Added MySQL Migration for CDM.
This commit is contained in:
Colin Erdman
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affe817632
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/*********************************************************************************
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# Copyright 2014 Observational Health Data Sciences and Informatics
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#
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#
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# Licensed under the Apache License, Version 2.0 (the "License");
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# you may not use this file except in compliance with the License.
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# You may obtain a copy of the License at
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#
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# http://www.apache.org/licenses/LICENSE-2.0
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#
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# Unless required by applicable law or agreed to in writing, software
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# distributed under the License is distributed on an "AS IS" BASIS,
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# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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# See the License for the specific language governing permissions and
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# limitations under the License.
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********************************************************************************/
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/************************
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####### # # ####### ###### ##### ###### # # ####### #####
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####### # # ####### # ##### ###### # # ## ##### ##### #### # # #### # # # # # # # # # ####
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script to create constraints within OMOP common data model, version 5.0 for PostgreSQL database
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last revised: 12 Oct 2014
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author: Patrick Ryan
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*************************/
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/************************
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*************************
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*************************
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*************************
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Primary key constraints
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*************************
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*************************
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*************************
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************************/
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/************************
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Standardized vocabulary
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************************/
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ALTER TABLE concept ADD CONSTRAINT xpk_concept PRIMARY KEY (concept_id);
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ALTER TABLE vocabulary ADD CONSTRAINT xpk_vocabulary PRIMARY KEY (vocabulary_id);
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ALTER TABLE domain ADD CONSTRAINT xpk_domain PRIMARY KEY (domain_id);
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ALTER TABLE concept_class ADD CONSTRAINT xpk_concept_class PRIMARY KEY (concept_class_id);
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ALTER TABLE concept_relationship ADD CONSTRAINT xpk_concept_relationship PRIMARY KEY (concept_id_1,concept_id_2,relationship_id);
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ALTER TABLE relationship ADD CONSTRAINT xpk_relationship PRIMARY KEY (relationship_id);
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ALTER TABLE concept_ancestor ADD CONSTRAINT xpk_concept_ancestor PRIMARY KEY (ancestor_concept_id,descendant_concept_id);
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ALTER TABLE source_to_concept_map ADD CONSTRAINT xpk_source_to_concept_map PRIMARY KEY (source_vocabulary_id,target_concept_id,source_code,valid_end_date);
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ALTER TABLE drug_strength ADD CONSTRAINT xpk_drug_strength PRIMARY KEY (drug_concept_id, ingredient_concept_id);
