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OHDSI / CommonDataModel

Definition and DDLs for the OMOP Common Data Model (CDM)
https://ohdsi.github.io/CommonDataModel
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Clickhouse support DDL #630

Open dridk opened 5 months ago

dridk commented 5 months ago

Hi,

it would be greate to have an omop shema for clickhouse. It is a column oriented sgbd very suitable for analytical

https://clickhouse.com/

dridk commented 5 months ago

Let me work on this

dridk commented 5 months ago

Ok.. it looks like you generate DDL automatically from a script . I wonder how can I optimize shema data type. For instance using Uint8 for age and Uint32 for index.

dridk commented 5 months ago

Just for sharing mine .. Note: clickhouse doesn't have concept of Foreign key or index. It is a column oriented database.

--clickhouse CDM DDL Specification for OMOP Common Data Model 5.4
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE cdmDatabaseSchema.person (
            person_id UInt32 NOT NULL,
            gender_concept_id UInt32 NOT NULL,
            year_of_birth UInt16 NOT NULL,
            month_of_birth UInt16 NULL,
            day_of_birth UInt16 NULL,
            birth_datetime DateTime NULL,
            race_concept_id UInt32 NOT NULL,
            ethnicity_concept_id UInt32 NOT NULL,
            location_id UInt32 NULL,
            provider_id UInt32 NULL,
            care_site_id UInt32 NULL,
            person_source_value String NULL,
            gender_source_value String NULL,
            gender_source_concept_id UInt32 NULL,
            race_source_value String NULL,
            race_source_concept_id UInt32 NULL,
            ethnicity_source_value String NULL,
            ethnicity_source_concept_id UInt32 NULL )
            ENGINE = MergeTree()
            PRIMARY KEY (person_id);

--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE cdmDatabaseSchema.observation_period (
            observation_period_id UInt32 NOT NULL,
            person_id UInt32 NOT NULL,
            observation_period_start_date Date NOT NULL,
            observation_period_end_date Date NOT NULL,
            period_type_concept_id UInt32 NOT NULL )
            ENGINE = MergeTree()
            PRIMARY KEY (observation_period_id);

--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE cdmDatabaseSchema.visit_occurrence (
            visit_occurrence_id UInt32 NOT NULL,
            person_id UInt32 NOT NULL,
            visit_concept_id UInt32 NOT NULL,
            visit_start_date Date NOT NULL,
            visit_start_datetime DateTime NULL,
            visit_end_date Date NOT NULL,
            visit_end_datetime DateTime NULL,
            visit_type_concept_id UInt32 NOT NULL,
            provider_id UInt32 NULL,
            care_site_id UInt32 NULL,
            visit_source_value String NULL,
            visit_source_concept_id UInt32 NULL,
            admitted_from_concept_id UInt32 NULL,
            admitted_from_source_value String NULL,
            discharged_to_concept_id UInt32 NULL,
            discharged_to_source_value String NULL,
            preceding_visit_occurrence_id UInt32 NULL )
            ENGINE = MergeTree()
            PRIMARY KEY (visit_occurrence_id);
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE cdmDatabaseSchema.visit_detail (
            visit_detail_id UInt32 NOT NULL,
            person_id UInt32 NOT NULL,
            visit_detail_concept_id UInt32 NOT NULL,
            visit_detail_start_date Date NOT NULL,
            visit_detail_start_datetime DateTime NULL,
            visit_detail_end_date Date NOT NULL,
            visit_detail_end_datetime DateTime NULL,
            visit_detail_type_concept_id UInt32 NOT NULL,
            provider_id UInt32 NULL,
            care_site_id UInt32 NULL,
            visit_detail_source_value String NULL,
            visit_detail_source_concept_id UInt32 NULL,
            admitted_from_concept_id UInt32 NULL,
            admitted_from_source_value String NULL,
            discharged_to_source_value String NULL,
            discharged_to_concept_id UInt32 NULL,
            preceding_visit_detail_id UInt32 NULL,
            parent_visit_detail_id UInt32 NULL,
            visit_occurrence_id UInt32 NOT NULL )
            ENGINE = MergeTree()
            PRIMARY KEY (visit_detail_id);

