id) REFERENCES person (person_id);
|
||||||
|
|
||||||
|
ALTER TABLE death ADD CONSTRAINT fpk_death_type_concept FOREIGN KEY (death_type_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE death ADD CONSTRAINT fpk_death_cause_concept FOREIGN KEY (cause_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE death ADD CONSTRAINT fpk_death_cause_concept_s FOREIGN KEY (cause_source_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
|
||||||
|
ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_person FOREIGN KEY (person_id) REFERENCES person (person_id);
|
||||||
|
|
||||||
|
ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_concept FOREIGN KEY (visit_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_type_concept FOREIGN KEY (visit_type_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
|
||||||
|
|
||||||
|
ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_care_site FOREIGN KEY (care_site_id) REFERENCES care_site (care_site_id);
|
||||||
|
|
||||||
|
ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_concept_s FOREIGN KEY (visit_source_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
|
||||||
|
ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_person FOREIGN KEY (person_id) REFERENCES person (person_id);
|
||||||
|
|
||||||
|
ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_concept FOREIGN KEY (procedure_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_type_concept FOREIGN KEY (procedure_type_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_modifier FOREIGN KEY (modifier_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
|
||||||
|
|
||||||
|
ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id);
|
||||||
|
|
||||||
|
ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_concept_s FOREIGN KEY (procedure_source_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
|
||||||
|
ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_person FOREIGN KEY (person_id) REFERENCES person (person_id);
|
||||||
|
|
||||||
|
ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_concept FOREIGN KEY (drug_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_type_concept FOREIGN KEY (drug_type_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_route_concept FOREIGN KEY (route_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_dose_unit_concept FOREIGN KEY (dose_unit_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
|
||||||
|
|
||||||
|
ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id);
|
||||||
|
|
||||||
|
ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_concept_s FOREIGN KEY (drug_source_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
|
||||||
|
ALTER TABLE device_exposure ADD CONSTRAINT fpk_device_person FOREIGN KEY (person_id) REFERENCES person (person_id);
|
||||||
|
|
||||||
|
ALTER TABLE device_exposure ADD CONSTRAINT fpk_device_concept FOREIGN KEY (device_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE device_exposure ADD CONSTRAINT fpk_device_type_concept FOREIGN KEY (device_type_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE device_exposure ADD CONSTRAINT fpk_device_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
|
||||||
|
|
||||||
|
ALTER TABLE device_exposure ADD CONSTRAINT fpk_device_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id);
|
||||||
|
|
||||||
|
ALTER TABLE device_exposure ADD CONSTRAINT fpk_device_concept_s FOREIGN KEY (device_source_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
|
||||||
|
ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_person FOREIGN KEY (person_id) REFERENCES person (person_id);
|
||||||
|
|
||||||
|
ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_concept FOREIGN KEY (condition_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_type_concept FOREIGN KEY (condition_type_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
|
||||||
|
|
||||||
|
ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id);
|
||||||
|
|
||||||
|
ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_concept_s FOREIGN KEY (condition_source_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
|
||||||
|
ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_person FOREIGN KEY (person_id) REFERENCES person (person_id);
|
||||||
|
|
||||||
|
ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_concept FOREIGN KEY (measurement_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_type_concept FOREIGN KEY (measurement_type_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_operator FOREIGN KEY (operator_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_value FOREIGN KEY (value_as_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_unit FOREIGN KEY (unit_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
|
||||||
|
|
||||||
|
ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id);
|
||||||
|
|
||||||
|
ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_concept_s FOREIGN KEY (measurement_source_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
|
||||||
|
ALTER TABLE note ADD CONSTRAINT fpk_note_person FOREIGN KEY (person_id) REFERENCES person (person_id);
|
||||||
|
|
||||||
|
ALTER TABLE note ADD CONSTRAINT fpk_note_type_concept FOREIGN KEY (note_type_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE note ADD CONSTRAINT fpk_note_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
|
||||||
|
|
||||||
|
ALTER TABLE note ADD CONSTRAINT fpk_note_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id);
|
||||||
|
|
||||||
|
|
||||||
|
ALTER TABLE observation ADD CONSTRAINT fpk_observation_person FOREIGN KEY (person_id) REFERENCES person (person_id);
|
||||||
|
|
||||||
|
ALTER TABLE observation ADD CONSTRAINT fpk_observation_concept FOREIGN KEY (observation_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE observation ADD CONSTRAINT fpk_observation_type_concept FOREIGN KEY (observation_type_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE observation ADD CONSTRAINT fpk_observation_value FOREIGN KEY (value_as_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE observation ADD CONSTRAINT fpk_observation_qualifier FOREIGN KEY (qualifier_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE observation ADD CONSTRAINT fpk_observation_unit FOREIGN KEY (unit_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE observation ADD CONSTRAINT fpk_observation_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