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ALTER TABLE cohort_definition ADD CONSTRAINT xpk_cohort_definition PRIMARY KEY (cohort_definition_id);
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ALTER TABLE attribute_definition ADD CONSTRAINT xpk_attribute_definition PRIMARY KEY (attribute_definition_id);
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/**************************
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Standardized meta-data
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***************************/
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/************************
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Standardized clinical data
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************************/
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/**PRIMARY KEY NONCLUSTERED constraints**/
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ALTER TABLE person ADD CONSTRAINT xpk_person PRIMARY KEY ( person_id ) ;
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ALTER TABLE observation_period ADD CONSTRAINT xpk_observation_period PRIMARY KEY ( observation_period_id ) ;
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ALTER TABLE specimen ADD CONSTRAINT xpk_specimen PRIMARY KEY ( specimen_id ) ;
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ALTER TABLE death ADD CONSTRAINT xpk_death PRIMARY KEY ( person_id ) ;
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ALTER TABLE visit_occurrence ADD CONSTRAINT xpk_visit_occurrence PRIMARY KEY ( visit_occurrence_id ) ;
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ALTER TABLE procedure_occurrence ADD CONSTRAINT xpk_procedure_occurrence PRIMARY KEY ( procedure_occurrence_id ) ;
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ALTER TABLE drug_exposure ADD CONSTRAINT xpk_drug_exposure PRIMARY KEY ( drug_exposure_id ) ;
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ALTER TABLE device_exposure ADD CONSTRAINT xpk_device_exposure PRIMARY KEY ( device_exposure_id ) ;
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ALTER TABLE condition_occurrence ADD CONSTRAINT xpk_condition_occurrence PRIMARY KEY ( condition_occurrence_id ) ;
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ALTER TABLE measurement ADD CONSTRAINT xpk_measurement PRIMARY KEY ( measurement_id ) ;
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ALTER TABLE note ADD CONSTRAINT xpk_note PRIMARY KEY ( note_id ) ;
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ALTER TABLE observation ADD CONSTRAINT xpk_observation PRIMARY KEY ( observation_id ) ;
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/************************
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Standardized health system data
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************************/
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ALTER TABLE location ADD CONSTRAINT xpk_location PRIMARY KEY ( location_id ) ;
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ALTER TABLE care_site ADD CONSTRAINT xpk_care_site PRIMARY KEY ( care_site_id ) ;
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ALTER TABLE provider ADD CONSTRAINT xpk_provider PRIMARY KEY ( provider_id ) ;
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/************************
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Standardized health economics
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************************/
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ALTER TABLE payer_plan_period ADD CONSTRAINT xpk_payer_plan_period PRIMARY KEY ( payer_plan_period_id ) ;
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ALTER TABLE visit_cost ADD CONSTRAINT xpk_visit_cost PRIMARY KEY ( visit_cost_id ) ;
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ALTER TABLE procedure_cost ADD CONSTRAINT xpk_procedure_cost PRIMARY KEY ( procedure_cost_id ) ;
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ALTER TABLE drug_cost ADD CONSTRAINT xpk_drug_cost PRIMARY KEY ( drug_cost_id ) ;
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ALTER TABLE device_cost ADD CONSTRAINT xpk_device_cost PRIMARY KEY ( device_cost_id ) ;
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/************************
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Standardized derived elements
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************************/
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ALTER TABLE cohort ADD CONSTRAINT xpk_cohort PRIMARY KEY ( cohort_definition_id, subject_id, cohort_start_date, cohort_end_date ) ;
