instancia de omop en postgres

instancia_omop_postgresql/Makefile

+db:
+	docker run --rm -d --name postgres -p 5432:5432 \
+  -e POSTGRES_DB=omop \
+  -e POSTGRES_USER=postgres \
+  -e POSTGRES_PASSWORD=postgres \
+  postgres:latest
+

instancia_omop_postgresql/omop_indexes_postgres.sql

+/*postgresql OMOP CDM Indices
+
+  There are no unique indices created because it is assumed that the primary key constraints have been run prior to
+  implementing indices.
+*/
+
+
+/************************
+
+Standardized clinical data
+
+************************/
+
+CREATE INDEX idx_person_id  ON omop.person  (person_id ASC);
+CLUSTER omop.person  USING idx_person_id ;
+CREATE INDEX idx_gender ON omop.person (gender_concept_id ASC);
+
+CREATE INDEX idx_observation_period_id_1  ON omop.observation_period  (person_id ASC);
+CLUSTER omop.observation_period  USING idx_observation_period_id_1 ;
+
+CREATE INDEX idx_visit_person_id_1  ON omop.visit_occurrence  (person_id ASC);
+CLUSTER omop.visit_occurrence  USING idx_visit_person_id_1 ;
+CREATE INDEX idx_visit_concept_id_1 ON omop.visit_occurrence (visit_concept_id ASC);
+
+CREATE INDEX idx_visit_det_person_id_1  ON omop.visit_detail  (person_id ASC);
+CLUSTER omop.visit_detail  USING idx_visit_det_person_id_1 ;
+CREATE INDEX idx_visit_det_concept_id_1 ON omop.visit_detail (visit_detail_concept_id ASC);
+CREATE INDEX idx_visit_det_occ_id ON omop.visit_detail (visit_occurrence_id ASC);
+
+CREATE INDEX idx_condition_person_id_1  ON omop.condition_occurrence  (person_id ASC);
+CLUSTER omop.condition_occurrence  USING idx_condition_person_id_1 ;
+CREATE INDEX idx_condition_concept_id_1 ON omop.condition_occurrence (condition_concept_id ASC);
+CREATE INDEX idx_condition_visit_id_1 ON omop.condition_occurrence (visit_occurrence_id ASC);
+
+CREATE INDEX idx_drug_person_id_1  ON omop.drug_exposure  (person_id ASC);
+CLUSTER omop.drug_exposure  USING idx_drug_person_id_1 ;
+CREATE INDEX idx_drug_concept_id_1 ON omop.drug_exposure (drug_concept_id ASC);
+CREATE INDEX idx_drug_visit_id_1 ON omop.drug_exposure (visit_occurrence_id ASC);
+
+CREATE INDEX idx_procedure_person_id_1  ON omop.procedure_occurrence  (person_id ASC);
+CLUSTER omop.procedure_occurrence  USING idx_procedure_person_id_1 ;
+CREATE INDEX idx_procedure_concept_id_1 ON omop.procedure_occurrence (procedure_concept_id ASC);
+CREATE INDEX idx_procedure_visit_id_1 ON omop.procedure_occurrence (visit_occurrence_id ASC);
+
+CREATE INDEX idx_device_person_id_1  ON omop.device_exposure  (person_id ASC);
+CLUSTER omop.device_exposure  USING idx_device_person_id_1 ;
+CREATE INDEX idx_device_concept_id_1 ON omop.device_exposure (device_concept_id ASC);
+CREATE INDEX idx_device_visit_id_1 ON omop.device_exposure (visit_occurrence_id ASC);
+
+CREATE INDEX idx_measurement_person_id_1  ON omop.measurement  (person_id ASC);
+CLUSTER omop.measurement  USING idx_measurement_person_id_1 ;
+CREATE INDEX idx_measurement_concept_id_1 ON omop.measurement (measurement_concept_id ASC);