|
||||||
|
|
||||||
|
ALTER TABLE observation ADD CONSTRAINT fpk_observation_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id);
|
||||||
|
|
||||||
|
ALTER TABLE observation ADD CONSTRAINT fpk_observation_concept_s FOREIGN KEY (observation_source_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
|
||||||
|
ALTER TABLE fact_relationship ADD CONSTRAINT fpk_fact_domain_1 FOREIGN KEY (domain_concept_id_1) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE fact_relationship ADD CONSTRAINT fpk_fact_domain_2 FOREIGN KEY (domain_concept_id_2) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE fact_relationship ADD CONSTRAINT fpk_fact_relationship FOREIGN KEY (relationship_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/************************
|
||||||
|
|
||||||
|
Standardized health system data
|
||||||
|
|
||||||
|
************************/
|
||||||
|
|
||||||
|
ALTER TABLE care_site ADD CONSTRAINT fpk_care_site_location FOREIGN KEY (location_id) REFERENCES location (location_id);
|
||||||
|
|
||||||
|
ALTER TABLE care_site ADD CONSTRAINT fpk_care_site_place FOREIGN KEY (place_of_service_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
|
||||||
|
ALTER TABLE provider ADD CONSTRAINT fpk_provider_specialty FOREIGN KEY (specialty_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE provider ADD CONSTRAINT fpk_provider_care_site FOREIGN KEY (care_site_id) REFERENCES care_site (care_site_id);
|
||||||
|
|
||||||
|
ALTER TABLE provider ADD CONSTRAINT fpk_provider_gender FOREIGN KEY (gender_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE provider ADD CONSTRAINT fpk_provider_specialty_s FOREIGN KEY (specialty_source_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE provider ADD CONSTRAINT fpk_provider_gender_s FOREIGN KEY (gender_source_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/************************
|
||||||
|
|
||||||
|
Standardized health economics
|
||||||
|
|
||||||
|
************************/
|
||||||
|
|
||||||
|
ALTER TABLE payer_plan_period ADD CONSTRAINT fpk_payer_plan_period FOREIGN KEY (person_id) REFERENCES person (person_id);
|
||||||
|
|
||||||
|
|
||||||
|
ALTER TABLE visit_cost ADD CONSTRAINT fpk_visit_cost_id FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id);
|
||||||
|
|
||||||
|
ALTER TABLE visit_cost ADD CONSTRAINT fpk_visit_cost_currency FOREIGN KEY (currency_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE visit_cost ADD CONSTRAINT fpk_visit_cost_period FOREIGN KEY (payer_plan_period_id) REFERENCES payer_plan_period (payer_plan_period_id);
|
||||||
|
|
||||||
|
|
||||||
|
ALTER TABLE procedure_cost ADD CONSTRAINT fpk_procedure_cost_id FOREIGN KEY (procedure_occurrence_id) REFERENCES procedure_occurrence (procedure_occurrence_id);
|
||||||
|
|
||||||
|
ALTER TABLE procedure_cost ADD CONSTRAINT fpk_procedure_cost_currency FOREIGN KEY (currency_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE procedure_cost ADD CONSTRAINT fpk_procedure_cost_period FOREIGN KEY (payer_plan_period_id) REFERENCES payer_plan_period (payer_plan_period_id);
|
||||||
|
|
||||||
|
ALTER TABLE procedure_cost ADD CONSTRAINT fpk_procedure_cost_revenue FOREIGN KEY (revenue_code_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
|
||||||
|
ALTER TABLE drug_cost ADD CONSTRAINT fpk_drug_cost_id FOREIGN KEY (drug_exposure_id) REFERENCES drug_exposure (drug_exposure_id);
|
||||||
|
|
||||||
|
ALTER TABLE drug_cost ADD CONSTRAINT fpk_drug_cost_currency FOREIGN KEY (currency_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE drug_cost ADD CONSTRAINT fpk_drug_cost_period FOREIGN KEY (payer_plan_period_id) REFERENCES payer_plan_period (payer_plan_period_id);
|
||||||
|
|
||||||
|
|
||||||
|
ALTER TABLE device_cost ADD CONSTRAINT fpk_device_cost_id FOREIGN KEY (device_exposure_id) REFERENCES device_exposure (device_exposure_id);
|
||||||
|
|
||||||
|
ALTER TABLE device_cost ADD CONSTRAINT fpk_device_cost_currency FOREIGN KEY (currency_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE device_cost ADD CONSTRAINT fpk_device_cost_period FOREIGN KEY (payer_plan_period_id) REFERENCES payer_plan_period (payer_plan_period_id);
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/************************
|
||||||
|
|
||||||
|
Standardized derived elements
|
||||||
|
|
||||||
|
************************/
|
||||||
|
|
||||||
|
|
||||||
|
ALTER TABLE cohort ADD CONSTRAINT fpk_cohort_definition FOREIGN KEY (cohort_definition_id) REFERENCES cohort_definition (cohort_definition_id);
|
||||||
|
|
||||||
|
|
||||||
|
ALTER TABLE cohort_attribute ADD CONSTRAINT fpk_ca_cohort_definition FOREIGN KEY (cohort_definition_id) REFERENCES cohort_definition (cohort_definition_id);
|
||||||
|
|
||||||
|
ALTER TABLE cohort_attribute ADD CONSTRAINT fpk_ca_attribute_definition FOREIGN KEY (attribute_definition_id) REFERENCES attribute_definition (attribute_definition_id);
|
||||||
|
|
||||||
|
ALTER TABLE cohort_attribute ADD CONSTRAINT fpk_ca_value FOREIGN KEY (value_as_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
|
||||||
|
ALTER TABLE drug_era ADD CONSTRAINT fpk_drug_era_person FOREIGN KEY (person_id) REFERENCES person (person_id);
|
||||||
|
|
||||||
|
ALTER TABLE drug_era ADD CONSTRAINT fpk_drug_era_concept FOREIGN KEY (drug_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
|
||||||
|
ALTER TABLE dose_era ADD CONSTRAINT fpk_dose_era_person FOREIGN KEY (person_id) REFERENCES person (person_id);
|
||||||
|
|
||||||
|
ALTER TABLE dose_era ADD CONSTRAINT fpk_dose_era_concept FOREIGN KEY (drug_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
ALTER TABLE dose_era ADD CONSTRAINT fpk_dose_era_unit_concept FOREIGN KEY (unit_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
|
||||||
|
ALTER TABLE condition_era ADD CONSTRAINT fpk_condition_era_person FOREIGN KEY (person_id) REFERENCES person (person_id);
|
||||||
|
|
||||||
|
ALTER TABLE condition_era ADD CONSTRAINT fpk_condition_era_concept FOREIGN KEY (condition_concept_id) REFERENCES concept (concept_id);
|
||||||
|
|
||||||
|
|
@ -0,0 +1,709 @@
|
||||||
|
/*********************************************************************************