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ALTER TABLE cohort_attribute ADD CONSTRAINT xpk_cohort_attribute PRIMARY KEY ( cohort_definition_id, subject_id, cohort_start_date, cohort_end_date, attribute_definition_id ) ;
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ALTER TABLE drug_era ADD CONSTRAINT xpk_drug_era PRIMARY KEY ( drug_era_id ) ;
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ALTER TABLE dose_era ADD CONSTRAINT xpk_dose_era PRIMARY KEY ( dose_era_id ) ;
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ALTER TABLE condition_era ADD CONSTRAINT xpk_condition_era PRIMARY KEY ( condition_era_id ) ;
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/************************
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*************************
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*************************
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*************************
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Foreign key constraints
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*************************
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*************************
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*************************
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************************/
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/************************
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Standardized vocabulary
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************************/
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ALTER TABLE concept ADD CONSTRAINT fpk_concept_domain FOREIGN KEY (domain_id) REFERENCES domain (domain_id);
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ALTER TABLE concept ADD CONSTRAINT fpk_concept_class FOREIGN KEY (concept_class_id) REFERENCES concept_class (concept_class_id);
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ALTER TABLE concept ADD CONSTRAINT fpk_concept_vocabulary FOREIGN KEY (vocabulary_id) REFERENCES vocabulary (vocabulary_id);
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ALTER TABLE vocabulary ADD CONSTRAINT fpk_vocabulary_concept FOREIGN KEY (vocabulary_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE domain ADD CONSTRAINT fpk_domain_concept FOREIGN KEY (domain_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE concept_class ADD CONSTRAINT fpk_concept_class_concept FOREIGN KEY (concept_class_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE concept_relationship ADD CONSTRAINT fpk_concept_relationship_c_1 FOREIGN KEY (concept_id_1) REFERENCES concept (concept_id);
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ALTER TABLE concept_relationship ADD CONSTRAINT fpk_concept_relationship_c_2 FOREIGN KEY (concept_id_2) REFERENCES concept (concept_id);
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ALTER TABLE concept_relationship ADD CONSTRAINT fpk_concept_relationship_id FOREIGN KEY (relationship_id) REFERENCES relationship (relationship_id);
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ALTER TABLE relationship ADD CONSTRAINT fpk_relationship_concept FOREIGN KEY (relationship_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE relationship ADD CONSTRAINT fpk_relationship_reverse FOREIGN KEY (reverse_relationship_id) REFERENCES relationship (relationship_id);
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ALTER TABLE concept_synonym ADD CONSTRAINT fpk_concept_synonym_concept FOREIGN KEY (concept_id) REFERENCES concept (concept_id);
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ALTER TABLE concept_ancestor ADD CONSTRAINT fpk_concept_ancestor_concept_1 FOREIGN KEY (ancestor_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE concept_ancestor ADD CONSTRAINT fpk_concept_ancestor_concept_2 FOREIGN KEY (descendant_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE source_to_concept_map ADD CONSTRAINT fpk_source_to_concept_map_v_1 FOREIGN KEY (source_vocabulary_id) REFERENCES vocabulary (vocabulary_id);
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ALTER TABLE source_to_concept_map ADD CONSTRAINT fpk_source_to_concept_map_v_2 FOREIGN KEY (target_vocabulary_id) REFERENCES vocabulary (vocabulary_id);