--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE cdmDatabaseSchema.condition_occurrence (
            condition_occurrence_id UInt32 NOT NULL,
            person_id UInt32 NOT NULL,
            condition_concept_id UInt32 NOT NULL,
            condition_start_date Date NOT NULL,
            condition_start_datetime DateTime NULL,
            condition_end_date Date NULL,
            condition_end_datetime DateTime NULL,
            condition_type_concept_id UInt32 NOT NULL,
            condition_status_concept_id UInt32 NULL,
            stop_reason String NULL,
            provider_id UInt32 NULL,
            visit_occurrence_id UInt32 NULL,
            visit_detail_id UInt32 NULL,
            condition_source_value String NULL,
            condition_source_concept_id UInt32 NULL,
            condition_status_source_value String NULL )
            ENGINE = MergeTree()
            PRIMARY KEY (condition_occurrence_id);

--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE cdmDatabaseSchema.drug_exposure (
            drug_exposure_id UInt32 NOT NULL,
            person_id UInt32 NOT NULL,
            drug_concept_id UInt32 NOT NULL,
            drug_exposure_start_date Date NOT NULL,
            drug_exposure_start_datetime DateTime NULL,
            drug_exposure_end_date Date NOT NULL,
            drug_exposure_end_datetime DateTime NULL,
            verbatim_end_date Date NULL,
            drug_type_concept_id UInt32 NOT NULL,
            stop_reason String NULL,
            refills UInt32 NULL,
            quantity Float64 NULL,
            days_supply UInt32 NULL,
            sig String NULL,
            route_concept_id UInt32 NULL,
            lot_number String NULL,
            provider_id UInt32 NULL,
            visit_occurrence_id UInt32 NULL,
            visit_detail_id UInt32 NULL,
            drug_source_value String NULL,
            drug_source_concept_id UInt32 NULL,
            route_source_value String NULL,
            dose_unit_source_value String NULL )
            ENGINE = MergeTree()
            PRIMARY KEY (drug_exposure_id);

--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE cdmDatabaseSchema.procedure_occurrence (
            procedure_occurrence_id UInt32 NOT NULL,
            person_id UInt32 NOT NULL,
            procedure_concept_id UInt32 NOT NULL,
            procedure_date Date NOT NULL,
            procedure_datetime DateTime NULL,
            procedure_end_date Date NULL,
            procedure_end_datetime DateTime NULL,
            procedure_type_concept_id UInt32 NOT NULL,
            modifier_concept_id UInt32 NULL,
            quantity UInt32 NULL,
            provider_id UInt32 NULL,
            visit_occurrence_id UInt32 NULL,
            visit_detail_id UInt32 NULL,
            procedure_source_value String NULL,
            procedure_source_concept_id UInt32 NULL,
            modifier_source_value String NULL )
            ENGINE = MergeTree()
            PRIMARY KEY (procedure_occurrence_id);

--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE cdmDatabaseSchema.device_exposure (
            device_exposure_id UInt32 NOT NULL,
            person_id UInt32 NOT NULL,
            device_concept_id UInt32 NOT NULL,
            device_exposure_start_date Date NOT NULL,
            device_exposure_start_datetime DateTime NULL,
            device_exposure_end_date Date NULL,
            device_exposure_end_datetime DateTime NULL,
            device_type_concept_id UInt32 NOT NULL,
            unique_device_id String NULL,
            production_id String NULL,
            quantity UInt32 NULL,
            provider_id UInt32 NULL,
            visit_occurrence_id UInt32 NULL,
            visit_detail_id UInt32 NULL,
            device_source_value String NULL,
            device_source_concept_id UInt32 NULL,
            unit_concept_id UInt32 NULL,
            unit_source_value String NULL,
            unit_source_concept_id UInt32 NULL )
            ENGINE = MergeTree()
            PRIMARY KEY (device_exposure_id);

--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE cdmDatabaseSchema.measurement (
            measurement_id UInt32 NOT NULL,
            person_id UInt32 NOT NULL,
            measurement_concept_id UInt32 NOT NULL,
            measurement_date Date NOT NULL,
            measurement_datetime DateTime NULL,
            measurement_time String NULL,
            measurement_type_concept_id UInt32 NOT NULL,
            operator_concept_id UInt32 NULL,
            value_as_number Float64 NULL,
            value_as_concept_id UInt32 NULL,
            unit_concept_id UInt32 NULL,
            range_low Float64 NULL,
            range_high Float64 NULL,
            provider_id UInt32 NULL,
            visit_occurrence_id UInt32 NULL,
            visit_detail_id UInt32 NULL,
            measurement_source_value String NULL,
            measurement_source_concept_id UInt32 NULL,
            unit_source_value String NULL,
            unit_source_concept_id UInt32 NULL,
            value_source_value String NULL,
            measurement_event_id UInt32 NULL,
            meas_event_field_concept_id UInt32 NULL )
            ENGINE = MergeTree()
            PRIMARY KEY (measurement_id);

