OMOP/Sql Server/OMOP CDM sql server pk indexes.txt

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sql server script to create the required primary keys and indices within the OMOP common data model, version 6.0

last revised: 30-Aug-2017

author:  Patrick Ryan, Clair Blacketer

description:  These primary keys and indices are considered a minimal requirement to ensure adequate performance of analyses.

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Primary key constraints

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Standardized vocabulary

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ALTER TABLE concept ADD CONSTRAINT xpk_concept PRIMARY KEY NONCLUSTERED (concept_id);

ALTER TABLE vocabulary ADD CONSTRAINT xpk_vocabulary PRIMARY KEY NONCLUSTERED (vocabulary_id);

ALTER TABLE domain ADD CONSTRAINT xpk_domain PRIMARY KEY NONCLUSTERED (domain_id);

ALTER TABLE concept_class ADD CONSTRAINT xpk_concept_class PRIMARY KEY NONCLUSTERED (concept_class_id);

ALTER TABLE concept_relationship ADD CONSTRAINT xpk_concept_relationship PRIMARY KEY NONCLUSTERED (concept_id_1,concept_id_2,relationship_id);

ALTER TABLE relationship ADD CONSTRAINT xpk_relationship PRIMARY KEY NONCLUSTERED (relationship_id);

ALTER TABLE concept_ancestor ADD CONSTRAINT xpk_concept_ancestor PRIMARY KEY NONCLUSTERED (ancestor_concept_id,descendant_concept_id);

ALTER TABLE source_to_concept_map ADD CONSTRAINT xpk_source_to_concept_map PRIMARY KEY NONCLUSTERED (source_vocabulary_id,target_concept_id,source_code,valid_end_date);

ALTER TABLE drug_strength ADD CONSTRAINT xpk_drug_strength PRIMARY KEY NONCLUSTERED (drug_concept_id, ingredient_concept_id);

ALTER TABLE cohort_definition ADD CONSTRAINT xpk_cohort_definition PRIMARY KEY NONCLUSTERED (cohort_definition_id);

ALTER TABLE attribute_definition ADD CONSTRAINT xpk_attribute_definition PRIMARY KEY NONCLUSTERED (attribute_definition_id);


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Standardized meta-data

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Standardized clinical data

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/**PRIMARY KEY NONCLUSTERED constraints**/

ALTER TABLE person ADD CONSTRAINT xpk_person PRIMARY KEY NONCLUSTERED ( person_id ) ;

ALTER TABLE observation_period ADD CONSTRAINT xpk_observation_period PRIMARY KEY NONCLUSTERED ( observation_period_id ) ;

ALTER TABLE specimen ADD CONSTRAINT xpk_specimen PRIMARY KEY NONCLUSTERED ( specimen_id ) ;

ALTER TABLE death ADD CONSTRAINT xpk_death PRIMARY KEY NONCLUSTERED ( person_id ) ;

ALTER TABLE visit_occurrence ADD CONSTRAINT xpk_visit_occurrence PRIMARY KEY NONCLUSTERED ( visit_occurrence_id ) ;

ALTER TABLE visit_detail ADD CONSTRAINT xpk_visit_detail PRIMARY KEY NONCLUSTERED ( visit_detail_id ) ;

ALTER TABLE procedure_occurrence ADD CONSTRAINT xpk_procedure_occurrence PRIMARY KEY NONCLUSTERED ( procedure_occurrence_id ) ;

ALTER TABLE drug_exposure ADD CONSTRAINT xpk_drug_exposure PRIMARY KEY NONCLUSTERED ( drug_exposure_id ) ;

ALTER TABLE device_exposure ADD CONSTRAINT xpk_device_exposure PRIMARY KEY NONCLUSTERED ( device_exposure_id ) ;

ALTER TABLE condition_occurrence ADD CONSTRAINT xpk_condition_occurrence PRIMARY KEY NONCLUSTERED ( condition_occurrence_id ) ;

ALTER TABLE measurement ADD CONSTRAINT xpk_measurement PRIMARY KEY NONCLUSTERED ( measurement_id ) ;

ALTER TABLE note ADD CONSTRAINT xpk_note PRIMARY KEY NONCLUSTERED ( note_id ) ;

ALTER TABLE note_nlp ADD CONSTRAINT xpk_note_nlp PRIMARY KEY NONCLUSTERED ( note_nlp_id ) ;

ALTER TABLE observation  ADD CONSTRAINT xpk_observation PRIMARY KEY NONCLUSTERED ( observation_id ) ;

ALTER TABLE survey ADD CONSTRAINT xpk_survey PRIMARY KEY NONCLUSTERED ( survey_occurrence_id ) ;