|
||||||
|
# Copyright 2014 Observational Health Data Sciences and Informatics
|
||||||
|
#
|
||||||
|
#
|
||||||
|
# Licensed under the Apache License, Version 2.0 (the "License");
|
||||||
|
# you may not use this file except in compliance with the License.
|
||||||
|
# You may obtain a copy of the License at
|
||||||
|
#
|
||||||
|
# http://www.apache.org/licenses/LICENSE-2.0
|
||||||
|
#
|
||||||
|
# Unless required by applicable law or agreed to in writing, software
|
||||||
|
# distributed under the License is distributed on an "AS IS" BASIS,
|
||||||
|
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
|
||||||
|
# See the License for the specific language governing permissions and
|
||||||
|
# limitations under the License.
|
||||||
|
********************************************************************************/
|
||||||
|
|
||||||
|
/************************
|
||||||
|
|
||||||
|
####### # # ####### ###### ##### ###### # # #######
|
||||||
|
# # ## ## # # # # # # # # ## ## # # #
|
||||||
|
# # # # # # # # # # # # # # # # # # # #
|
||||||
|
# # # # # # # ###### # # # # # # # # ######
|
||||||
|
# # # # # # # # # # # # # # #
|
||||||
|
# # # # # # # # # # # # # # # # #
|
||||||
|
####### # # ####### # ##### ###### # # ## #####
|
||||||
|
|
||||||
|
|
||||||
|
script to create OMOP common data model, version 5.0 for SQL Server database
|
||||||
|
|
||||||
|
last revised: 12 Oct 2014
|
||||||
|
|
||||||
|
author: Patrick Ryan
|
||||||
|
|
||||||
|
|
||||||
|
*************************/
|
||||||
|
|
||||||
|
|
||||||
|
/************************
|
||||||
|
|
||||||
|
Standardized vocabulary
|
||||||
|
|
||||||
|
************************/
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE concept (
|
||||||
|
concept_id INTEGER NOT NULL,
|
||||||
|
concept_name VARCHAR(255) NOT NULL,
|
||||||
|
domain_id VARCHAR(20) NOT NULL,
|
||||||
|
vocabulary_id VARCHAR(20) NOT NULL,
|
||||||
|
concept_class_id VARCHAR(20) NOT NULL,
|
||||||
|
standard_concept VARCHAR(1) NULL,
|
||||||
|
concept_code VARCHAR(50) NOT NULL,
|
||||||
|
valid_start_date DATE NOT NULL,
|
||||||
|
valid_end_date DATE NOT NULL,
|
||||||
|
invalid_reason VARCHAR(1) NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE vocabulary (
|
||||||
|
vocabulary_id VARCHAR(20) NOT NULL,
|
||||||
|
vocabulary_name VARCHAR(255) NOT NULL,
|
||||||
|
vocabulary_reference VARCHAR(255) NULL,
|
||||||
|
vocabulary_version VARCHAR(255) NULL,
|
||||||
|
vocabulary_concept_id INTEGER NOT NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE domain (
|
||||||
|
domain_id VARCHAR(20) NOT NULL,
|
||||||
|
domain_name VARCHAR(255) NOT NULL,
|
||||||
|
domain_concept_id INTEGER NOT NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE concept_class (
|
||||||
|
concept_class_id VARCHAR(20) NOT NULL,
|
||||||
|
concept_class_name VARCHAR(255) NOT NULL,
|
||||||
|
concept_class_concept_id INTEGER NOT NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE concept_relationship (
|
||||||
|
concept_id_1 INTEGER NOT NULL,
|
||||||
|
concept_id_2 INTEGER NOT NULL,
|
||||||
|
relationship_id VARCHAR(20) NOT NULL,
|
||||||
|
valid_start_date DATE NOT NULL,
|
||||||
|
valid_end_date DATE NOT NULL,
|
||||||
|
invalid_reason VARCHAR(1) NULL)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE relationship (
|
||||||
|
relationship_id VARCHAR(20) NOT NULL,
|
||||||
|
relationship_name VARCHAR(255) NOT NULL,
|
||||||
|
is_hierarchical VARCHAR(1) NOT NULL,
|
||||||
|
defines_ancestry VARCHAR(1) NOT NULL,
|
||||||
|
reverse_relationship_id VARCHAR(20) NOT NULL,
|
||||||
|
relationship_concept_id INTEGER NOT NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE concept_synonym (
|
||||||
|
concept_id INTEGER NOT NULL,
|
||||||
|
concept_synonym_name VARCHAR(1000) NOT NULL,
|
||||||
|
language_concept_id INTEGER NOT NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE concept_ancestor (
|
||||||
|
ancestor_concept_id INTEGER NOT NULL,
|
||||||
|
descendant_concept_id INTEGER NOT NULL,
|
||||||
|
min_levels_of_separation INTEGER NOT NULL,
|
||||||
|
max_levels_of_separation INTEGER NOT NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE source_to_concept_map (
|
||||||
|
source_code VARCHAR(50) NOT NULL,
|
||||||
|
source_concept_id INTEGER NOT NULL,
|
||||||
|
source_vocabulary_id VARCHAR(20) NOT NULL,
|
||||||
|
source_code_description VARCHAR(255) NULL,
|
||||||
|
target_concept_id INTEGER NOT NULL,
|
||||||
|
target_vocabulary_id VARCHAR(20) NOT NULL,
|
||||||
|
valid_start_date DATE NOT NULL,
|
||||||
|
valid_end_date DATE NOT NULL,
|
||||||
|
invalid_reason VARCHAR(1) NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE drug_strength (
|
||||||
|
drug_concept_id INTEGER NOT NULL,
|
||||||
|
ingredient_concept_id INTEGER NOT NULL,
|
||||||
|
amount_value FLOAT NULL,
|
||||||
|
amount_unit_concept_id INTEGER NULL,
|
||||||
|
numerator_value FLOAT NULL,
|
||||||
|
numerator_unit_concept_id INTEGER NULL,
|
||||||
|
denominator_unit_concept_id INTEGER NULL,
|
||||||
|
valid_start_date DATE NOT NULL,
|
||||||
|
valid_end_date DATE NOT NULL,
|
||||||
|
invalid_reason VARCHAR(1) NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE cohort_definition (
|
||||||
|
cohort_definition_id INTEGER NOT NULL,
|
||||||
|
cohort_definition_name VARCHAR(255) NOT NULL,
|
||||||
|
cohort_definition_description VARCHAR(MAX) NULL,
|
||||||