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ALTER TABLE source_to_concept_map ADD CONSTRAINT fpk_source_to_concept_map_c_1 FOREIGN KEY (target_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE drug_strength ADD CONSTRAINT fpk_drug_strength_concept_1 FOREIGN KEY (drug_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE drug_strength ADD CONSTRAINT fpk_drug_strength_concept_2 FOREIGN KEY (ingredient_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE drug_strength ADD CONSTRAINT fpk_drug_strength_unit_1 FOREIGN KEY (amount_unit_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE drug_strength ADD CONSTRAINT fpk_drug_strength_unit_2 FOREIGN KEY (numerator_unit_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE drug_strength ADD CONSTRAINT fpk_drug_strength_unit_3 FOREIGN KEY (denominator_unit_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE cohort_definition ADD CONSTRAINT fpk_cohort_definition_concept FOREIGN KEY (definition_type_concept_id) REFERENCES concept (concept_id);
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/**************************
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Standardized meta-data
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/************************
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Standardized clinical data
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************************/
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ALTER TABLE person ADD CONSTRAINT fpk_person_gender_concept FOREIGN KEY (gender_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE person ADD CONSTRAINT fpk_person_race_concept FOREIGN KEY (race_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE person ADD CONSTRAINT fpk_person_ethnicity_concept FOREIGN KEY (ethnicity_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE person ADD CONSTRAINT fpk_person_gender_concept_s FOREIGN KEY (gender_source_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE person ADD CONSTRAINT fpk_person_race_concept_s FOREIGN KEY (race_source_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE person ADD CONSTRAINT fpk_person_ethnicity_concept_s FOREIGN KEY (ethnicity_source_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE person ADD CONSTRAINT fpk_person_location FOREIGN KEY (location_id) REFERENCES location (location_id);
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ALTER TABLE person ADD CONSTRAINT fpk_person_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
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ALTER TABLE person ADD CONSTRAINT fpk_person_care_site FOREIGN KEY (care_site_id) REFERENCES care_site (care_site_id);
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ALTER TABLE observation_period ADD CONSTRAINT fpk_observation_period_person FOREIGN KEY (person_id) REFERENCES person (person_id);
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ALTER TABLE observation_period ADD CONSTRAINT fpk_observation_period_concept FOREIGN KEY (period_type_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE specimen ADD CONSTRAINT fpk_specimen_person FOREIGN KEY (person_id) REFERENCES person (person_id);
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ALTER TABLE specimen ADD CONSTRAINT fpk_specimen_concept FOREIGN KEY (specimen_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE specimen ADD CONSTRAINT fpk_specimen_type_concept FOREIGN KEY (specimen_type_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE specimen ADD CONSTRAINT fpk_specimen_unit_concept FOREIGN KEY (unit_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE specimen ADD CONSTRAINT fpk_specimen_site_concept FOREIGN KEY (anatomic_site_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE specimen ADD CONSTRAINT fpk_specimen_status_concept FOREIGN KEY (disease_status_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE death ADD CONSTRAINT fpk_death_person FOREIGN KEY (person_id) REFERENCES person (person_id);
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ALTER TABLE death ADD CONSTRAINT fpk_death_type_concept FOREIGN KEY (death_type_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE death ADD CONSTRAINT fpk_death_cause_concept FOREIGN KEY (cause_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE death ADD CONSTRAINT fpk_death_cause_concept_s FOREIGN KEY (cause_source_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_person FOREIGN KEY (person_id) REFERENCES person (person_id);
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ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_concept FOREIGN KEY (visit_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_type_concept FOREIGN KEY (visit_type_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
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ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_care_site FOREIGN KEY (care_site_id) REFERENCES care_site (care_site_id);
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ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_concept_s FOREIGN KEY (visit_source_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_person FOREIGN KEY (person_id) REFERENCES person (person_id);