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Standardized health system data

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ALTER TABLE location ADD CONSTRAINT xpk_location PRIMARY KEY NONCLUSTERED ( location_id ) ;

ALTER TABLE location_history ADD CONSTRAINT xpk_location_history PRIMARY KEY NONCLUSTERED ( location_history_id ) ; --Assuming this should be added

ALTER TABLE care_site ADD CONSTRAINT xpk_care_site PRIMARY KEY NONCLUSTERED ( care_site_id ) ;

ALTER TABLE provider ADD CONSTRAINT xpk_provider PRIMARY KEY NONCLUSTERED ( provider_id ) ;



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Standardized health economics

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ALTER TABLE payer_plan_period ADD CONSTRAINT xpk_payer_plan_period PRIMARY KEY NONCLUSTERED ( payer_plan_period_id ) ;

ALTER TABLE cost ADD CONSTRAINT xpk_visit_cost PRIMARY KEY NONCLUSTERED ( cost_id ) ;


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Standardized derived elements

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ALTER TABLE cohort ADD CONSTRAINT xpk_cohort PRIMARY KEY NONCLUSTERED ( cohort_definition_id, subject_id, cohort_start_date, cohort_end_date  ) ;

ALTER TABLE cohort_attribute ADD CONSTRAINT xpk_cohort_attribute PRIMARY KEY NONCLUSTERED ( cohort_definition_id, subject_id, cohort_start_date, cohort_end_date, attribute_definition_id ) ;

ALTER TABLE drug_era ADD CONSTRAINT xpk_drug_era PRIMARY KEY NONCLUSTERED ( drug_era_id ) ;

ALTER TABLE dose_era  ADD CONSTRAINT xpk_dose_era PRIMARY KEY NONCLUSTERED ( dose_era_id ) ;

ALTER TABLE condition_era ADD CONSTRAINT xpk_condition_era PRIMARY KEY NONCLUSTERED ( condition_era_id ) ;


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Indices

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Standardized vocabulary

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CREATE UNIQUE CLUSTERED INDEX idx_concept_concept_id ON concept (concept_id ASC);
CREATE INDEX idx_concept_code ON concept (concept_code ASC);
CREATE INDEX idx_concept_vocabluary_id ON concept (vocabulary_id ASC);
CREATE INDEX idx_concept_domain_id ON concept (domain_id ASC);
CREATE INDEX idx_concept_class_id ON concept (concept_class_id ASC);

CREATE UNIQUE CLUSTERED INDEX idx_vocabulary_vocabulary_id ON vocabulary (vocabulary_id ASC);

CREATE UNIQUE CLUSTERED INDEX idx_domain_domain_id ON domain (domain_id ASC);

CREATE UNIQUE CLUSTERED INDEX idx_concept_class_class_id ON concept_class (concept_class_id ASC);

CREATE INDEX idx_concept_relationship_id_1 ON concept_relationship (concept_id_1 ASC);
CREATE INDEX idx_concept_relationship_id_2 ON concept_relationship (concept_id_2 ASC);
CREATE INDEX idx_concept_relationship_id_3 ON concept_relationship (relationship_id ASC);

CREATE UNIQUE CLUSTERED INDEX idx_relationship_rel_id ON relationship (relationship_id ASC);

CREATE CLUSTERED INDEX idx_concept_synonym_id ON concept_synonym (concept_id ASC);

CREATE CLUSTERED INDEX idx_concept_ancestor_id_1 ON concept_ancestor (ancestor_concept_id ASC);
CREATE INDEX idx_concept_ancestor_id_2 ON concept_ancestor (descendant_concept_id ASC);

CREATE CLUSTERED INDEX idx_source_to_concept_map_id_3 ON source_to_concept_map (target_concept_id ASC);
CREATE INDEX idx_source_to_concept_map_id_1 ON source_to_concept_map (source_vocabulary_id ASC);
CREATE INDEX idx_source_to_concept_map_id_2 ON source_to_concept_map (target_vocabulary_id ASC);
CREATE INDEX idx_source_to_concept_map_code ON source_to_concept_map (source_code ASC);

CREATE CLUSTERED INDEX idx_drug_strength_id_1 ON drug_strength (drug_concept_id ASC);
CREATE INDEX idx_drug_strength_id_2 ON drug_strength (ingredient_concept_id ASC);

CREATE CLUSTERED INDEX idx_cohort_definition_id ON cohort_definition (cohort_definition_id ASC);

CREATE CLUSTERED INDEX idx_attribute_definition_id ON attribute_definition (attribute_definition_id ASC);


