/********************************************************************************* # Copyright 2017-11 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. ********************************************************************************/ /************************ ####### # # ####### ###### ##### ###### # # ####### ##### # # ## ## # # # # # # # # ## ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # ###### # # # # # # # # ###### ##### # # # # # # # # # # # # # # # ### # # # # # # # # # # # # # # # # # # ### # # ####### # # ####### # ##### ###### # # ## ##### ### ##### postgresql script to create OMOP common data model version 5.3 last revised: 6-Nov-2017 Authors: Patrick Ryan, Christian Reich, Clair Blacketer *************************/ /************************ 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) NOT NULL, vocabulary_version VARCHAR(255) NOT 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_value NUMERIC NULL, denominator_unit_concept_id INTEGER NULL, box_size 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 ) ; CREATE TABLE metadata ( metadata_concept_id INTEGER NOT NULL , metadata_type_concept_id INTEGER NOT NULL , name VARCHAR(250) NOT NULL , value_as_string TEXT NULL , value_as_concept_id INTEGER NULL , metadata_date DATE NULL , metadata_datetime TIMESTAMP NULL ) ; /************************ Standardized clinical data ************************/ --HINT DISTRIBUTE_ON_KEY(person_id) 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, birth_datetime TIMESTAMP 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 ) ; --HINT DISTRIBUTE_ON_KEY(person_id) 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 ) ; --HINT DISTRIBUTE_ON_KEY(person_id) 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_datetime TIMESTAMP 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 ) ; --HINT DISTRIBUTE_ON_KEY(person_id) CREATE TABLE death ( person_id INTEGER NOT NULL , death_date DATE NOT NULL , death_datetime TIMESTAMP 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 ) ; --HINT DISTRIBUTE_ON_KEY(person_id) 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_datetime TIMESTAMP NULL , visit_end_date DATE NOT NULL , visit_end_datetime TIMESTAMP 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 , admitting_source_concept_id INTEGER NULL , admitting_source_value VARCHAR(50) NULL , discharge_to_concept_id INTEGER NULL , discharge_to_source_value VARCHAR(50) NULL , preceding_visit_occurrence_id INTEGER NULL ) ; --HINT DISTRIBUTE_ON_KEY(person_id) CREATE TABLE visit_detail ( visit_detail_id INTEGER NOT NULL , person_id INTEGER NOT NULL , visit_detail_concept_id INTEGER NOT NULL , visit_start_date DATE NOT NULL , visit_start_datetime TIMESTAMP NULL , visit_end_date DATE NOT NULL , visit_end_datetime TIMESTAMP NULL , visit_type_concept_id INTEGER NOT NULL , provider_id INTEGER NULL , care_site_id INTEGER NULL , admitting_source_concept_id INTEGER NULL , discharge_to_concept_id INTEGER NULL , preceding_visit_detail_id INTEGER NULL , visit_source_value VARCHAR(50) NULL , visit_source_concept_id INTEGER NULL , admitting_source_value VARCHAR(50) NULL , discharge_to_source_value VARCHAR(50) NULL , visit_detail_parent_id INTEGER NULL , visit_occurrence_id INTEGER NOT NULL ) ; --HINT DISTRIBUTE_ON_KEY(person_id) 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_datetime TIMESTAMP 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 , visit_detail_id INTEGER NULL , procedure_source_value VARCHAR(50) NULL , procedure_source_concept_id INTEGER NULL , modifier_source_value VARCHAR(50) NULL ) ; --HINT DISTRIBUTE_ON_KEY(person_id) 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_start_datetime TIMESTAMP NULL , drug_exposure_end_date DATE NOT NULL , drug_exposure_end_datetime TIMESTAMP NULL , verbatim_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 , lot_number VARCHAR(50) NULL , provider_id INTEGER NULL , visit_occurrence_id INTEGER NULL , visit_detail_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 ) ; --HINT DISTRIBUTE_ON_KEY(person_id) 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_start_datetime TIMESTAMP NULL , device_exposure_end_date DATE NULL , device_exposure_end_datetime TIMESTAMP 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 , visit_detail_id INTEGER NULL , device_source_value VARCHAR(100) NULL , device_source_concept_id INTEGER NULL ) ; --HINT DISTRIBUTE_ON_KEY(person_id) 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_start_datetime TIMESTAMP NULL , condition_end_date DATE NULL , condition_end_datetime TIMESTAMP NULL , condition_type_concept_id INTEGER NOT NULL , stop_reason VARCHAR(20) NULL , provider_id INTEGER NULL , visit_occurrence_id INTEGER NULL , visit_detail_id INTEGER NULL , condition_source_value VARCHAR(50) NULL , condition_source_concept_id INTEGER NULL , condition_status_source_value VARCHAR(50) NULL , condition_status_concept_id INTEGER NULL ) ; --HINT DISTRIBUTE_ON_KEY(person_id) 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_datetime TIMESTAMP 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 , visit_detail_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 ) ; --HINT DISTRIBUTE_ON_KEY(person_id) CREATE TABLE note ( note_id INTEGER NOT NULL , person_id INTEGER NOT NULL , note_date DATE NOT NULL , note_datetime TIMESTAMP NULL , note_type_concept_id INTEGER NOT NULL , note_class_concept_id INTEGER NOT NULL , note_title VARCHAR(250) NULL , note_text TEXT NULL , encoding_concept_id INTEGER NOT NULL , language_concept_id INTEGER NOT NULL , provider_id INTEGER NULL , visit_occurrence_id INTEGER NULL , visit_detail_id INTEGER NULL , note_source_value VARCHAR(50) NULL ) ; CREATE TABLE note_nlp ( note_nlp_id BIGINT NOT NULL , note_id INTEGER NOT NULL , section_concept_id INTEGER NULL , snippet VARCHAR(250) NULL , "offset" VARCHAR(250) NULL , lexical_variant VARCHAR(250) NOT NULL , note_nlp_concept_id INTEGER NULL , note_nlp_source_concept_id INTEGER NULL , nlp_system VARCHAR(250) NULL , nlp_date DATE NOT NULL , nlp_datetime TIMESTAMP NULL , term_exists VARCHAR(1) NULL , term_temporal VARCHAR(50) NULL , term_modifiers VARCHAR(2000) NULL ) ; --HINT DISTRIBUTE_ON_KEY(person_id) 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_datetime TIMESTAMP 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 , visit_detail_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 ************************/ --HINT DISTRIBUTE_ON_KEY(person_id) 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_concept_id INTEGER NULL , payer_source_value VARCHAR(50) NULL , payer_source_concept_id INTEGER NULL , plan_concept_id INTEGER NULL , plan_source_value VARCHAR(50) NULL , plan_source_concept_id INTEGER NULL , sponsor_concept_id INTEGER NULL , sponsor_source_value VARCHAR(50) NULL , sponsor_source_concept_id INTEGER NULL , family_source_value VARCHAR(50) NULL , stop_reason_concept_id INTEGER NULL , stop_reason_source_value INTEGER NULL , stop_reason_source_concept_id INTEGER NULL ) ; CREATE TABLE cost ( cost_id INTEGER NOT NULL , cost_event_id INTEGER NOT NULL , cost_domain_id VARCHAR(20) NOT NULL , cost_type_concept_id INTEGER NOT NULL , currency_concept_id INTEGER NULL , total_charge NUMERIC NULL , total_cost NUMERIC NULL , total_paid NUMERIC NULL , paid_by_payer NUMERIC NULL , paid_by_patient NUMERIC NULL , paid_patient_copay NUMERIC NULL , paid_patient_coinsurance NUMERIC NULL , paid_patient_deductible NUMERIC NULL , paid_by_primary NUMERIC NULL , paid_ingredient_cost NUMERIC NULL , paid_dispensing_fee NUMERIC NULL , payer_plan_period_id INTEGER NULL , amount_allowed NUMERIC NULL , revenue_code_concept_id INTEGER NULL , reveue_code_source_value VARCHAR(50) NULL, drg_concept_id INTEGER NULL, drg_source_value VARCHAR(3) NULL ) ; /************************ Standardized derived elements ************************/ --HINT DISTRIBUTE_ON_KEY(subject_id) 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 ) ; --HINT DISTRIBUTE_ON_KEY(subject_id) CREATE TABLE cohort_attribute ( cohort_definition_id INTEGER NOT NULL , subject_id INTEGER NOT NULL , cohort_start_date DATE NOT NULL , cohort_end_date DATE NOT NULL , attribute_definition_id INTEGER NOT NULL , value_as_number NUMERIC NULL , value_as_concept_id INTEGER NULL ) ; --HINT DISTRIBUTE_ON_KEY(person_id) 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 ) ; --HINT DISTRIBUTE_ON_KEY(person_id) 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 ) ; --HINT DISTRIBUTE_ON_KEY(person_id) 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 ) ;