/********************************************************************************* # Copyright 2018-08 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. ********************************************************************************/ /************************ ####### # # ####### ###### ##### ###### # # ##### ### # # ## ## # # # # # # # # ## ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # ###### # # # # # # # # ###### # # # # # # # # # # # # # # # # # # ### # # # # # # # # # # # # # # # # # # # ### # # ####### # # ####### # ##### ###### # # ## ##### ### ### impala script to create OMOP common data model version 6.0 last revised: 27-Aug-2018 Authors: Patrick Ryan, Christian Reich, Clair Blacketer *************************/ /************************ Standardized vocabulary ************************/ --HINT DISTRIBUTE ON RANDOM CREATE TABLE ohdsi.concept ( concept_id INTEGER NOT NULL , concept_name VARCHAR(255) , domain_id VARCHAR(20) , vocabulary_id VARCHAR(20) , concept_class_id VARCHAR(20) , standard_concept VARCHAR(1) , concept_code VARCHAR(50) , valid_start_date TIMESTAMP , valid_end_date TIMESTAMP , invalid_reason VARCHAR(1) ) ; --HINT DISTRIBUTE ON RANDOM CREATE TABLE ohdsi.vocabulary ( vocabulary_id VARCHAR(20), vocabulary_name VARCHAR(255), vocabulary_reference VARCHAR(255), vocabulary_version VARCHAR(255), vocabulary_concept_id INTEGER NOT NULL ) ; --HINT DISTRIBUTE ON RANDOM CREATE TABLE ohdsi.domain ( domain_id VARCHAR(20), domain_name VARCHAR(255), domain_concept_id INTEGER NOT NULL ) ; --HINT DISTRIBUTE ON RANDOM CREATE TABLE ohdsi.concept_class ( concept_class_id VARCHAR(20), concept_class_name VARCHAR(255), concept_class_concept_id INTEGER NOT NULL ) ; --HINT DISTRIBUTE ON RANDOM CREATE TABLE ohdsi.concept_relationship ( concept_id_1 INTEGER NOT NULL, concept_id_2 INTEGER NOT NULL, relationship_id VARCHAR(20), valid_start_date TIMESTAMP, valid_end_date TIMESTAMP, invalid_reason VARCHAR(1) ) ; --HINT DISTRIBUTE ON RANDOM CREATE TABLE ohdsi.relationship ( relationship_id VARCHAR(20), relationship_name VARCHAR(255), is_hierarchical VARCHAR(1), defines_ancestry VARCHAR(1), reverse_relationship_id VARCHAR(20), relationship_concept_id INTEGER NOT NULL ) ; --HINT DISTRIBUTE ON RANDOM CREATE TABLE ohdsi.concept_synonym ( concept_id INTEGER NOT NULL, concept_synonym_name VARCHAR(1000), language_concept_id INTEGER NOT NULL ) ; --HINT DISTRIBUTE ON RANDOM CREATE TABLE ohdsi.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 ) ; --HINT DISTRIBUTE ON RANDOM CREATE TABLE ohdsi.source_to_concept_map ( source_code VARCHAR(50), source_concept_id INTEGER NOT NULL, source_vocabulary_id VARCHAR(20), source_code_description VARCHAR(255), target_concept_id INTEGER NOT NULL, target_vocabulary_id VARCHAR(20), valid_start_date TIMESTAMP, valid_end_date TIMESTAMP, invalid_reason VARCHAR(1) ) ; --HINT DISTRIBUTE ON RANDOM CREATE TABLE ohdsi.drug_strength ( drug_concept_id INTEGER NOT NULL, ingredient_concept_id INTEGER NOT NULL, amount_value FLOAT, amount_unit_concept_id INTEGER NULL, numerator_value FLOAT, numerator_unit_concept_id INTEGER NULL, denominator_value FLOAT, denominator_unit_concept_id INTEGER NULL, box_size INTEGER NULL, valid_start_date TIMESTAMP, valid_end_date TIMESTAMP, invalid_reason VARCHAR(1) ) ; /************************** Standardized meta-data ***************************/ --HINT DISTRIBUTE ON RANDOM CREATE TABLE ohdsi.cdm_source ( cdm_source_name VARCHAR(255) , cdm_source_abbreviation VARCHAR(25) , cdm_holder VARCHAR(255) , source_description