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ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_concept FOREIGN KEY (procedure_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_type_concept FOREIGN KEY (procedure_type_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_modifier FOREIGN KEY (modifier_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
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ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id);
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ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_concept_s FOREIGN KEY (procedure_source_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_person FOREIGN KEY (person_id) REFERENCES person (person_id);
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ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_concept FOREIGN KEY (drug_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_type_concept FOREIGN KEY (drug_type_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_route_concept FOREIGN KEY (route_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_dose_unit_concept FOREIGN KEY (dose_unit_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
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ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id);
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ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_concept_s FOREIGN KEY (drug_source_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE device_exposure ADD CONSTRAINT fpk_device_person FOREIGN KEY (person_id) REFERENCES person (person_id);
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ALTER TABLE device_exposure ADD CONSTRAINT fpk_device_concept FOREIGN KEY (device_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE device_exposure ADD CONSTRAINT fpk_device_type_concept FOREIGN KEY (device_type_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE device_exposure ADD CONSTRAINT fpk_device_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
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ALTER TABLE device_exposure ADD CONSTRAINT fpk_device_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id);
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ALTER TABLE device_exposure ADD CONSTRAINT fpk_device_concept_s FOREIGN KEY (device_source_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_person FOREIGN KEY (person_id) REFERENCES person (person_id);
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ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_concept FOREIGN KEY (condition_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_type_concept FOREIGN KEY (condition_type_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
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ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id);
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ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_concept_s FOREIGN KEY (condition_source_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_person FOREIGN KEY (person_id) REFERENCES person (person_id);
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ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_concept FOREIGN KEY (measurement_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_type_concept FOREIGN KEY (measurement_type_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_operator FOREIGN KEY (operator_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_value FOREIGN KEY (value_as_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_unit FOREIGN KEY (unit_concept_id) REFERENCES concept (concept_id);
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ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id);
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|
||||
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 +1,700 @@
|
|||
/*********************************************************************************
|
||||
# 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 INT(11) 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 INT(11) NOT NULL
|
||||
);
|
||||
|
||||
|
||||
|
||||
|
||||
CREATE TABLE domain (
|
||||
domain_id VARCHAR(20) NOT NULL,
|
||||
domain_name VARCHAR(255) NOT NULL,
|
||||
domain_concept_id INT(11) NOT NULL
|
||||
);
|
||||
|
||||
|
||||
|
||||
CREATE TABLE concept_class (
|
||||
concept_class_id VARCHAR(20) NOT NULL,
|
||||
concept_class_name VARCHAR(255) NOT NULL,
|
||||
concept_class_concept_id INT(11) NOT NULL
|
||||
);
|
||||
|
||||
|
||||
|
||||
|
||||
CREATE TABLE concept_relationship (
|
||||
concept_id_1 INT(11) NOT NULL,
|
||||
concept_id_2 INT(11) 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 INT(11) NOT NULL
|
||||
);
|
||||
|
||||
|
||||