|
definition_type_concept_id INTEGER NOT NULL,
|
||||||
|
cohort_definition_syntax VARCHAR(MAX) NULL,
|
||||||
|
subject_concept_id INTEGER NOT NULL,
|
||||||
|
cohort_initiation_date DATE NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE attribute_definition (
|
||||||
|
attribute_definition_id INTEGER NOT NULL,
|
||||||
|
attribute_name VARCHAR(255) NOT NULL,
|
||||||
|
attribute_description VARCHAR(MAX) NULL,
|
||||||
|
attribute_type_concept_id INTEGER NOT NULL,
|
||||||
|
attribute_syntax VARCHAR(MAX) NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
/**************************
|
||||||
|
|
||||||
|
Standardized meta-data
|
||||||
|
|
||||||
|
***************************/
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE cdm_source
|
||||||
|
(
|
||||||
|
cdm_source_name VARCHAR(255) NOT NULL,
|
||||||
|
cdm_source_abbreviation VARCHAR(25) NULL,
|
||||||
|
cdm_holder VARCHAR(255) NULL,
|
||||||
|
source_description VARCHAR(MAX) NULL,
|
||||||
|
source_documentation_reference VARCHAR(255) NULL,
|
||||||
|
cdm_etl_reference VARCHAR(255) NULL,
|
||||||
|
source_release_date DATE NULL,
|
||||||
|
cdm_release_date DATE NULL,
|
||||||
|
cdm_version VARCHAR(10) NULL,
|
||||||
|
vocabulary_version VARCHAR(20) NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/************************
|
||||||
|
|
||||||
|
Standardized clinical data
|
||||||
|
|
||||||
|
************************/
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE person
|
||||||
|
(
|
||||||
|
person_id INTEGER NOT NULL ,
|
||||||
|
gender_concept_id INTEGER NOT NULL ,
|
||||||
|
year_of_birth INTEGER NOT NULL ,
|
||||||
|
month_of_birth INTEGER NULL,
|
||||||
|
day_of_birth INTEGER NULL,
|
||||||
|
time_of_birth VARCHAR(10) NULL,
|
||||||
|
race_concept_id INTEGER NOT NULL,
|
||||||
|
ethnicity_concept_id INTEGER NOT NULL,
|
||||||
|
location_id INTEGER NULL,
|
||||||
|
provider_id INTEGER NULL,
|
||||||
|
care_site_id INTEGER NULL,
|
||||||
|
person_source_value VARCHAR(50) NULL,
|
||||||
|
gender_source_value VARCHAR(50) NULL,
|
||||||
|
gender_source_concept_id INTEGER NULL,
|
||||||
|
race_source_value VARCHAR(50) NULL,
|
||||||
|
race_source_concept_id INTEGER NULL,
|
||||||
|
ethnicity_source_value VARCHAR(50) NULL,
|
||||||
|
ethnicity_source_concept_id INTEGER NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE observation_period
|
||||||
|
(
|
||||||
|
observation_period_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
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE specimen
|
||||||
|
(
|
||||||
|
specimen_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 ,
|
||||||
|
specimen_time VARCHAR(10) NULL ,
|
||||||
|
quantity FLOAT NULL ,
|
||||||
|
unit_concept_id INTEGER NULL ,
|
||||||
|
anatomic_site_concept_id INTEGER NULL ,
|
||||||
|
disease_status_concept_id INTEGER NULL ,
|
||||||
|
specimen_source_id VARCHAR(50) NULL ,
|
||||||
|
specimen_source_value VARCHAR(50) NULL ,
|
||||||
|
unit_source_value VARCHAR(50) NULL ,
|
||||||
|
anatomic_site_source_value VARCHAR(50) NULL ,
|
||||||
|
disease_status_source_value VARCHAR(50) NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE death
|
||||||
|
(
|
||||||
|
person_id INTEGER NOT NULL ,
|
||||||
|
death_date DATE NOT NULL ,
|
||||||
|
death_type_concept_id INTEGER NOT NULL ,
|
||||||
|
cause_concept_id INTEGER NULL ,
|
||||||
|
cause_source_value VARCHAR(50) NULL,
|
||||||
|
cause_source_concept_id INTEGER NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE visit_occurrence
|
||||||
|
(
|
||||||
|
visit_occurrence_id INTEGER NOT NULL ,
|
||||||
|
person_id INTEGER NOT NULL ,
|
||||||
|
visit_concept_id INTEGER NOT NULL ,
|
||||||
|
visit_start_date DATE NOT NULL ,
|
||||||
|
visit_start_time VARCHAR(10) NULL ,
|
||||||
|
visit_end_date DATE NOT NULL ,
|
||||||
|
visit_end_time VARCHAR(10) NULL ,
|
||||||
|
visit_type_concept_id INTEGER NOT NULL ,
|
||||||
|
provider_id INTEGER NULL,
|
||||||
|
care_site_id INTEGER NULL,
|
||||||
|
visit_source_value VARCHAR(50) NULL,
|
||||||
|
visit_source_concept_id INTEGER NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE procedure_occurrence
|
||||||
|
(
|
||||||
|
procedure_occurrence_id INTEGER NOT NULL ,
|
||||||
|
person_id INTEGER NOT NULL ,
|
||||||
|
procedure_concept_id INTEGER NOT NULL ,
|
||||||
|
procedure_date DATE NOT NULL ,
|
||||||
|
procedure_type_concept_id INTEGER NOT NULL ,
|
||||||
|
modifier_concept_id INTEGER NULL ,
|
||||||
|
quantity INTEGER NULL ,
|
||||||
|
provider_id INTEGER NULL ,
|
||||||
|
visit_occurrence_id INTEGER NULL ,
|
||||||
|
procedure_source_value VARCHAR(50) NULL ,
|
||||||
|
procedure_source_concept_id INTEGER NULL ,
|
||||||
|
qualifier_source_value VARCHAR(50) NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE drug_exposure
|
||||||
|
(
|
||||||
|
drug_exposure_id INTEGER NOT NULL ,
|
||||||
|
person_id INTEGER NOT NULL ,
|
||||||
|
drug_concept_id INTEGER NOT NULL ,
|
||||||
|
drug_exposure_start_date DATE NOT NULL ,
|
||||||
|
drug_exposure_end_date DATE NULL ,
|
||||||
|
drug_type_concept_id INTEGER NOT NULL ,
|
||||||
|
stop_reason VARCHAR(20) NULL ,
|
||||||
|
refills INTEGER NULL ,
|
||||||
|
quantity FLOAT NULL ,
|
||||||
|
days_supply INTEGER NULL ,
|
||||||
|
sig VARCHAR(MAX) NULL ,
|
||||||
|
route_concept_id INTEGER NULL ,
|
||||||
|
effective_drug_dose FLOAT NULL ,
|
||||||
|
dose_unit_concept_id INTEGER NULL ,