--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE cdmDatabaseSchema.observation (
            observation_id UInt32 NOT NULL,
            person_id UInt32 NOT NULL,
            observation_concept_id UInt32 NOT NULL,
            observation_date Date NOT NULL,
            observation_datetime DateTime NULL,
            observation_type_concept_id UInt32 NOT NULL,
            value_as_number Float64 NULL,
            value_as_string String NULL,
            value_as_concept_id UInt32 NULL,
            qualifier_concept_id UInt32 NULL,
            unit_concept_id UInt32 NULL,
            provider_id UInt32 NULL,
            visit_occurrence_id UInt32 NULL,
            visit_detail_id UInt32 NULL,
            observation_source_value String NULL,
            observation_source_concept_id UInt32 NULL,
            unit_source_value String NULL,
            qualifier_source_value String NULL,
            value_source_value String NULL,
            observation_event_id UInt32 NULL,
            obs_event_field_concept_id UInt32 NULL )
            ENGINE = MergeTree()
            PRIMARY KEY (observation_id);

--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE cdmDatabaseSchema.death (
            person_id UInt32 NOT NULL,
            death_date Date NOT NULL,
            death_datetime DateTime NULL,
            death_type_concept_id UInt32 NULL,
            cause_concept_id UInt32 NULL,
            cause_source_value String NULL,
            cause_source_concept_id UInt32 NULL )
            ENGINE = MergeTree()
            PRIMARY KEY (person_id);

--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE cdmDatabaseSchema.note (
            note_id UInt32 NOT NULL,
            person_id UInt32 NOT NULL,
            note_date Date NOT NULL,
            note_datetime DateTime NULL,
            note_type_concept_id UInt32 NOT NULL,
            note_class_concept_id UInt32 NOT NULL,
            note_title String NULL,
            note_String String NOT NULL,
            encoding_concept_id UInt32 NOT NULL,
            language_concept_id UInt32 NOT NULL,
            provider_id UInt32 NULL,
            visit_occurrence_id UInt32 NULL,
            visit_detail_id UInt32 NULL,
            note_source_value String NULL,
            note_event_id UInt32 NULL,
            note_event_field_concept_id UInt32 NULL )
            ENGINE = MergeTree()
            PRIMARY KEY (note_id);

--HINT DISTRIBUTE ON RANDOM
CREATE TABLE cdmDatabaseSchema.note_nlp (
            note_nlp_id UInt32 NOT NULL,
            note_id UInt32 NOT NULL,
            section_concept_id UInt32 NULL,
            snippet String NULL,
            offset String NULL,
            lexical_variant String NOT NULL,
            note_nlp_concept_id UInt32 NULL,
            note_nlp_source_concept_id UInt32 NULL,
            nlp_system String NULL,
            nlp_date Date NOT NULL,
            nlp_datetime DateTime NULL,
            term_exists FixedString(1) NULL,
            term_temporal String NULL,
            term_modifiers String NULL )
            ENGINE = MergeTree()
            PRIMARY KEY (note_nlp_id);

--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE cdmDatabaseSchema.specimen (
            specimen_id UInt32 NOT NULL,
            person_id UInt32 NOT NULL,
            specimen_concept_id UInt32 NOT NULL,
            specimen_type_concept_id UInt32 NOT NULL,
            specimen_date Date NOT NULL,
            specimen_datetime DateTime NULL,
            quantity Float64 NULL,
            unit_concept_id UInt32 NULL,
            anatomic_site_concept_id UInt32 NULL,
            disease_status_concept_id UInt32 NULL,
            specimen_source_id String NULL,
            specimen_source_value String NULL,
            unit_source_value String NULL,
            anatomic_site_source_value String NULL,
            disease_status_source_value String NULL )
            ENGINE = MergeTree()
            PRIMARY KEY (specimen_id);

--HINT DISTRIBUTE ON RANDOM
CREATE TABLE cdmDatabaseSchema.fact_relationship (
            domain_concept_id_1 UInt32 NOT NULL,
            fact_id_1 UInt32 NOT NULL,
            domain_concept_id_2 UInt32 NOT NULL,
            fact_id_2 UInt32 NOT NULL,
            relationship_concept_id UInt32 NOT NULL )
            ENGINE = MergeTree()
            PRIMARY KEY (fact_id_1,fact_id_2);