CREATE TABLE concept_synonym (
|
||||
concept_id INT(11) NOT NULL,
|
||||
concept_synonym_name VARCHAR(1000) NOT NULL,
|
||||
language_concept_id INT(11) NOT NULL
|
||||
);
|
||||
|
||||
|
||||
CREATE TABLE concept_ancestor (
|
||||
ancestor_concept_id INT(11) NOT NULL,
|
||||
descendant_concept_id INT(11) NOT NULL,
|
||||
min_levels_of_separation INT(11) NOT NULL,
|
||||
max_levels_of_separation INT(11) NOT NULL
|
||||
);
|
||||
|
||||
|
||||
|
||||
CREATE TABLE source_to_concept_map (
|
||||
source_code VARCHAR(50) NOT NULL,
|
||||
source_concept_id INT(11) NOT NULL,
|
||||
source_vocabulary_id VARCHAR(20) NOT NULL,
|
||||
source_code_description VARCHAR(255) NULL,
|
||||
target_concept_id INT(11) 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 INT(11) NOT NULL,
|
||||
ingredient_concept_id INT(11) NOT NULL,
|
||||
amount_value NUMERIC NULL,
|
||||
amount_unit_concept_id INT(11) NULL,
|
||||
numerator_value NUMERIC NULL,
|
||||
numerator_unit_concept_id INT(11) NULL,
|
||||
denominator_unit_concept_id INT(11) 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 INT(11) NOT NULL,
|
||||
cohort_definition_name VARCHAR(255) NOT NULL,
|
||||
cohort_definition_description TEXT NULL,
|
||||
definition_type_concept_id INT(11) NOT NULL,
|
||||
cohort_definition_syntax TEXT NULL,
|
||||
subject_concept_id INT(11) NOT NULL,
|
||||
cohort_initiation_date DATE NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
CREATE TABLE attribute_definition (
|
||||
attribute_definition_id INT(11) NOT NULL,
|
||||
attribute_name VARCHAR(255) NOT NULL,
|
||||
attribute_description TEXT NULL,
|
||||
attribute_type_concept_id INT(11) 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 INT(11) NOT NULL ,
|
||||
gender_concept_id INT(11) NOT NULL ,
|
||||
year_of_birth INT(11) NOT NULL ,
|
||||
month_of_birth INT(11) NULL,
|
||||
day_of_birth INT(11) NULL,
|
||||
time_of_birth VARCHAR(10) NULL,
|
||||
race_concept_id INT(11) NOT NULL,
|
||||
ethnicity_concept_id INT(11) NOT NULL,
|
||||
location_id INT(11) NULL,
|
||||
provider_id INT(11) NULL,
|
||||
care_site_id INT(11) NULL,
|
||||
person_source_value VARCHAR(50) NULL,
|
||||
gender_source_value VARCHAR(50) NULL,
|
||||
gender_source_concept_id INT(11) NULL,
|
||||
race_source_value VARCHAR(50) NULL,
|
||||
race_source_concept_id INT(11) NULL,
|
||||
ethnicity_source_value VARCHAR(50) NULL,
|
||||
ethnicity_source_concept_id INT(11) NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
CREATE TABLE observation_period
|
||||
(
|
||||
observation_period_id INT(11) NOT NULL ,
|
||||
person_id INT(11) NOT NULL ,
|
||||
observation_period_start_date DATE NOT NULL ,
|
||||
observation_period_end_date DATE NOT NULL ,
|
||||
period_type_concept_id INT(11) NOT NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
CREATE TABLE specimen
|
||||
(
|
||||
specimen_id INT(11) NOT NULL ,
|
||||
person_id INT(11) NOT NULL ,
|
||||
specimen_concept_id INT(11) NOT NULL ,
|
||||
specimen_type_concept_id INT(11) NOT NULL ,
|
||||
specimen_date DATE NOT NULL ,
|
||||
specimen_time VARCHAR(10) NULL ,
|
||||
quantity NUMERIC NULL ,
|
||||
unit_concept_id INT(11) NULL ,
|
||||
anatomic_site_concept_id INT(11) NULL ,
|
||||
disease_status_concept_id INT(11) 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 INT(11) NOT NULL ,
|
||||
death_date DATE NOT NULL ,
|
||||
death_type_concept_id INT(11) NOT NULL ,
|
||||
cause_concept_id INT(11) NULL ,
|
||||
cause_source_value VARCHAR(50) NULL,
|
||||
cause_source_concept_id INT(11) NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
CREATE TABLE visit_occurrence
|
||||
(
|
||||
visit_occurrence_id INT(11) NOT NULL ,
|
||||
person_id INT(11) NOT NULL ,
|
||||
visit_concept_id INT(11) 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 INT(11) NOT NULL ,
|
||||
provider_id INT(11) NULL,
|
||||
care_site_id INT(11) NULL,
|
||||
visit_source_value VARCHAR(50) NULL,
|
||||
visit_source_concept_id INT(11) NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
CREATE TABLE procedure_occurrence
|
||||
(
|
||||
procedure_occurrence_id INT(11) NOT NULL ,
|
||||
person_id INT(11) NOT NULL ,
|
||||
procedure_concept_id INT(11) NOT NULL ,
|
||||
procedure_date DATE NOT NULL ,
|
||||
procedure_type_concept_id INT(11) NOT NULL ,
|
||||
modifier_concept_id INT(11) NULL ,
|
||||
quantity INT(11) NULL ,
|
||||
provider_id INT(11) NULL ,
|
||||
visit_occurrence_id INT(11) NULL ,
|
||||
procedure_source_value VARCHAR(50) NULL ,
|
||||
procedure_source_concept_id INT(11) NULL ,
|
||||
qualifier_source_value VARCHAR(50) NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
CREATE TABLE drug_exposure
|
||||
(
|
||||
drug_exposure_id INT(11) NOT NULL ,
|
||||
person_id INT(11) NOT NULL ,
|
||||
drug_concept_id INT(11) NOT NULL ,