|
||||||
|
lot_number VARCHAR(50) NULL ,
|
||||||
|
provider_id INTEGER NULL ,
|
||||||
|
visit_occurrence_id INTEGER NULL ,
|
||||||
|
drug_source_value VARCHAR(50) NULL ,
|
||||||
|
drug_source_concept_id INTEGER NULL ,
|
||||||
|
route_source_value VARCHAR(50) NULL ,
|
||||||
|
dose_unit_source_value VARCHAR(50) NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE device_exposure
|
||||||
|
(
|
||||||
|
device_exposure_id INTEGER NOT NULL ,
|
||||||
|
person_id INTEGER NOT NULL ,
|
||||||
|
device_concept_id INTEGER NOT NULL ,
|
||||||
|
device_exposure_start_date DATE NOT NULL ,
|
||||||
|
device_exposure_end_date DATE NULL ,
|
||||||
|
device_type_concept_id INTEGER NOT NULL ,
|
||||||
|
unique_device_id VARCHAR(50) NULL ,
|
||||||
|
quantity INTEGER NULL ,
|
||||||
|
provider_id INTEGER NULL ,
|
||||||
|
visit_occurrence_id INTEGER NULL ,
|
||||||
|
device_source_value VARCHAR(100) NULL ,
|
||||||
|
device_source_concept_id INTEGER NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE condition_occurrence
|
||||||
|
(
|
||||||
|
condition_occurrence_id INTEGER NOT NULL ,
|
||||||
|
person_id INTEGER NOT NULL ,
|
||||||
|
condition_concept_id INTEGER NOT NULL ,
|
||||||
|
condition_start_date DATE NOT NULL ,
|
||||||
|
condition_end_date DATE NULL ,
|
||||||
|
condition_type_concept_id INTEGER NOT NULL ,
|
||||||
|
stop_reason VARCHAR(20) NULL ,
|
||||||
|
provider_id INTEGER NULL ,
|
||||||
|
visit_occurrence_id INTEGER NULL ,
|
||||||
|
condition_source_value VARCHAR(50) NULL ,
|
||||||
|
condition_source_concept_id INTEGER NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE measurement
|
||||||
|
(
|
||||||
|
measurement_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 ,
|
||||||
|
measurement_type_concept_id INTEGER NOT NULL ,
|
||||||
|
operator_concept_id INTEGER NULL ,
|
||||||
|
value_as_number FLOAT NULL ,
|
||||||
|
value_as_concept_id INTEGER NULL ,
|
||||||
|
unit_concept_id INTEGER NULL ,
|
||||||
|
range_low FLOAT NULL ,
|
||||||
|
range_high FLOAT NULL ,
|
||||||
|
provider_id INTEGER NULL ,
|
||||||
|
visit_occurrence_id INTEGER NULL ,
|
||||||
|
measurement_source_value VARCHAR(50) NULL ,
|
||||||
|
measurement_source_concept_id INTEGER NULL ,
|
||||||
|
unit_source_value VARCHAR(50) NULL ,
|
||||||
|
value_source_value VARCHAR(50) NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE note
|
||||||
|
(
|
||||||
|
note_id INTEGER NOT NULL ,
|
||||||
|
person_id INTEGER NOT NULL ,
|
||||||
|
note_date DATE NOT NULL ,
|
||||||
|
note_time VARCHAR(10) NULL ,
|
||||||
|
note_type_concept_id INTEGER NOT NULL ,
|
||||||
|
note_text VARCHAR(MAX) NOT NULL ,
|
||||||
|
provider_id INTEGER NULL ,
|
||||||
|
visit_occurrence_id INTEGER NULL ,
|
||||||
|
note_source_value VARCHAR(50) NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE observation
|
||||||
|
(
|
||||||
|
observation_id INTEGER NOT NULL ,
|
||||||
|
person_id INTEGER NOT NULL ,
|
||||||
|
observation_concept_id INTEGER NOT NULL ,
|
||||||
|
observation_date DATE NOT NULL ,
|
||||||
|
observation_time VARCHAR(10) NULL ,
|
||||||
|
observation_type_concept_id INTEGER NOT NULL ,
|
||||||
|
value_as_number FLOAT NULL ,
|
||||||
|
value_as_string VARCHAR(60) NULL ,
|
||||||
|
value_as_concept_id INTEGER NULL ,
|
||||||
|
qualifier_concept_id INTEGER NULL ,
|
||||||
|
unit_concept_id INTEGER NULL ,
|
||||||
|
provider_id INTEGER NULL ,
|
||||||
|
visit_occurrence_id INTEGER NULL ,
|
||||||
|
observation_source_value VARCHAR(50) NULL ,
|
||||||
|
observation_source_concept_id INTEGER NULL ,
|
||||||
|
unit_source_value VARCHAR(50) NULL ,
|
||||||
|
qualifier_source_value VARCHAR(50) NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE fact_relationship
|
||||||
|
(
|
||||||
|
domain_concept_id_1 INTEGER NOT NULL ,
|
||||||
|
fact_id_1 INTEGER NOT NULL ,
|
||||||
|
domain_concept_id_2 INTEGER NOT NULL ,
|
||||||
|
fact_id_2 INTEGER NOT NULL ,
|
||||||
|
relationship_concept_id INTEGER NOT NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/************************
|
||||||
|
|
||||||
|
Standardized health system data
|
||||||
|
|
||||||
|
************************/
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE location
|
||||||
|
(
|
||||||
|
location_id INTEGER NOT NULL ,
|
||||||
|
address_1 VARCHAR(50) NULL ,
|
||||||
|
address_2 VARCHAR(50) NULL ,
|
||||||
|
city VARCHAR(50) NULL ,
|
||||||
|
state VARCHAR(2) NULL ,
|
||||||
|
zip VARCHAR(9) NULL ,
|
||||||
|
county VARCHAR(20) NULL ,
|
||||||
|
location_source_value VARCHAR(50) NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE care_site
|
||||||
|
(
|
||||||
|
care_site_id INTEGER NOT NULL ,
|
||||||
|
care_site_name VARCHAR(255) NULL ,
|
||||||
|
place_of_service_concept_id INTEGER NULL ,
|
||||||
|
location_id INTEGER NULL ,
|
||||||
|
care_site_source_value VARCHAR(50) NULL ,
|
||||||
|
place_of_service_source_value VARCHAR(50) NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE provider
|
||||||
|
(
|
||||||
|
provider_id INTEGER NOT NULL ,
|
||||||
|
provider_name VARCHAR(255) NULL ,
|
||||||
|
NPI VARCHAR(20) NULL ,
|
||||||
|
DEA VARCHAR(20) NULL ,
|
||||||
|
specialty_concept_id INTEGER NULL ,
|
||||||
|
care_site_id INTEGER NULL ,
|
||||||
|
year_of_birth INTEGER NULL ,
|
||||||
|
gender_concept_id INTEGER NULL ,
|
||||||
|
provider_source_value VARCHAR(50) NULL ,
|
||||||
|