--HINT DISTRIBUTE ON RANDOM
CREATE TABLE cdmDatabaseSchema.location (
            location_id UInt32 NOT NULL,
            address_1 String NULL,
            address_2 String NULL,
            city String NULL,
            state String NULL,
            zip String NULL,
            county String NULL,
            location_source_value String NULL,
            country_concept_id UInt32 NULL,
            country_source_value String NULL,
            latitude Float64 NULL,
            longitude Float64 NULL )
            ENGINE = MergeTree()
            PRIMARY KEY (location_id);

--HINT DISTRIBUTE ON RANDOM
CREATE TABLE cdmDatabaseSchema.care_site (
            care_site_id UInt32 NOT NULL,
            care_site_name String NULL,
            place_of_service_concept_id UInt32 NULL,
            location_id UInt32 NULL,
            care_site_source_value String NULL,
            place_of_service_source_value String NULL )
            ENGINE = MergeTree()
            PRIMARY KEY (care_site_id);

            --HINT DISTRIBUTE ON RANDOM
CREATE TABLE cdmDatabaseSchema.provider (
            provider_id UInt32 NOT NULL,
            provider_name String NULL,
            npi String NULL,
            dea String NULL,
            specialty_concept_id UInt32 NULL,
            care_site_id UInt32 NULL,
            year_of_birth UInt32 NULL,
            gender_concept_id UInt32 NULL,
            provider_source_value String NULL,
            specialty_source_value String NULL,
            specialty_source_concept_id UInt32 NULL,
            gender_source_value String NULL,
            gender_source_concept_id UInt32 NULL )
            ENGINE = MergeTree()
            PRIMARY KEY (provider_id);

--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE cdmDatabaseSchema.payer_plan_period (
            payer_plan_period_id UInt32 NOT NULL,
            person_id UInt32 NOT NULL,
            payer_plan_period_start_date Date NOT NULL,
            payer_plan_period_end_date Date NOT NULL,
            payer_concept_id UInt32 NULL,
            payer_source_value String NULL,
            payer_source_concept_id UInt32 NULL,
            plan_concept_id UInt32 NULL,
            plan_source_value String NULL,
            plan_source_concept_id UInt32 NULL,
            sponsor_concept_id UInt32 NULL,
            sponsor_source_value String NULL,
            sponsor_source_concept_id UInt32 NULL,
            family_source_value String NULL,
            stop_reason_concept_id UInt32 NULL,
            stop_reason_source_value String NULL,
            stop_reason_source_concept_id UInt32 NULL )
            ENGINE = MergeTree()
            PRIMARY KEY (payer_plan_period_id);

--HINT DISTRIBUTE ON RANDOM
CREATE TABLE cdmDatabaseSchema.cost (
            cost_id UInt32 NOT NULL,
            cost_event_id UInt32 NOT NULL,
            cost_domain_id String NOT NULL,
            cost_type_concept_id UInt32 NOT NULL,
            currency_concept_id UInt32 NULL,
            total_charge Float64 NULL,
            total_cost Float64 NULL,
            total_paid Float64 NULL,
            paid_by_payer Float64 NULL,
            paid_by_patient Float64 NULL,
            paid_patient_copay Float64 NULL,
            paid_patient_coinsurance Float64 NULL,
            paid_patient_deductible Float64 NULL,
            paid_by_primary Float64 NULL,
            paid_ingredient_cost Float64 NULL,
            paid_dispensing_fee Float64 NULL,
            payer_plan_period_id UInt32 NULL,
            amount_allowed Float64 NULL,
            revenue_code_concept_id UInt32 NULL,
            revenue_code_source_value String NULL,
            drg_concept_id UInt32 NULL,
            drg_source_value String NULL )
            ENGINE = MergeTree()
            PRIMARY KEY (cost_id);

--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE cdmDatabaseSchema.drug_era (
            drug_era_id UInt32 NOT NULL,
            person_id UInt32 NOT NULL,
            drug_concept_id UInt32 NOT NULL,
            drug_era_start_date Date NOT NULL,
            drug_era_end_date Date NOT NULL,
            drug_exposure_count UInt32 NULL,
            gap_days UInt32 NULL )
            ENGINE = MergeTree()
            PRIMARY KEY (drug_era_id);