+CREATE INDEX idx_measurement_visit_id_1 ON omop.measurement (visit_occurrence_id ASC);
+
+CREATE INDEX idx_observation_person_id_1  ON omop.observation  (person_id ASC);
+CLUSTER omop.observation  USING idx_observation_person_id_1 ;
+CREATE INDEX idx_observation_concept_id_1 ON omop.observation (observation_concept_id ASC);
+CREATE INDEX idx_observation_visit_id_1 ON omop.observation (visit_occurrence_id ASC);
+
+CREATE INDEX idx_death_person_id_1  ON omop.death  (person_id ASC);
+CLUSTER omop.death  USING idx_death_person_id_1 ;
+
+CREATE INDEX idx_note_person_id_1  ON omop.note  (person_id ASC);
+CLUSTER omop.note  USING idx_note_person_id_1 ;
+CREATE INDEX idx_note_concept_id_1 ON omop.note (note_type_concept_id ASC);
+CREATE INDEX idx_note_visit_id_1 ON omop.note (visit_occurrence_id ASC);
+
+CREATE INDEX idx_note_nlp_note_id_1  ON omop.note_nlp  (note_id ASC);
+CLUSTER omop.note_nlp  USING idx_note_nlp_note_id_1 ;
+CREATE INDEX idx_note_nlp_concept_id_1 ON omop.note_nlp (note_nlp_concept_id ASC);
+
+CREATE INDEX idx_specimen_person_id_1  ON omop.specimen  (person_id ASC);
+CLUSTER omop.specimen  USING idx_specimen_person_id_1 ;
+CREATE INDEX idx_specimen_concept_id_1 ON omop.specimen (specimen_concept_id ASC);
+
+CREATE INDEX idx_fact_relationship_id1 ON omop.fact_relationship (domain_concept_id_1 ASC);
+CREATE INDEX idx_fact_relationship_id2 ON omop.fact_relationship (domain_concept_id_2 ASC);
+CREATE INDEX idx_fact_relationship_id3 ON omop.fact_relationship (relationship_concept_id ASC);
+
+/************************
+
+Standardized health system data
+
+************************/
+
+CREATE INDEX idx_location_id_1  ON omop.location  (location_id ASC);
+CLUSTER omop.location  USING idx_location_id_1 ;
+
+CREATE INDEX idx_care_site_id_1  ON omop.care_site  (care_site_id ASC);
+CLUSTER omop.care_site  USING idx_care_site_id_1 ;
+
+CREATE INDEX idx_provider_id_1  ON omop.provider  (provider_id ASC);
+CLUSTER omop.provider  USING idx_provider_id_1 ;
+
+/************************
+
+Standardized health economics
+
+************************/
+
+CREATE INDEX idx_period_person_id_1  ON omop.payer_plan_period  (person_id ASC);
+CLUSTER omop.payer_plan_period  USING idx_period_person_id_1 ;
+
+CREATE INDEX idx_cost_event_id  ON omop.cost (cost_event_id ASC);
+
+/************************
+
+Standardized derived elements
+
+************************/
+
+CREATE INDEX idx_drug_era_person_id_1  ON omop.drug_era  (person_id ASC);
+CLUSTER omop.drug_era  USING idx_drug_era_person_id_1 ;
+CREATE INDEX idx_drug_era_concept_id_1 ON omop.drug_era (drug_concept_id ASC);
+
+CREATE INDEX idx_dose_era_person_id_1  ON omop.dose_era  (person_id ASC);
+CLUSTER omop.dose_era  USING idx_dose_era_person_id_1 ;
+CREATE INDEX idx_dose_era_concept_id_1 ON omop.dose_era (drug_concept_id ASC);
+
+CREATE INDEX idx_condition_era_person_id_1  ON omop.condition_era  (person_id ASC);
+CLUSTER omop.condition_era  USING idx_condition_era_person_id_1 ;