specialty_source_value VARCHAR(50) NULL ,
|
||||||
|
specialty_source_concept_id INTEGER NULL ,
|
||||||
|
gender_source_value VARCHAR(50) NULL ,
|
||||||
|
gender_source_concept_id INTEGER NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/************************
|
||||||
|
|
||||||
|
Standardized health economics
|
||||||
|
|
||||||
|
************************/
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE payer_plan_period
|
||||||
|
(
|
||||||
|
payer_plan_period_id INTEGER NOT NULL ,
|
||||||
|
person_id INTEGER NOT NULL ,
|
||||||
|
payer_plan_period_start_date DATE NOT NULL ,
|
||||||
|
payer_plan_period_end_date DATE NOT NULL ,
|
||||||
|
payer_source_value VARCHAR (50) NULL ,
|
||||||
|
plan_source_value VARCHAR (50) NULL ,
|
||||||
|
family_source_value VARCHAR (50) NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE visit_cost
|
||||||
|
(
|
||||||
|
visit_cost_id INTEGER NOT NULL ,
|
||||||
|
visit_occurrence_id INTEGER NOT NULL ,
|
||||||
|
currency_concept_id INTEGER NULL ,
|
||||||
|
paid_copay FLOAT NULL ,
|
||||||
|
paid_coinsurance FLOAT NULL ,
|
||||||
|
paid_toward_deductible FLOAT NULL ,
|
||||||
|
paid_by_payer FLOAT NULL ,
|
||||||
|
paid_by_coordination_benefits FLOAT NULL ,
|
||||||
|
total_out_of_pocket FLOAT NULL ,
|
||||||
|
total_paid FLOAT NULL ,
|
||||||
|
payer_plan_period_id INTEGER NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE procedure_cost
|
||||||
|
(
|
||||||
|
procedure_cost_id INTEGER NOT NULL ,
|
||||||
|
procedure_occurrence_id INTEGER NOT NULL ,
|
||||||
|
currency_concept_id INTEGER NULL ,
|
||||||
|
paid_copay FLOAT NULL ,
|
||||||
|
paid_coinsurance FLOAT NULL ,
|
||||||
|
paid_toward_deductible FLOAT NULL ,
|
||||||
|
paid_by_payer FLOAT NULL ,
|
||||||
|
paid_by_coordination_benefits FLOAT NULL ,
|
||||||
|
total_out_of_pocket FLOAT NULL ,
|
||||||
|
total_paid FLOAT NULL ,
|
||||||
|
revenue_code_concept_id INTEGER NULL ,
|
||||||
|
payer_plan_period_id INTEGER NULL ,
|
||||||
|
revenue_code_source_value VARCHAR(50) NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE drug_cost
|
||||||
|
(
|
||||||
|
drug_cost_id INTEGER NOT NULL ,
|
||||||
|
drug_exposure_id INTEGER NOT NULL ,
|
||||||
|
currency_concept_id INTEGER NULL ,
|
||||||
|
paid_copay FLOAT NULL ,
|
||||||
|
paid_coinsurance FLOAT NULL ,
|
||||||
|
paid_toward_deductible FLOAT NULL ,
|
||||||
|
paid_by_payer FLOAT NULL ,
|
||||||
|
paid_by_coordination_benefits FLOAT NULL ,
|
||||||
|
total_out_of_pocket FLOAT NULL ,
|
||||||
|
total_paid FLOAT NULL ,
|
||||||
|
ingredient_cost FLOAT NULL ,
|
||||||
|
dispensing_fee FLOAT NULL ,
|
||||||
|
average_wholesale_price FLOAT NULL ,
|
||||||
|
payer_plan_period_id INTEGER NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE device_cost
|
||||||
|
(
|
||||||
|
device_cost_id INTEGER NOT NULL ,
|
||||||
|
device_exposure_id INTEGER NOT NULL ,
|
||||||
|
currency_concept_id INTEGER NULL ,
|
||||||
|
paid_copay FLOAT NULL ,
|
||||||
|
paid_coinsurance FLOAT NULL ,
|
||||||
|
paid_toward_deductible FLOAT NULL ,
|
||||||
|
paid_by_payer FLOAT NULL ,
|
||||||
|
paid_by_coordination_benefits FLOAT NULL ,
|
||||||
|
total_out_of_pocket FLOAT NULL ,
|
||||||
|
total_paid FLOAT NULL ,
|
||||||
|
payer_plan_period_id INTEGER NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/************************
|
||||||
|
|
||||||
|
Standardized derived elements
|
||||||
|
|
||||||
|
************************/
|
||||||
|
|
||||||
|
CREATE TABLE cohort
|
||||||
|
(
|
||||||
|
cohort_definition_id INTEGER NOT NULL ,
|
||||||
|
subject_id INTEGER NOT NULL ,
|
||||||
|
cohort_start_date DATE NOT NULL ,
|
||||||
|
cohort_end_date DATE NOT NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE cohort_attribute
|
||||||
|
(
|
||||||
|
cohort_definition_id INTEGER NOT NULL ,
|
||||||
|
cohort_start_date DATE NOT NULL ,
|
||||||
|
cohort_end_date DATE NOT NULL ,
|
||||||
|
subject_id INTEGER NOT NULL ,
|
||||||
|
attribute_definition_id INTEGER NOT NULL ,
|
||||||
|
value_as_number FLOAT NULL ,
|
||||||
|
value_as_concept_id INTEGER NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE drug_era
|
||||||
|
(
|
||||||
|
drug_era_id INTEGER NOT NULL ,
|
||||||
|
person_id INTEGER NOT NULL ,
|
||||||
|
drug_concept_id INTEGER NOT NULL ,
|
||||||
|
drug_era_start_date DATE NOT NULL ,
|
||||||
|
drug_era_end_date DATE NOT NULL ,
|
||||||
|
drug_exposure_count INTEGER NULL ,
|
||||||
|
gap_days INTEGER NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE dose_era
|
||||||
|
(
|
||||||
|
dose_era_id INTEGER NOT NULL ,
|
||||||
|
person_id INTEGER NOT NULL ,
|
||||||
|
drug_concept_id INTEGER NOT NULL ,
|
||||||
|
unit_concept_id INTEGER NOT NULL ,
|
||||||
|
dose_value FLOAT NOT NULL ,
|
||||||
|
dose_era_start_date DATE NOT NULL ,
|
||||||
|
dose_era_end_date DATE NOT NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
CREATE TABLE condition_era
|
||||||
|
(
|
||||||
|
condition_era_id INTEGER NOT NULL ,
|
||||||
|
person_id INTEGER NOT NULL ,
|
||||||
|
condition_concept_id INTEGER NOT NULL ,
|
||||||
|
condition_era_start_date DATE NOT NULL ,
|
||||||
|
condition_era_end_date DATE NOT NULL ,
|
||||||
|
condition_occurrence_count INTEGER NULL
|
||||||
|
)
|
||||||
|
;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
@ -0,0 +1,187 @@
|
||||||
|
/*********************************************************************************