VARCHAR(MAX) , source_documentation_reference VARCHAR(255) , cdm_etl_reference VARCHAR(255) , source_release_date TIMESTAMP , cdm_release_date TIMESTAMP , cdm_version VARCHAR(10) , vocabulary_version VARCHAR(20) ) ; --HINT DISTRIBUTE ON RANDOM CREATE TABLE ohdsi.metadata ( metadata_concept_id INTEGER NOT NULL , metadata_type_concept_id INTEGER NOT NULL , name VARCHAR(250) , value_as_string VARCHAR(MAX) , value_as_concept_id INTEGER NULL , metadata_date TIMESTAMP , metadata_datetime TIMESTAMP ) ; INSERT INTO ohdsi.metadata (metadata_concept_id, metadata_type_concept_id, name, value_as_string, value_as_concept_id, metadata_date, metadata_datetime) --Added cdm version record VALUES (0,0,'CDM Version', '6.0',0,NULL,NULL) ; /************************ Standardized clinical data ************************/ --HINT DISTRIBUTE_ON_KEY(person_id) CREATE TABLE ohdsi.person ( person_id BIGINT , 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, death_datetime TIMESTAMP, race_concept_id INTEGER NOT NULL, ethnicity_concept_id INTEGER NOT NULL, location_id BIGINT, provider_id BIGINT, care_site_id BIGINT, person_source_value VARCHAR(50), gender_source_value VARCHAR(50), gender_source_concept_id INTEGER NOT NULL, race_source_value VARCHAR(50), race_source_concept_id INTEGER NOT NULL, ethnicity_source_value VARCHAR(50), ethnicity_source_concept_id INTEGER NOT NULL ) ; --HINT DISTRIBUTE_ON_KEY(person_id) CREATE TABLE ohdsi.observation_period ( observation_period_id BIGINT , person_id BIGINT , observation_period_start_date TIMESTAMP , observation_period_end_date TIMESTAMP , period_type_concept_id INTEGER NOT NULL ) ; --HINT DISTRIBUTE_ON_KEY(person_id) CREATE TABLE ohdsi.specimen ( specimen_id BIGINT , person_id BIGINT , specimen_concept_id INTEGER NOT NULL , specimen_type_concept_id INTEGER NOT NULL , specimen_date TIMESTAMP , specimen_datetime TIMESTAMP , quantity FLOAT , unit_concept_id INTEGER NULL , anatomic_site_concept_id INTEGER NOT NULL , disease_status_concept_id INTEGER NOT NULL , specimen_source_id VARCHAR(50) , specimen_source_value VARCHAR(50) , unit_source_value VARCHAR(50) , anatomic_site_source_value VARCHAR(50) , disease_status_source_value VARCHAR(50) ) ; --HINT DISTRIBUTE_ON_KEY(person_id) CREATE TABLE ohdsi.visit_occurrence ( visit_occurrence_id BIGINT , person_id BIGINT , visit_concept_id INTEGER NOT NULL , visit_start_date TIMESTAMP , visit_start_datetime TIMESTAMP , visit_end_date TIMESTAMP , visit_end_datetime TIMESTAMP , visit_type_concept_id INTEGER NOT NULL , provider_id BIGINT, care_site_id BIGINT, visit_source_value VARCHAR(50), visit_source_concept_id INTEGER NOT NULL , admitted_from_concept_id INTEGER NOT NULL , admitted_from_source_value VARCHAR(50) , discharge_to_source_value VARCHAR(50) , discharge_to_concept_id INTEGER NOT NULL , preceding_visit_occurrence_id BIGINT ) ; --HINT DISTRIBUTE_ON_KEY(person_id) CREATE TABLE ohdsi.visit_detail ( visit_detail_id BIGINT , person_id BIGINT , visit_detail_concept_id INTEGER NOT NULL , visit_detail_start_date TIMESTAMP , visit_detail_start_datetime TIMESTAMP , visit_detail_end_date TIMESTAMP , visit_detail_end_datetime TIMESTAMP , visit_detail_type_concept_id INTEGER NOT NULL , provider_id BIGINT , care_site_id BIGINT , discharge_to_concept_id INTEGER NOT NULL , admitted_from_concept_id INTEGER NOT NULL , admitted_from_source_value VARCHAR(50) , visit_detail_source_value VARCHAR(50) , visit_detail_source_concept_id INTEGER NOT NULL , discharge_to_source_value VARCHAR(50) , preceding_visit_detail_id BIGINT , visit_detail_parent_id BIGINT , visit_occurrence_id BIGINT ) ; --HINT DISTRIBUTE_ON_KEY(person_id) CREATE TABLE ohdsi.procedure_occurrence ( procedure_occurrence_id BIGINT , person_id BIGINT , procedure_concept_id INTEGER NOT NULL , procedure_date TIMESTAMP , procedure_datetime TIMESTAMP , procedure_type_concept_id INTEGER NOT NULL , modifier_concept_id INTEGER NOT NULL , quantity INTEGER NULL , provider_id BIGINT , visit_occurrence_id BIGINT , visit_detail_id BIGINT , procedure_source_value VARCHAR(50) , procedure_source_concept_id INTEGER NOT NULL , modifier_source_value VARCHAR(50) ) ; --HINT DISTRIBUTE_ON_KEY(person_id) CREATE TABLE ohdsi.drug_exposure ( drug_exposure_id BIGINT , person_id BIGINT , drug_concept_id INTEGER NOT NULL , drug_exposure_start_date TIMESTAMP , drug_exposure_start_datetime TIMESTAMP , drug_exposure_end_date TIMESTAMP , drug_exposure_end_datetime TIMESTAMP , verbatim_end_date TIMESTAMP , drug_type_concept_id INTEGER NOT NULL , stop_reason VARCHAR(20) , refills INTEGER NULL , quantity FLOAT , days_supply INTEGER NULL , sig VARCHAR(MAX) , route_concept_id INTEGER NOT NULL , lot_number VARCHAR(50) , provider_id BIGINT , visit_occurrence_id BIGINT , visit_detail_id BIGINT , drug_source_value VARCHAR(50) , drug_source_concept_id INTEGER NOT NULL , route_source_value VARCHAR(50) , dose_unit_source_value VARCHAR(50) ) ; --HINT DISTRIBUTE_ON_KEY(person_id) CREATE TABLE ohdsi.device_exposure ( device_exposure_id BIGINT , person_id BIGINT , device_concept_id INTEGER NOT NULL , device_exposure_start_date TIMESTAMP , device_exposure_start_datetime TIMESTAMP , device_exposure_end_date TIMESTAMP , device_exposure_end_datetime TIMESTAMP , device_type_concept_id INTEGER NOT NULL , unique_device_id VARCHAR(50) , quantity INTEGER NULL , provider_id BIGINT , visit_occurrence_id BIGINT , visit_detail_id BIGINT , device_source_value VARCHAR(100) , device_source_concept_id INTEGER NOT NULL ) ; --HINT DISTRIBUTE_ON_KEY(person_id) CREATE TABLE ohdsi.condition_occurrence ( condition_occurrence_id BIGINT , person_id BIGINT , condition_concept_id INTEGER NOT NULL , condition_start_date TIMESTAMP , condition_start_datetime TIMESTAMP , condition_end_date TIMESTAMP , condition_end_datetime TIMESTAMP , condition_type_concept_id INTEGER NOT NULL , condition_status_concept_id INTEGER NOT NULL , stop_reason VARCHAR(20) , provider_id BIGINT , visit_occurrence_id BIGINT , visit_detail_id BIGINT , condition_source_value VARCHAR(50) , condition_source_concept_id INTEGER NOT NULL , condition_status_source_value VARCHAR(50) ) ; --HINT DISTRIBUTE_ON_KEY(person_id) CREATE TABLE ohdsi.measurement ( measurement_id BIGINT , person_id BIGINT , measurement_concept_id INTEGER NOT NULL , measurement_date TIMESTAMP , measurement_datetime TIMESTAMP , measurement_time VARCHAR(10), measurement_type_concept_id INTEGER NOT NULL , operator_concept_id INTEGER NULL , value_as_number FLOAT , value_as_concept_id INTEGER NULL , unit_concept_id INTEGER NULL , range_low FLOAT , range_high FLOAT , provider_id BIGINT , visit_occurrence_id BIGINT , visit_detail_id BIGINT , measurement_source_value VARCHAR(50) , measurement_source_concept_id INTEGER NOT NULL , unit_source_value VARCHAR(50) , value_source_value VARCHAR(50), modifier_of_event_id BIGINT, modifier_of_field_concept_id INTEGER NULL ) ; --HINT DISTRIBUTE_ON_KEY(person_id) CREATE TABLE ohdsi.note ( note_id BIGINT , person_id BIGINT , note_event_id BIGINT , note_event_field_concept_id INTEGER NOT NULL , note_date TIMESTAMP , note_datetime TIMESTAMP , note_type_concept_id INTEGER NOT NULL , note_class_concept_id INTEGER NOT NULL , note_title VARCHAR(250) , note_text VARCHAR(MAX) , encoding_concept_id INTEGER NOT NULL , language_concept_id INTEGER NOT NULL , provider_id BIGINT , visit_occurrence_id BIGINT , visit_detail_id BIGINT , note_source_value VARCHAR(50) ) ; --HINT DISTRIBUTE ON RANDOM CREATE TABLE ohdsi.note_nlp ( note_nlp_id BIGINT , note_id BIGINT , section_concept_id INTEGER NOT NULL , snippet VARCHAR(250) , "offset" VARCHAR(250) , lexical_variant VARCHAR(250) , note_nlp_concept_id INTEGER NOT NULL , nlp_system VARCHAR(250) , nlp_date TIMESTAMP , nlp_datetime TIMESTAMP , term_exists VARCHAR(1) , term_temporal VARCHAR(50) , term_modifiers VARCHAR(2000) , note_nlp_source_concept_id INTEGER NOT NULL ) ; --HINT DISTRIBUTE_ON_KEY(person_id) CREATE TABLE ohdsi.observation ( observation_id BIGINT , person_id BIGINT , observation_concept_id INTEGER NOT NULL , observation_date TIMESTAMP , observation_datetime TIMESTAMP , observation_type_concept_id INTEGER NOT NULL , value_as_number FLOAT , value_as_string VARCHAR(60) , value_as_concept_id INTEGER NULL , qualifier_concept_id INTEGER NULL , unit_concept_id INTEGER NULL , provider_id INTEGER NULL , visit_occurrence_id BIGINT , visit_detail_id BIGINT , observation_source_value VARCHAR(50) , observation_source_concept_id INTEGER NOT NULL , unit_source_value VARCHAR(50) , qualifier_source_value VARCHAR(50) , observation_event_id BIGINT , obs_event_field_concept_id INTEGER NOT NULL , value_as_datetime TIMESTAMP ) ; --HINT DISTRIBUTE ON KEY(person_id) CREATE TABLE ohdsi.survey_conduct ( survey_conduct_id BIGINT , person_id BIGINT , survey_concept_id INTEGER NOT NULL , survey_start_date TIMESTAMP , survey_start_datetime TIMESTAMP , survey_end_date TIMESTAMP , survey_end_datetime TIMESTAMP , provider_id BIGINT , assisted_concept_id INTEGER NOT NULL , respondent_type_concept_id INTEGER NOT NULL , timing_concept_id INTEGER NOT NULL , collection_method_concept_id INTEGER NOT NULL , assisted_source_value VARCHAR(50) , respondent_type_source_value VARCHAR(100) , timing_source_value VARCHAR(100) , collection_method_source_value VARCHAR(100) , survey_source_value VARCHAR(100) , survey_source_concept_id INTEGER NOT NULL , survey_source_identifier VARCHAR(100) , validated_survey_concept_id INTEGER NOT NULL , validated_survey_source_value VARCHAR(100) , survey_version_number VARCHAR(20) , visit_occurrence_id BIGINT , visit_detail_id BIGINT , response_visit_occurrence_id BIGINT ) ; --HINT DISTRIBUTE ON RANDOM CREATE TABLE ohdsi.fact_relationship ( domain_concept_id_1 INTEGER NOT NULL , fact_id_1 BIGINT , domain_concept_id_2 INTEGER NOT NULL , fact_id_2 BIGINT , relationship_concept_id INTEGER NOT NULL ) ; CREATE TABLE ohdsi.episode ( episode_id BIGINT, person_id BIGINT, episode_start_datetime TIMESTAMP, episode_end_datetime TIMESTAMP, episode_concept_id INTEGER NOT NULL, episode_parent_id INTEGER NULL, episode_number INTEGER NULL, episode_object_concept_id INTEGER NOT NULL, episode_type_concept_id INTEGER NOT NULL, episode_source_value VARCHAR(50), episode_source_concept_id INTEGER NULL ) ; -- Episode_Event CREATE TABLE ohdsi.episode_event ( episode_id BIGINT, event_id BIGINT, event_field_concept_id INTEGER NOT NULL ) ; /************************ Standardized health system data ************************/ --HINT DISTRIBUTE ON RANDOM CREATE TABLE ohdsi.