+CREATE INDEX idx_condition_era_concept_id_1 ON omop.condition_era (condition_concept_id ASC);
+
+/**************************
+
+Standardized meta-data
+
+***************************/
+
+CREATE INDEX idx_metadata_concept_id_1  ON omop.metadata  (metadata_concept_id ASC);
+CLUSTER omop.metadata  USING idx_metadata_concept_id_1 ;
+
+/**************************
+
+Standardized vocabularies
+
+***************************/
+
+CREATE INDEX idx_concept_concept_id  ON omop.concept  (concept_id ASC);
+CLUSTER omop.concept  USING idx_concept_concept_id ;
+CREATE INDEX idx_concept_code ON omop.concept (concept_code ASC);
+CREATE INDEX idx_concept_vocabluary_id ON omop.concept (vocabulary_id ASC);
+CREATE INDEX idx_concept_domain_id ON omop.concept (domain_id ASC);
+CREATE INDEX idx_concept_class_id ON omop.concept (concept_class_id ASC);
+
+CREATE INDEX idx_vocabulary_vocabulary_id  ON omop.vocabulary  (vocabulary_id ASC);
+CLUSTER omop.vocabulary  USING idx_vocabulary_vocabulary_id ;
+
+CREATE INDEX idx_domain_domain_id  ON omop.domain  (domain_id ASC);
+CLUSTER omop.domain  USING idx_domain_domain_id ;
+
+CREATE INDEX idx_concept_class_class_id  ON omop.concept_class  (concept_class_id ASC);
+CLUSTER omop.concept_class  USING idx_concept_class_class_id ;
+
+CREATE INDEX idx_concept_relationship_id_1  ON omop.concept_relationship  (concept_id_1 ASC);
+CLUSTER omop.concept_relationship  USING idx_concept_relationship_id_1 ;
+CREATE INDEX idx_concept_relationship_id_2 ON omop.concept_relationship (concept_id_2 ASC);
+CREATE INDEX idx_concept_relationship_id_3 ON omop.concept_relationship (relationship_id ASC);
+
+CREATE INDEX idx_relationship_rel_id  ON omop.relationship  (relationship_id ASC);
+CLUSTER omop.relationship  USING idx_relationship_rel_id ;
+
+CREATE INDEX idx_concept_synonym_id  ON omop.concept_synonym  (concept_id ASC);
+CLUSTER omop.concept_synonym  USING idx_concept_synonym_id ;
+
+CREATE INDEX idx_concept_ancestor_id_1  ON omop.concept_ancestor  (ancestor_concept_id ASC);
+CLUSTER omop.concept_ancestor  USING idx_concept_ancestor_id_1 ;
+CREATE INDEX idx_concept_ancestor_id_2 ON omop.concept_ancestor (descendant_concept_id ASC);
+
+CREATE INDEX idx_source_to_concept_map_3  ON omop.source_to_concept_map  (target_concept_id ASC);
+CLUSTER omop.source_to_concept_map  USING idx_source_to_concept_map_3 ;
+CREATE INDEX idx_source_to_concept_map_1 ON omop.source_to_concept_map (source_vocabulary_id ASC);
+CREATE INDEX idx_source_to_concept_map_2 ON omop.source_to_concept_map (target_vocabulary_id ASC);
+CREATE INDEX idx_source_to_concept_map_c ON omop.source_to_concept_map (source_code ASC);
+
+CREATE INDEX idx_drug_strength_id_1  ON omop.drug_strength  (drug_concept_id ASC);
+CLUSTER omop.drug_strength  USING idx_drug_strength_id_1 ;
+CREATE INDEX idx_drug_strength_id_2 ON omop.drug_strength (ingredient_concept_id ASC);
+
+
+--Additional v6.0 indices
+
+--CREATE CLUSTERED INDEX idx_survey_person_id_1 ON omop.survey_conduct (person_id ASC);
+
+
+--CREATE CLUSTERED INDEX idx_episode_person_id_1 ON omop.episode (person_id ASC);