|
||||||
|
# Copyright 2014 Observational Health Data Sciences and Informatics
|
||||||
|
#
|
||||||
|
#
|
||||||
|
# Licensed under the Apache License, Version 2.0 (the "License");
|
||||||
|
# you may not use this file except in compliance with the License.
|
||||||
|
# You may obtain a copy of the License at
|
||||||
|
#
|
||||||
|
# http://www.apache.org/licenses/LICENSE-2.0
|
||||||
|
#
|
||||||
|
# Unless required by applicable law or agreed to in writing, software
|
||||||
|
# distributed under the License is distributed on an "AS IS" BASIS,
|
||||||
|
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
|
||||||
|
# See the License for the specific language governing permissions and
|
||||||
|
# limitations under the License.
|
||||||
|
********************************************************************************/
|
||||||
|
|
||||||
|
/************************
|
||||||
|
|
||||||
|
####### # # ####### ###### ##### ###### # # ####### ###
|
||||||
|
# # ## ## # # # # # # # # ## ## # # # # # # ##### ###### # # ###### ####
|
||||||
|
# # # # # # # # # # # # # # # # # # # # # ## # # # # # # # #
|
||||||
|
# # # # # # # ###### # # # # # # # # ###### # # # # # # ##### ## ##### ####
|
||||||
|
# # # # # # # # # # # # # # # # # # # # # # ## # #
|
||||||
|
# # # # # # # # # # # # # # # # # # # ## # # # # # # # #
|
||||||
|
####### # # ####### # ##### ###### # # ## ##### ### # # ##### ###### # # ###### ####
|
||||||
|
|
||||||
|
|
||||||
|
script to create the required indexes within OMOP common data model, version 5.0 for SQL Server database
|
||||||
|
|
||||||
|
last revised: 12 Oct 2014
|
||||||
|
|
||||||
|
author: Patrick Ryan
|
||||||
|
|
||||||
|
description: These indices are considered a minimal requirement to ensure adequate performance of analyses.
|
||||||
|
|
||||||
|
*************************/
|
||||||
|
|
||||||
|
|
||||||
|
/************************
|
||||||
|
|
||||||
|
Standardized vocabulary
|
||||||
|
|
||||||
|
************************/
|
||||||
|
|
||||||
|
CREATE UNIQUE CLUSTERED INDEX idx_concept_concept_id ON concept (concept_id ASC);
|
||||||
|
CREATE INDEX idx_concept_code ON concept (concept_code ASC);
|
||||||
|
CREATE INDEX idx_concept_vocabluary_id ON concept (vocabulary_id ASC);
|
||||||
|
CREATE INDEX idx_concept_domain_id ON concept (domain_id ASC);
|
||||||
|
CREATE INDEX idx_concept_class_id ON concept (concept_class_id ASC);
|
||||||
|
|
||||||
|
CREATE UNIQUE CLUSTERED INDEX idx_vocabulary_vocabulary_id ON vocabulary (vocabulary_id ASC);
|
||||||
|
|
||||||
|
CREATE UNIQUE CLUSTERED INDEX idx_domain_domain_id ON domain (domain_id ASC);
|
||||||
|
|
||||||
|
CREATE UNIQUE CLUSTERED INDEX idx_concept_class_class_id ON concept_class (concept_class_id ASC);
|
||||||
|
|
||||||
|
CREATE INDEX idx_concept_relationship_id_1 ON concept_relationship (concept_id_1 ASC);
|
||||||
|
CREATE INDEX idx_concept_relationship_id_2 ON concept_relationship (concept_id_2 ASC);
|
||||||
|
CREATE INDEX idx_concept_relationship_id_3 ON concept_relationship (relationship_id ASC);
|
||||||
|
|
||||||
|
CREATE UNIQUE CLUSTERED INDEX idx_relationship_rel_id ON relationship (relationship_id ASC);
|
||||||
|
|
||||||
|
CREATE CLUSTERED INDEX idx_concept_synonym_id ON concept_synonym (concept_id ASC);
|
||||||
|
|
||||||
|
CREATE CLUSTERED INDEX idx_concept_ancestor_id_1 ON concept_ancestor (ancestor_concept_id ASC);
|
||||||
|
CREATE INDEX idx_concept_ancestor_id_2 ON concept_ancestor (descendant_concept_id ASC);
|
||||||
|
|
||||||
|
CREATE CLUSTERED INDEX idx_source_to_concept_map_id_3 ON source_to_concept_map (target_concept_id ASC);
|
||||||
|
CREATE INDEX idx_source_to_concept_map_id_1 ON source_to_concept_map (source_vocabulary_id ASC);
|
||||||
|
CREATE INDEX idx_source_to_concept_map_id_2 ON source_to_concept_map (target_vocabulary_id ASC);
|
||||||
|
CREATE INDEX idx_source_to_concept_map_code ON source_to_concept_map (source_code ASC);
|
||||||
|
|
||||||
|
CREATE CLUSTERED INDEX idx_drug_strength_id_1 ON drug_strength (drug_concept_id ASC);
|
||||||
|
CREATE INDEX idx_drug_strength_id_2 ON drug_strength (ingredient_concept_id ASC);
|
||||||
|
|
||||||
|
CREATE CLUSTERED INDEX idx_cohort_definition_id ON cohort_definition (cohort_definition_id ASC);
|
||||||
|
|
||||||
|
CREATE CLUSTERED INDEX idx_attribute_definition_id ON attribute_definition (attribute_definition_id ASC);
|
||||||
|
|
||||||
|
|
||||||
|
/**************************
|
||||||
|
|
||||||
|
Standardized meta-data
|
||||||
|
|
||||||
|
***************************/
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/************************
|
||||||
|
|
||||||
|
Standardized clinical data