|
||||
drug_exposure_start_date DATE NOT NULL ,
|
||||
drug_exposure_end_date DATE NULL ,
|
||||
drug_type_concept_id INT(11) NOT NULL ,
|
||||
stop_reason VARCHAR(20) NULL ,
|
||||
refills INT(11) NULL ,
|
||||
quantity NUMERIC NULL ,
|
||||
days_supply INT(11) NULL ,
|
||||
sig TEXT NULL ,
|
||||
route_concept_id INT(11) NULL ,
|
||||
effective_drug_dose NUMERIC NULL ,
|
||||
dose_unit_concept_id INT(11) NULL ,
|
||||
lot_number VARCHAR(50) NULL ,
|
||||
provider_id INT(11) NULL ,
|
||||
visit_occurrence_id INT(11) NULL ,
|
||||
drug_source_value VARCHAR(50) NULL ,
|
||||
drug_source_concept_id INT(11) NULL ,
|
||||
route_source_value VARCHAR(50) NULL ,
|
||||
dose_unit_source_value VARCHAR(50) NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
CREATE TABLE device_exposure
|
||||
(
|
||||
device_exposure_id INT(11) NOT NULL ,
|
||||
person_id INT(11) NOT NULL ,
|
||||
device_concept_id INT(11) NOT NULL ,
|
||||
device_exposure_start_date DATE NOT NULL ,
|
||||
device_exposure_end_date DATE NULL ,
|
||||
device_type_concept_id INT(11) NOT NULL ,
|
||||
unique_device_id VARCHAR(50) NULL ,
|
||||
quantity INT(11) NULL ,
|
||||
provider_id INT(11) NULL ,
|
||||
visit_occurrence_id INT(11) NULL ,
|
||||
device_source_value VARCHAR(100) NULL ,
|
||||
device_source_concept_id INT(11) NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
CREATE TABLE condition_occurrence
|
||||
(
|
||||
condition_occurrence_id INT(11) NOT NULL ,
|
||||
person_id INT(11) NOT NULL ,
|
||||
condition_concept_id INT(11) NOT NULL ,
|
||||
condition_start_date DATE NOT NULL ,
|
||||
condition_end_date DATE NULL ,
|
||||
condition_type_concept_id INT(11) NOT NULL ,
|
||||
stop_reason VARCHAR(20) NULL ,
|
||||
provider_id INT(11) NULL ,
|
||||
visit_occurrence_id INT(11) NULL ,
|
||||
condition_source_value VARCHAR(50) NULL ,
|
||||
condition_source_concept_id INT(11) NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
CREATE TABLE measurement
|
||||
(
|
||||
measurement_id INT(11) NOT NULL ,
|
||||
person_id INT(11) NOT NULL ,
|
||||
measurement_concept_id INT(11) NOT NULL ,
|
||||
measurement_date DATE NOT NULL ,
|
||||
measurement_time VARCHAR(10) NULL ,
|
||||
measurement_type_concept_id INT(11) NOT NULL ,
|
||||
operator_concept_id INT(11) NULL ,
|
||||
value_as_number NUMERIC NULL ,
|
||||
value_as_concept_id INT(11) NULL ,
|
||||
unit_concept_id INT(11) NULL ,
|
||||
range_low NUMERIC NULL ,
|
||||
range_high NUMERIC NULL ,
|
||||
provider_id INT(11) NULL ,
|
||||
visit_occurrence_id INT(11) NULL ,
|
||||
measurement_source_value VARCHAR(50) NULL ,
|
||||
measurement_source_concept_id INT(11) NULL ,
|
||||
unit_source_value VARCHAR(50) NULL ,
|
||||
value_source_value VARCHAR(50) NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
CREATE TABLE note
|
||||
(
|
||||
note_id INT(11) NOT NULL ,
|
||||
person_id INT(11) NOT NULL ,
|
||||
note_date DATE NOT NULL ,
|
||||
note_time VARCHAR(10) NULL ,
|
||||
note_type_concept_id INT(11) NOT NULL ,
|
||||
note_text TEXT NOT NULL ,
|
||||
provider_id INT(11) NULL ,
|
||||
visit_occurrence_id INT(11) NULL ,
|
||||
note_source_value VARCHAR(50) NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
CREATE TABLE observation
|
||||
(
|
||||
observation_id INT(11) NOT NULL ,
|
||||
person_id INT(11) NOT NULL ,
|
||||
observation_concept_id INT(11) NOT NULL ,
|
||||
observation_date DATE NOT NULL ,
|
||||
observation_time VARCHAR(10) NULL ,
|
||||
observation_type_concept_id INT(11) NOT NULL ,
|
||||
value_as_number NUMERIC NULL ,
|
||||
value_as_string VARCHAR(60) NULL ,
|
||||
value_as_concept_id INT(11) NULL ,
|
||||
qualifier_concept_id INT(11) NULL ,
|
||||
unit_concept_id INT(11) NULL ,
|
||||
provider_id INT(11) NULL ,
|
||||
visit_occurrence_id INT(11) NULL ,
|
||||
observation_source_value VARCHAR(50) NULL ,
|
||||
observation_source_concept_id INT(11) NULL ,
|
||||
unit_source_value VARCHAR(50) NULL ,
|
||||
qualifier_source_value VARCHAR(50) NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
CREATE TABLE fact_relationship
|
||||
(
|
||||
domain_concept_id_1 INT(11) NOT NULL ,
|
||||
fact_id_1 INT(11) NOT NULL ,
|
||||
domain_concept_id_2 INT(11) NOT NULL ,
|
||||
fact_id_2 INT(11) NOT NULL ,
|
||||
relationship_concept_id INT(11) NOT NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
|
||||
/************************
|
||||
|
||||
Standardized health system data
|
||||
|
||||
************************/
|
||||
|
||||
|
||||
|
||||
CREATE TABLE location
|
||||
(
|
||||
location_id INT(11) 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 INT(11) NOT NULL ,
|
||||
care_site_name VARCHAR(255) NULL ,
|
||||
place_of_service_concept_id INT(11) NULL ,
|
||||
location_id INT(11) NULL ,
|
||||
care_site_source_value VARCHAR(50) NULL ,