+--CREATE INDEX idx_episode_concept_id_1 ON omop.episode (episode_concept_id ASC);
+
+--CREATE CLUSTERED INDEX idx_episode_event_id_1 ON omop.episode_event (episode_id ASC);
+--CREATE INDEX idx_ee_field_concept_id_1 ON omop.episode_event (event_field_concept_id ASC);
+

instancia_omop_postgresql/omop_pk_postgres.sql

+--postgresql CDM Primary Key Constraints for OMOP Common Data Model 5.4
+
+ALTER TABLE omop.PERSON ADD CONSTRAINT xpk_PERSON PRIMARY KEY (person_id);
+
+ALTER TABLE omop.OBSERVATION_PERIOD ADD CONSTRAINT xpk_OBSERVATION_PERIOD PRIMARY KEY (observation_period_id);
+
+ALTER TABLE omop.VISIT_OCCURRENCE ADD CONSTRAINT xpk_VISIT_OCCURRENCE PRIMARY KEY (visit_occurrence_id);
+
+ALTER TABLE omop.VISIT_DETAIL ADD CONSTRAINT xpk_VISIT_DETAIL PRIMARY KEY (visit_detail_id);
+
+ALTER TABLE omop.CONDITION_OCCURRENCE ADD CONSTRAINT xpk_CONDITION_OCCURRENCE PRIMARY KEY (condition_occurrence_id);
+
+ALTER TABLE omop.DRUG_EXPOSURE ADD CONSTRAINT xpk_DRUG_EXPOSURE PRIMARY KEY (drug_exposure_id);
+
+ALTER TABLE omop.PROCEDURE_OCCURRENCE ADD CONSTRAINT xpk_PROCEDURE_OCCURRENCE PRIMARY KEY (procedure_occurrence_id);
+
+ALTER TABLE omop.DEVICE_EXPOSURE ADD CONSTRAINT xpk_DEVICE_EXPOSURE PRIMARY KEY (device_exposure_id);
+
+ALTER TABLE omop.MEASUREMENT ADD CONSTRAINT xpk_MEASUREMENT PRIMARY KEY (measurement_id);
+
+ALTER TABLE omop.OBSERVATION ADD CONSTRAINT xpk_OBSERVATION PRIMARY KEY (observation_id);
+
+ALTER TABLE omop.NOTE ADD CONSTRAINT xpk_NOTE PRIMARY KEY (note_id);
+
+ALTER TABLE omop.NOTE_NLP ADD CONSTRAINT xpk_NOTE_NLP PRIMARY KEY (note_nlp_id);
+
+ALTER TABLE omop.SPECIMEN ADD CONSTRAINT xpk_SPECIMEN PRIMARY KEY (specimen_id);
+
+ALTER TABLE omop.LOCATION ADD CONSTRAINT xpk_LOCATION PRIMARY KEY (location_id);
+
+ALTER TABLE omop.CARE_SITE ADD CONSTRAINT xpk_CARE_SITE PRIMARY KEY (care_site_id);
+
+ALTER TABLE omop.PROVIDER ADD CONSTRAINT xpk_PROVIDER PRIMARY KEY (provider_id);
+
+ALTER TABLE omop.PAYER_PLAN_PERIOD ADD CONSTRAINT xpk_PAYER_PLAN_PERIOD PRIMARY KEY (payer_plan_period_id);
+
+ALTER TABLE omop.COST ADD CONSTRAINT xpk_COST PRIMARY KEY (cost_id);
+
+ALTER TABLE omop.DRUG_ERA ADD CONSTRAINT xpk_DRUG_ERA PRIMARY KEY (drug_era_id);
+
+ALTER TABLE omop.DOSE_ERA ADD CONSTRAINT xpk_DOSE_ERA PRIMARY KEY (dose_era_id);
+
+ALTER TABLE omop.CONDITION_ERA ADD CONSTRAINT xpk_CONDITION_ERA PRIMARY KEY (condition_era_id);
+
+ALTER TABLE omop.EPISODE ADD CONSTRAINT xpk_EPISODE PRIMARY KEY (episode_id);
+
+ALTER TABLE omop.METADATA ADD CONSTRAINT xpk_METADATA PRIMARY KEY (metadata_id);
+
+ALTER TABLE omop.CONCEPT ADD CONSTRAINT xpk_CONCEPT PRIMARY KEY (concept_id);
+
+ALTER TABLE omop.VOCABULARY ADD CONSTRAINT xpk_VOCABULARY PRIMARY KEY (vocabulary_id);
+
+ALTER TABLE omop.DOMAIN ADD CONSTRAINT xpk_DOMAIN PRIMARY KEY (domain_id);
+
+ALTER TABLE omop.CONCEPT_CLASS ADD CONSTRAINT xpk_CONCEPT_CLASS PRIMARY KEY (concept_class_id);
+
+ALTER TABLE omop.RELATIONSHIP ADD CONSTRAINT xpk_RELATIONSHIP PRIMARY KEY (relationship_id);
+