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Standardized meta-data

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Standardized clinical data

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CREATE UNIQUE CLUSTERED INDEX idx_person_id ON person (person_id ASC);

CREATE CLUSTERED INDEX idx_observation_period_id ON observation_period (person_id ASC);

CREATE CLUSTERED INDEX idx_specimen_person_id ON specimen (person_id ASC);
CREATE INDEX idx_specimen_concept_id ON specimen (specimen_concept_id ASC);

CREATE CLUSTERED INDEX idx_death_person_id ON death (person_id ASC);

CREATE CLUSTERED INDEX idx_visit_person_id ON visit_occurrence (person_id ASC);
CREATE INDEX idx_visit_concept_id ON visit_occurrence (visit_concept_id ASC);

CREATE CLUSTERED INDEX idx_visit_detail_person_id ON visit_detail (person_id ASC);
CREATE INDEX idx_visit_detail_concept_id ON visit_detail (visit_detail_concept_id ASC);

CREATE CLUSTERED INDEX idx_procedure_person_id ON procedure_occurrence (person_id ASC);
CREATE INDEX idx_procedure_concept_id ON procedure_occurrence (procedure_concept_id ASC);
CREATE INDEX idx_procedure_visit_id ON procedure_occurrence (visit_occurrence_id ASC);

CREATE CLUSTERED INDEX idx_drug_person_id ON drug_exposure (person_id ASC);
CREATE INDEX idx_drug_concept_id ON drug_exposure (drug_concept_id ASC);
CREATE INDEX idx_drug_visit_id ON drug_exposure (visit_occurrence_id ASC);

CREATE CLUSTERED INDEX idx_device_person_id ON device_exposure (person_id ASC);
CREATE INDEX idx_device_concept_id ON device_exposure (device_concept_id ASC);
CREATE INDEX idx_device_visit_id ON device_exposure (visit_occurrence_id ASC);

CREATE CLUSTERED INDEX idx_condition_person_id ON condition_occurrence (person_id ASC);
CREATE INDEX idx_condition_concept_id ON condition_occurrence (condition_concept_id ASC);
CREATE INDEX idx_condition_visit_id ON condition_occurrence (visit_occurrence_id ASC);

CREATE CLUSTERED INDEX idx_measurement_person_id ON measurement (person_id ASC);
CREATE INDEX idx_measurement_concept_id ON measurement (measurement_concept_id ASC);
CREATE INDEX idx_measurement_visit_id ON measurement (visit_occurrence_id ASC);

CREATE CLUSTERED INDEX idx_note_person_id ON note (person_id ASC);
CREATE INDEX idx_note_concept_id ON note (note_type_concept_id ASC);
CREATE INDEX idx_note_visit_id ON note (visit_occurrence_id ASC);

CREATE CLUSTERED INDEX idx_note_nlp_note_id ON note_nlp (note_id ASC);
CREATE INDEX idx_note_nlp_concept_id ON note_nlp (note_nlp_concept_id ASC);

CREATE CLUSTERED INDEX idx_observation_person_id ON observation (person_id ASC);
CREATE INDEX idx_observation_concept_id ON observation (observation_concept_id ASC);
CREATE INDEX idx_observation_visit_id ON observation (visit_occurrence_id ASC);

CREATE CLUSTERED INDEX idx_survey_person_id ON survey (person_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);



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Standardized health system data

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Standardized health economics

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CREATE CLUSTERED INDEX idx_period_person_id ON payer_plan_period (person_id ASC);

CREATE CLUSTERED INDEX idx_cost_person_id ON cost (person_id ASC);


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Standardized derived elements

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CREATE INDEX idx_cohort_subject_id ON cohort (subject_id ASC);
CREATE INDEX idx_cohort_c_definition_id ON cohort (cohort_definition_id ASC);

CREATE INDEX idx_ca_subject_id ON cohort_attribute (subject_id ASC);
CREATE INDEX idx_ca_definition_id ON cohort_attribute (cohort_definition_id ASC);

CREATE CLUSTERED INDEX idx_drug_era_person_id ON drug_era (person_id ASC);
CREATE INDEX idx_drug_era_concept_id ON drug_era (drug_concept_id ASC);

CREATE CLUSTERED INDEX idx_dose_era_person_id ON dose_era (person_id ASC);
CREATE INDEX idx_dose_era_concept_id ON dose_era (drug_concept_id ASC);

CREATE CLUSTERED INDEX idx_condition_era_person_id ON condition_era (person_id ASC);
CREATE INDEX idx_condition_era_concept_id ON condition_era (condition_concept_id ASC);