|
||||
place_of_service_source_value VARCHAR(50) NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
CREATE TABLE provider
|
||||
(
|
||||
provider_id INT(11) NOT NULL ,
|
||||
provider_name VARCHAR(255) NULL ,
|
||||
NPI VARCHAR(20) NULL ,
|
||||
DEA VARCHAR(20) NULL ,
|
||||
specialty_concept_id INT(11) NULL ,
|
||||
care_site_id INT(11) NULL ,
|
||||
year_of_birth INT(11) NULL ,
|
||||
gender_concept_id INT(11) NULL ,
|
||||
provider_source_value VARCHAR(50) NULL ,
|
||||
specialty_source_value VARCHAR(50) NULL ,
|
||||
specialty_source_concept_id INT(11) NULL ,
|
||||
gender_source_value VARCHAR(50) NULL ,
|
||||
gender_source_concept_id INT(11) NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
|
||||
/************************
|
||||
|
||||
Standardized health economics
|
||||
|
||||
************************/
|
||||
|
||||
|
||||
CREATE TABLE payer_plan_period
|
||||
(
|
||||
payer_plan_period_id INT(11) NOT NULL ,
|
||||
person_id INT(11) 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 INT(11) NOT NULL ,
|
||||
visit_occurrence_id INT(11) NOT NULL ,
|
||||
currency_concept_id INT(11) 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 INT(11) NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
CREATE TABLE procedure_cost
|
||||
(
|
||||
procedure_cost_id INT(11) NOT NULL ,
|
||||
procedure_occurrence_id INT(11) NOT NULL ,
|
||||
currency_concept_id INT(11) 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 INT(11) NULL ,
|
||||
payer_plan_period_id INT(11) NULL ,
|
||||
revenue_code_source_value VARCHAR(50) NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
CREATE TABLE drug_cost
|
||||
(
|
||||
drug_cost_id INT(11) NOT NULL ,
|
||||
drug_exposure_id INT(11) NOT NULL ,
|
||||
currency_concept_id INT(11) 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 INT(11) NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
CREATE TABLE device_cost
|
||||
(
|
||||
device_cost_id INT(11) NOT NULL ,
|
||||
device_exposure_id INT(11) NOT NULL ,
|
||||
currency_concept_id INT(11) 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 INT(11) NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
|
||||
/************************
|
||||
|
||||
Standardized derived elements
|
||||
|
||||
************************/
|
||||
|
||||
CREATE TABLE cohort
|
||||
(
|
||||
cohort_definition_id INT(11) NOT NULL ,
|
||||
subject_id INT(11) NOT NULL ,
|
||||
cohort_start_date DATE NOT NULL ,
|
||||
cohort_end_date DATE NOT NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
CREATE TABLE cohort_attribute
|
||||
(
|
||||
cohort_definition_id INT(11) NOT NULL ,
|
||||
cohort_start_date DATE NOT NULL ,
|
||||
cohort_end_date DATE NOT NULL ,
|
||||
subject_id INT(11) NOT NULL ,
|
||||
attribute_definition_id INT(11) NOT NULL ,
|
||||
value_as_number NUMERIC NULL ,
|
||||
value_as_concept_id INT(11) NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
|
||||
CREATE TABLE drug_era
|
||||
(
|
||||
drug_era_id INT(11) NOT NULL ,
|
||||
person_id INT(11) NOT NULL ,
|
||||
drug_concept_id INT(11) NOT NULL ,
|
||||
drug_era_start_date DATE NOT NULL ,
|
||||
drug_era_end_date DATE NOT NULL ,
|
||||
drug_exposure_count INT(11) NULL ,
|
||||
gap_days INT(11) NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
CREATE TABLE dose_era
|
||||
(
|
||||
dose_era_id INT(11) NOT NULL ,
|
||||
person_id INT(11) NOT NULL ,
|
||||
drug_concept_id INT(11) NOT NULL ,
|
||||
unit_concept_id INT(11) 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 INT(11) NOT NULL ,
|
||||
person_id INT(11) NOT NULL ,
|
||||
condition_concept_id INT(11) NOT NULL ,
|
||||
condition_era_start_date DATE NOT NULL ,
|
||||
condition_era_end_date DATE NOT NULL ,
|
||||
condition_occurrence_count INT(11) 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 +1,18 @@
|
|||
Common-Data-Model / PostgreSQL
|
||||
=================
|
||||
|
||||
This folder contains the SQL scripts for PostgreSQL.
|
||||
|
||||
In order to create your instantiation of the Common Data Model, we recommend following these steps:
|
||||
|
||||
1. Create an empty schema.
|
||||
|
||||
2. Execute the script `OMOP CDM ddl - MySQL.sql` to create the tables and fields.
|
||||
|
||||
3. Load your data into the schema.
|
||||
|
||||
4. Execute the script `OMOP CDM indexes required - PostgreSQL.sql` to add the minimum set of indexes we recommend (required before fk creation in MySQL).
|
||||
|
||||
5. Execute the script `OMOP CDM constraints - PostgreSQL.sql` to add the constraints (primary and foreign keys).
|
||||
|
||||
Note: you could also apply the constraints and/or the indexes before loading the data, but this will slow down the insertion of the data considerably.
|
||||
Loading…
Reference in New Issue