--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE cdmDatabaseSchema.dose_era (
            dose_era_id UInt32 NOT NULL,
            person_id UInt32 NOT NULL,
            drug_concept_id UInt32 NOT NULL,
            unit_concept_id UInt32 NOT NULL,
            dose_value Float64 NOT NULL,
            dose_era_start_date Date NOT NULL,
            dose_era_end_date Date NOT NULL )
            ENGINE = MergeTree()
            PRIMARY KEY (dose_era_id);

--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE cdmDatabaseSchema.condition_era (
            condition_era_id UInt32 NOT NULL,
            person_id UInt32 NOT NULL,
            condition_concept_id UInt32 NOT NULL,
            condition_era_start_date Date NOT NULL,
            condition_era_end_date Date NOT NULL,
            condition_occurrence_count UInt32 NULL )
            ENGINE = MergeTree()
            PRIMARY KEY (condition_era_id);

--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE cdmDatabaseSchema.episode (
            episode_id UInt32 NOT NULL,
            person_id UInt32 NOT NULL,
            episode_concept_id UInt32 NOT NULL,
            episode_start_date Date NOT NULL,
            episode_start_datetime DateTime NULL,
            episode_end_date Date NULL,
            episode_end_datetime DateTime NULL,
            episode_parent_id UInt32 NULL,
            episode_number UInt32 NULL,
            episode_object_concept_id UInt32 NOT NULL,
            episode_type_concept_id UInt32 NOT NULL,
            episode_source_value String NULL,
            episode_source_concept_id UInt32 NULL )
            ENGINE = MergeTree()
            PRIMARY KEY (episode_id);

--HINT DISTRIBUTE ON RANDOM
CREATE TABLE cdmDatabaseSchema.episode_event (
            episode_id UInt32 NOT NULL,
            event_id UInt32 NOT NULL,
            episode_event_field_concept_id UInt32 NOT NULL )
            ENGINE = MergeTree()
            PRIMARY KEY (episode_id);

--HINT DISTRIBUTE ON RANDOM
CREATE TABLE cdmDatabaseSchema.metadata (
            metadata_id UInt32 NOT NULL,
            metadata_concept_id UInt32 NOT NULL,
            metadata_type_concept_id UInt32 NOT NULL,
            name String NOT NULL,
            value_as_string String NULL,
            value_as_concept_id UInt32 NULL,
            value_as_number Float64 NULL,
            metadata_date Date NULL,
            metadata_datetime DateTime NULL )
            ENGINE = MergeTree()
            PRIMARY KEY (metadata_id);

--HINT DISTRIBUTE ON RANDOM
CREATE TABLE cdmDatabaseSchema.cdm_source (
            cdm_source_name String NOT NULL,
            cdm_source_abbreviation String NOT NULL,
            cdm_holder String NOT NULL,
            source_description String NULL,
            source_documentation_reference String NULL,
            cdm_etl_reference String NULL,
            source_release_date Date NOT NULL,
            cdm_release_date Date NOT NULL,
            cdm_version String NULL,
            cdm_version_concept_id UInt32 NOT NULL,
            vocabulary_version String NOT NULL )
            ENGINE = MergeTree()
            PRIMARY KEY (cdm_source_name);

--HINT DISTRIBUTE ON RANDOM
CREATE TABLE cdmDatabaseSchema.concept (
            concept_id UInt32 NOT NULL,
            concept_name String NOT NULL,
            domain_id String NOT NULL,
            vocabulary_id String NOT NULL,
            concept_class_id String NOT NULL,
            standard_concept String NULL,
            concept_code String NOT NULL,
            valid_start_date Date NOT NULL,
            valid_end_date Date NOT NULL,
            invalid_reason FixedString(1) NULL )
            ENGINE = MergeTree()
            PRIMARY KEY (concept_id);

--HINT DISTRIBUTE ON RANDOM
CREATE TABLE cdmDatabaseSchema.vocabulary (
            vocabulary_id String NOT NULL,
            vocabulary_name String NOT NULL,
            vocabulary_reference String NULL,
            vocabulary_version String NULL,
            vocabulary_concept_id UInt32 NOT NULL )
            ENGINE = MergeTree()
            PRIMARY KEY (vocabulary_id);

--HINT DISTRIBUTE ON RANDOM
CREATE TABLE cdmDatabaseSchema.domain (
            domain_id String NOT NULL,
            domain_name String NOT NULL,
            domain_concept_id UInt32 NOT NULL )
            ENGINE = MergeTree()
            PRIMARY KEY (domain_id);