|
||||||
|
|
||||||
|
************************/
|
||||||
|
|
||||||
|
CREATE UNIQUE CLUSTERED INDEX idx_person_id ON person (person_id ASC);
|
||||||
|
|
||||||
|
CREATE CLUSTERED INDEX idx_observation_period_id ON observation_period (person_id ASC);
|
||||||
|
|
||||||
|
CREATE CLUSTERED INDEX idx_specimen_person_id ON specimen (person_id ASC);
|
||||||
|
CREATE INDEX idx_specimen_concept_id ON specimen (specimen_concept_id ASC);
|
||||||
|
|
||||||
|
CREATE CLUSTERED INDEX idx_death_person_id ON death (person_id ASC);
|
||||||
|
|
||||||
|
CREATE CLUSTERED INDEX idx_visit_person_id ON visit_occurrence (person_id ASC);
|
||||||
|
CREATE INDEX idx_visit_concept_id ON visit_occurrence (visit_concept_id ASC);
|
||||||
|
|
||||||
|
CREATE CLUSTERED INDEX idx_procedure_person_id ON procedure_occurrence (person_id ASC);
|
||||||
|
CREATE INDEX idx_procedure_concept_id ON procedure_occurrence (procedure_concept_id ASC);
|
||||||
|
CREATE INDEX idx_procedure_visit_id ON procedure_occurrence (visit_occurrence_id ASC);
|
||||||
|
|
||||||
|
CREATE CLUSTERED INDEX idx_drug_person_id ON drug_exposure (person_id ASC);
|
||||||
|
CREATE INDEX idx_drug_concept_id ON drug_exposure (drug_concept_id ASC);
|
||||||
|
CREATE INDEX idx_drug_visit_id ON drug_exposure (visit_occurrence_id ASC);
|
||||||
|
|
||||||
|
CREATE CLUSTERED INDEX idx_device_person_id ON device_exposure (person_id ASC);
|
||||||
|
CREATE INDEX idx_device_concept_id ON device_exposure (device_concept_id ASC);
|
||||||
|
CREATE INDEX idx_device_visit_id ON device_exposure (visit_occurrence_id ASC);
|
||||||
|
|
||||||
|
CREATE CLUSTERED INDEX idx_condition_person_id ON condition_occurrence (person_id ASC);
|
||||||
|
CREATE INDEX idx_condition_concept_id ON condition_occurrence (condition_concept_id ASC);
|
||||||
|
CREATE INDEX idx_condition_visit_id ON condition_occurrence (visit_occurrence_id ASC);
|
||||||
|
|
||||||
|
CREATE CLUSTERED INDEX idx_measurement_person_id ON measurement (person_id ASC);
|
||||||
|
CREATE INDEX idx_measurement_concept_id ON measurement (measurement_concept_id ASC);
|
||||||
|
CREATE INDEX idx_measurement_visit_id ON measurement (visit_occurrence_id ASC);
|
||||||
|
|
||||||
|
CREATE CLUSTERED INDEX idx_note_person_id ON note (person_id ASC);
|
||||||
|
CREATE INDEX idx_note_concept_id ON note (note_type_concept_id ASC);
|
||||||
|
CREATE INDEX idx_note_visit_id ON note (visit_occurrence_id ASC);
|
||||||
|
|
||||||
|
CREATE CLUSTERED INDEX idx_observation_person_id ON observation (person_id ASC);
|
||||||
|
CREATE INDEX idx_observation_concept_id ON observation (observation_concept_id ASC);
|
||||||
|
CREATE INDEX idx_observation_visit_id ON observation (visit_occurrence_id ASC);
|
||||||
|
|
||||||
|
CREATE INDEX idx_fact_relationship_id_1 ON fact_relationship (domain_concept_id_1 ASC);
|
||||||
|
CREATE INDEX idx_fact_relationship_id_2 ON fact_relationship (domain_concept_id_2 ASC);
|
||||||
|
CREATE INDEX idx_fact_relationship_id_3 ON fact_relationship (relationship_concept_id ASC);
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/************************
|
||||||
|
|
||||||
|
Standardized health system data
|
||||||
|
|
||||||
|
************************/
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/************************
|
||||||
|
|
||||||
|
Standardized health economics
|
||||||
|
|
||||||
|
************************/
|
||||||
|
|
||||||
|
CREATE CLUSTERED INDEX idx_period_person_id ON payer_plan_period (person_id ASC);
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/************************
|
||||||
|
|
||||||
|
Standardized derived elements
|
||||||
|
|
||||||
|
************************/
|
||||||
|
|
||||||
|
|
||||||
|
CREATE INDEX idx_cohort_subject_id ON cohort (subject_id ASC);
|
||||||
|
CREATE INDEX idx_cohort_c_definition_id ON cohort (cohort_definition_id ASC);
|
||||||
|
|
||||||
|
CREATE INDEX idx_ca_subject_id ON cohort_attribute (subject_id ASC);
|
||||||
|
CREATE INDEX idx_ca_definition_id ON cohort_attribute (cohort_definition_id ASC);
|
||||||
|
|
||||||
|
CREATE CLUSTERED INDEX idx_drug_era_person_id ON drug_era (person_id ASC);
|
||||||
|
CREATE INDEX idx_drug_era_concept_id ON drug_era (drug_concept_id ASC);
|
||||||
|
|
||||||
|
CREATE CLUSTERED INDEX idx_dose_era_person_id ON dose_era (person_id ASC);
|
||||||
|
CREATE INDEX idx_dose_era_concept_id ON dose_era (drug_concept_id ASC);
|
||||||
|
|
||||||
|
CREATE CLUSTERED INDEX idx_condition_era_person_id ON condition_era (person_id ASC);
|
||||||
|
CREATE INDEX idx_condition_era_concept_id ON condition_era (condition_concept_id ASC);
|
||||||
|
|
||||||
Loading…
Reference in New Issue