`location` ( location_id BIGINT , address_1 VARCHAR(50) , address_2 VARCHAR(50) , city VARCHAR(50) , state VARCHAR(2) , zip VARCHAR(9) , county VARCHAR(20) , country VARCHAR(100) , location_source_value VARCHAR(50) , latitude FLOAT , longitude FLOAT , region_concept_id INTEGER NULL ) ; --HINT DISTRIBUTE ON RANDOM CREATE TABLE ohdsi.location_history --Table added ( location_history_id BIGINT , location_id BIGINT , relationship_type_concept_id INTEGER NOT NULL , domain_id VARCHAR(50) , entity_id BIGINT , start_date TIMESTAMP , end_date TIMESTAMP ) ; --HINT DISTRIBUTE ON RANDOM CREATE TABLE ohdsi.care_site ( care_site_id BIGINT , care_site_name VARCHAR(255) , place_of_service_concept_id INTEGER NOT NULL , location_id BIGINT , care_site_source_value VARCHAR(50) , place_of_service_source_value VARCHAR(50) ) ; --HINT DISTRIBUTE ON RANDOM CREATE TABLE ohdsi.provider ( provider_id BIGINT , provider_name VARCHAR(255) , NPI VARCHAR(20) , DEA VARCHAR(20) , specialty_concept_id INTEGER NOT NULL , care_site_id BIGINT , year_of_birth INTEGER NULL , gender_concept_id INTEGER NOT NULL , provider_source_value VARCHAR(50) , specialty_source_value VARCHAR(50) , specialty_source_concept_id INTEGER NOT NULL , gender_source_value VARCHAR(50) , gender_source_concept_id INTEGER NOT NULL ) ; /************************ Standardized health economics ************************/ --HINT DISTRIBUTE_ON_KEY(person_id) CREATE TABLE ohdsi.payer_plan_period ( payer_plan_period_id BIGINT , person_id BIGINT , contract_person_id BIGINT , payer_plan_period_start_date TIMESTAMP , payer_plan_period_end_date TIMESTAMP , payer_concept_id INTEGER NOT NULL , plan_concept_id INTEGER NOT NULL , contract_concept_id INTEGER NOT NULL , sponsor_concept_id INTEGER NOT NULL , stop_reason_concept_id INTEGER NOT NULL , payer_source_value VARCHAR(50) , payer_source_concept_id INTEGER NOT NULL , plan_source_value VARCHAR(50) , plan_source_concept_id INTEGER NOT NULL , contract_source_value VARCHAR(50) , contract_source_concept_id INTEGER NOT NULL , sponsor_source_value VARCHAR(50) , sponsor_source_concept_id INTEGER NOT NULL , family_source_value VARCHAR(50) , stop_reason_source_value VARCHAR(50) , stop_reason_source_concept_id INTEGER NOT NULL ) ; --HINT DISTRIBUTE ON KEY(person_id) CREATE TABLE ohdsi.cost ( cost_id BIGINT , person_id BIGINT, cost_event_id BIGINT , cost_event_field_concept_id INTEGER NOT NULL , cost_concept_id INTEGER NOT NULL , cost_type_concept_id INTEGER NOT NULL , currency_concept_id INTEGER NOT NULL , cost FLOAT , incurred_date TIMESTAMP , billed_date TIMESTAMP , paid_date TIMESTAMP , revenue_code_concept_id INTEGER NOT NULL , drg_concept_id INTEGER NOT NULL , cost_source_value VARCHAR(50) , cost_source_concept_id INTEGER NOT NULL , revenue_code_source_value VARCHAR(50) , drg_source_value VARCHAR(3) , payer_plan_period_id BIGINT ) ; /************************ Standardized derived elements ************************/ --HINT DISTRIBUTE_ON_KEY(person_id) CREATE TABLE ohdsi.drug_era ( drug_era_id BIGINT , person_id BIGINT , drug_concept_id INTEGER NOT NULL , drug_era_start_datetime TIMESTAMP , drug_era_end_datetime TIMESTAMP , drug_exposure_count INTEGER NULL , gap_days INTEGER NULL ) ; --HINT DISTRIBUTE_ON_KEY(person_id) CREATE TABLE ohdsi.dose_era ( dose_era_id BIGINT , person_id BIGINT , drug_concept_id INTEGER NOT NULL , unit_concept_id INTEGER NOT NULL , dose_value FLOAT , dose_era_start_datetime TIMESTAMP , dose_era_end_datetime TIMESTAMP ) ; --HINT DISTRIBUTE_ON_KEY(person_id) CREATE TABLE ohdsi.condition_era ( condition_era_id BIGINT , person_id BIGINT , condition_concept_id INTEGER NOT NULL , condition_era_start_datetime TIMESTAMP , condition_era_end_datetime TIMESTAMP , condition_occurrence_count INTEGER NULL ) ;