omop postgresql revisado

.gitignore

+vocabulary/
+instancia_omop_postgresql/vocabulary_download_v5.zip

instancia_omop_postgresql/Makefile

@@ -3,7 +3,7 @@ db:
   -e POSTGRES_DB=omop \
   -e POSTGRES_USER=postgres \
   -e POSTGRES_PASSWORD=postgres \
-  postgres:latest
+  postgres:15.4
 
 stop: 
 	docker kill postgres

instancia_omop_postgresql/docker-compose.yml

+  volumes:
+    db-data:
+      name: db-data
+
+  services:
+    db: 
+      image: postgres:15.2-alpine
+      env_file: .env
+
+      ports:
+        - 5432:5432
+      volumes:
+        - ./db-data:/var/lib/postgres/data
+      healthcheck:
+        test: ["CMD-SHELL", "pg_isready -U postgres"]
+        interval: 5s
+        timeout: 5s
+        retries: 10

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);
-
-ALTER TABLE omop.COHORT_DEFINITION ADD CONSTRAINT xpk_COHORT_DEFINITION PRIMARY KEY (cohort_definition_id); 

instancia_omop_postgresql/omop_indexes_postgres.sql → instancia_omop_postgresql/postgresql/OMOPCDM_postgresql_5.4_indices.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/postgresql/OMOPCDM_postgresql_5.4_primary_keys.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);

instancia_omop_postgresql/vocab_load.sql

+/*********************************************************************************
+# Copyright 2014 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.
+********************************************************************************/
+
+/************************
+
+ ####### #     # ####### ######      #####  ######  #     #           ####### 
+ #     # ##   ## #     # #     #    #     # #     # ##   ##    #    # #       
+ #     # # # # # #     # #     #    #       #     # # # # #    #    # #       
+ #     # #  #  # #     # ######     #       #     # #  #  #    #    # ######  
+ #     # #     # #     # #          #       #     # #     #    #    #       # 
+ #     # #     # #     # #          #     # #     # #     #     #  #  #     # 
+ ####### #     # ####### #           #####  ######  #     #      ##    #####  
+                                                                              
+
+Script to load the common data model, version 5.0 vocabulary tables for PostgreSQL database on Windows (MS-DOS style file paths)
+The database account running this script must have the "superuser" permission in the database.
+
+Notes
+
+1) There is no data file load for the SOURCE_TO_CONCEPT_MAP table because that table is deprecated in CDM version 5.0
+2) This script assumes the CDM version 5 vocabulary zip file has been unzipped into the "C:\CDMV5VOCAB" directory. 
+3) If you unzipped your CDM version 5 vocabulary files into a different directory then replace all file paths below, with your directory path.
+4) Truncate each table that will be lodaed below, before running this script.
+
+last revised: 5 Dec 2014
+
+author:  Lee Evans
+
+
+*************************/
+SET session_replication_role = 'replica';
+
+
+\copy omop.DRUG_STRENGTH FROM './vocabulary/DRUG_STRENGTH.csv' WITH DELIMITER E'\t' CSV HEADER QUOTE E'\b' ;
+
+\copy omop.CONCEPT FROM './vocabulary/CONCEPT.csv' WITH DELIMITER E'\t' CSV HEADER QUOTE E'\b' ;
+
+\copy  omop.CONCEPT_RELATIONSHIP FROM './vocabulary/CONCEPT_RELATIONSHIP.csv' WITH DELIMITER E'\t' CSV HEADER QUOTE E'\b' ;
+
+\copy omop.CONCEPT_ANCESTOR FROM './vocabulary/CONCEPT_ANCESTOR.csv' WITH DELIMITER E'\t' CSV HEADER QUOTE E'\b' ;
+
+\copy omop.CONCEPT_SYNONYM FROM './vocabulary/CONCEPT_SYNONYM.csv' WITH DELIMITER E'\t' CSV HEADER QUOTE E'\b' ;
+
+\copy omop.VOCABULARY FROM './vocabulary/VOCABULARY.csv' WITH DELIMITER E'\t' CSV HEADER QUOTE E'\b' ;
+
+\copy omop.RELATIONSHIP FROM './vocabulary/RELATIONSHIP.csv' WITH DELIMITER E'\t' CSV HEADER QUOTE E'\b' ;
+
+\copy omop.CONCEPT_CLASS FROM './vocabulary/CONCEPT_CLASS.csv' WITH DELIMITER E'\t' CSV HEADER QUOTE E'\b' ;
+
+\copy omop.DOMAIN FROM './vocabulary/DOMAIN.csv' WITH DELIMITER E'\t' CSV HEADER QUOTE E'\b' ;
+
+SET session_replication_role = 'origin';