--HINT DISTRIBUTE ON RANDOM
CREATE TABLE cdmDatabaseSchema.concept_class (
            concept_class_id String NOT NULL,
            concept_class_name String NOT NULL,
            concept_class_concept_id UInt32 NOT NULL )
            ENGINE = MergeTree()
            PRIMARY KEY (concept_class_id);

--HINT DISTRIBUTE ON RANDOM
CREATE TABLE cdmDatabaseSchema.concept_relationship (
            concept_id_1 UInt32 NOT NULL,
            concept_id_2 UInt32 NOT NULL,
            relationship_id String NOT NULL,
            valid_start_date Date NOT NULL,
            valid_end_date Date NOT NULL,
            invalid_reason String NULL )
            ENGINE = MergeTree()
            PRIMARY KEY (concept_id_1,concept_id_2);

--HINT DISTRIBUTE ON RANDOM
CREATE TABLE cdmDatabaseSchema.relationship (
            relationship_id String NOT NULL,
            relationship_name String NOT NULL,
            is_hierarchical String NOT NULL,
            defines_ancestry String NOT NULL,
            reverse_relationship_id String NOT NULL,
            relationship_concept_id UInt32 NOT NULL )
            ENGINE = MergeTree()
            PRIMARY KEY (relationship_id);

--HINT DISTRIBUTE ON RANDOM
CREATE TABLE cdmDatabaseSchema.concept_synonym (
            concept_id UInt32 NOT NULL,
            concept_synonym_name String NOT NULL,
            language_concept_id UInt32 NOT NULL )
            ENGINE = MergeTree()
            PRIMARY KEY (concept_id);

--HINT DISTRIBUTE ON RANDOM
CREATE TABLE cdmDatabaseSchema.concept_ancestor (
            ancestor_concept_id UInt32 NOT NULL,
            descendant_concept_id UInt32 NOT NULL,
            min_levels_of_separation UInt32 NOT NULL,
            max_levels_of_separation UInt32 NOT NULL )
            ENGINE = MergeTree()
            PRIMARY KEY (ancestor_concept_id,descendant_concept_id);

--HINT DISTRIBUTE ON RANDOM
CREATE TABLE cdmDatabaseSchema.source_to_concept_map (
            source_code String NOT NULL,
            source_concept_id UInt32 NOT NULL,
            source_vocabulary_id String NOT NULL,
            source_code_description String NULL,
            target_concept_id UInt32 NOT NULL,
            target_vocabulary_id String NOT NULL,
            valid_start_date Date NOT NULL,
            valid_end_date Date NOT NULL,
            invalid_reason String NULL )
            ENGINE = MergeTree()
            PRIMARY KEY (source_code);

--HINT DISTRIBUTE ON RANDOM
CREATE TABLE cdmDatabaseSchema.drug_strength (
            drug_concept_id UInt32 NOT NULL,
            ingredient_concept_id UInt32 NOT NULL,
            amount_value Float64 NULL,
            amount_unit_concept_id UInt32 NULL,
            numerator_value Float64 NULL,
            numerator_unit_concept_id UInt32 NULL,
            denominator_value Float64 NULL,
            denominator_unit_concept_id UInt32 NULL,
            box_size UInt32 NULL,
            valid_start_date Date NOT NULL,
            valid_end_date Date NOT NULL,
            invalid_reason String NULL )
            ENGINE = MergeTree()
            PRIMARY KEY (drug_concept_id);

--HINT DISTRIBUTE ON RANDOM
CREATE TABLE cdmDatabaseSchema.cohort (
            cohort_definition_id UInt32 NOT NULL,
            subject_id UInt32 NOT NULL,
            cohort_start_date Date NOT NULL,
            cohort_end_date Date NOT NULL )
            ENGINE = MergeTree()
            PRIMARY KEY (cohort_definition_id);

--HINT DISTRIBUTE ON RANDOM
CREATE TABLE cdmDatabaseSchema.cohort_definition (
            cohort_definition_id UInt32 NOT NULL,
            cohort_definition_name String NOT NULL,
            cohort_definition_description String NULL,
            definition_type_concept_id UInt32 NOT NULL,
            cohort_definition_syntax String NULL,
            subject_concept_id UInt32 NOT NULL,
            cohort_initiation_date Date NULL )
            ENGINE = MergeTree()
            PRIMARY KEY (cohort_definition_id);
clairblacketer commented 1 week ago

Hi, thank you so much for this! Have you had any experience running any OHDSI tools like the HADES stack https://ohdsi.github.io/Hades/ on clickhouse?