From a5b12716dd9bf58fd814cf9d3cb0c55a7d7b13d3 Mon Sep 17 00:00:00 2001 From: clairblacketer Date: Fri, 17 Nov 2017 15:18:32 -0500 Subject: [PATCH] Updated indices to include primary keys and moved foreign keys to their own files. --- DDLGeneratr/codeToRun.R | 4 +- .../sql/sql_server/OMOP CDM constraints.sql | 151 +- .../sql_server/OMOP CDM indexes required.sql | 151 +- .../oracle/OMOP CDM oracle constraints.txt | 189 +- .../output/oracle/OMOP CDM oracle indexes.txt | 184 +- .../output/pdw/OMOP CDM pdw constraints.txt | 421 +++ .../output/pdw/OMOP CDM pdw indexes.txt | 342 ++ .../OMOP CDM postgresql constraints.txt | 421 +++ .../OMOP CDM postgresql indexes.txt | 371 ++ .../OMOP CDM sql server constraints.txt | 421 +++ .../OMOP CDM sql server indexes.txt | 342 ++ DDLGeneratr/reports/OMOP_CDM_PDF.Rmd | 101 +- DDLGeneratr/reports/OMOP_CDM_v5_3.pdf | 3004 +++++++++-------- 13 files changed, 4243 insertions(+), 1859 deletions(-) create mode 100644 DDLGeneratr/output/pdw/OMOP CDM pdw constraints.txt create mode 100644 DDLGeneratr/output/pdw/OMOP CDM pdw indexes.txt create mode 100644 DDLGeneratr/output/postgresql/OMOP CDM postgresql constraints.txt create mode 100644 DDLGeneratr/output/postgresql/OMOP CDM postgresql indexes.txt create mode 100644 DDLGeneratr/output/sql server/OMOP CDM sql server constraints.txt create mode 100644 DDLGeneratr/output/sql server/OMOP CDM sql server indexes.txt diff --git a/DDLGeneratr/codeToRun.R b/DDLGeneratr/codeToRun.R index 6acd326..9023460 100644 --- a/DDLGeneratr/codeToRun.R +++ b/DDLGeneratr/codeToRun.R @@ -14,14 +14,14 @@ writeDDL("postgresql") writeDDL("redshift") writeDDL("sql server") -# Step 3: Run the following code to create indices for Oracle, Postgres, PDW and Sql Server +# Step 3: Run the following code to create the primary key constraints and index files for Oracle, Postgres, PDW and Sql Server writeIndex("oracle") writeIndex("postgresql") writeIndex("pdw") writeIndex("sql server") -# Step 4: Run the following code to create constraints for Oracle, Postgres, PDW and Sql Server +# Step 4: Run the following code to create foreign key constraints for Oracle, Postgres, PDW and Sql Server writeConstraints("oracle") writeConstraints("postgresql") diff --git a/DDLGeneratr/inst/sql/sql_server/OMOP CDM constraints.sql b/DDLGeneratr/inst/sql/sql_server/OMOP CDM constraints.sql index 0fb138b..17f363a 100644 --- a/DDLGeneratr/inst/sql/sql_server/OMOP CDM constraints.sql +++ b/DDLGeneratr/inst/sql/sql_server/OMOP CDM constraints.sql @@ -26,7 +26,7 @@ ####### # # ####### # ##### ###### # # ## ##### ### ##### ##### #### # # #### # # # # # # # # # #### -@targetdialect script to create constraints within OMOP common data model, version 5.3.0 +@targetdialect script to create foreign key constraints within OMOP common data model, version 5.3.0 last revised: 15-November-2017 @@ -36,155 +36,6 @@ author: Patrick Ryan, Clair Blacketer *************************/ -/************************ -************************* -************************* -************************* - -Primary key constraints - -************************* -************************* -************************* -************************/ - - - -/************************ - -Standardized vocabulary - -************************/ - - - -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); - - -/************************** - -Standardized meta-data - -***************************/ - - - - - - - - - -/************************ - -Standardized clinical data - -************************/ - - -/**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 ) ; - - - - -/************************ - -Standardized health system data - -************************/ - - -ALTER TABLE location ADD CONSTRAINT xpk_location PRIMARY KEY NONCLUSTERED ( location_id ) ; - -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 ) ; - - - -/************************ - -Standardized health economics - -************************/ - - -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 ) ; - - -/************************ - -Standardized derived elements - -************************/ - -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 ) ; - - - - - - - - /************************ ************************* ************************* diff --git a/DDLGeneratr/inst/sql/sql_server/OMOP CDM indexes required.sql b/DDLGeneratr/inst/sql/sql_server/OMOP CDM indexes required.sql index 7ed41c2..83bd1a3 100644 --- a/DDLGeneratr/inst/sql/sql_server/OMOP CDM indexes required.sql +++ b/DDLGeneratr/inst/sql/sql_server/OMOP CDM indexes required.sql @@ -32,11 +32,160 @@ last revised: 14-November-2017 author: Patrick Ryan, Clair Blacketer -description: These indices are considered a minimal requirement to ensure adequate performance of analyses. +description: These primary keys and indices are considered a minimal requirement to ensure adequate performance of analyses. *************************/ +/************************ +************************* +************************* +************************* + +Primary key constraints + +************************* +************************* +************************* +************************/ + + + +/************************ + +Standardized vocabulary + +************************/ + + + +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); + + +/************************** + +Standardized meta-data + +***************************/ + + + +/************************ + +Standardized clinical data + +************************/ + + +/**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 ) ; + + + + +/************************ + +Standardized health system data + +************************/ + + +ALTER TABLE location ADD CONSTRAINT xpk_location PRIMARY KEY NONCLUSTERED ( location_id ) ; + +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 ) ; + + + +/************************ + +Standardized health economics + +************************/ + + +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 ) ; + + +/************************ + +Standardized derived elements + +************************/ + +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 ) ; + + +/************************ +************************* +************************* +************************* + +Indices + +************************* +************************* +************************* +************************/ + /************************ Standardized vocabulary diff --git a/DDLGeneratr/output/oracle/OMOP CDM oracle constraints.txt b/DDLGeneratr/output/oracle/OMOP CDM oracle constraints.txt index 6a0ce77..facbafa 100644 --- a/DDLGeneratr/output/oracle/OMOP CDM oracle constraints.txt +++ b/DDLGeneratr/output/oracle/OMOP CDM oracle constraints.txt @@ -26,7 +26,7 @@ ####### # # ####### # ##### ###### # # ## ##### ### ##### ##### #### # # #### # # # # # # # # # #### -oracle script to create constraints within OMOP common data model, version 5.3.0 +oracle script to create foreign key constraints within OMOP common data model, version 5.3.0 last revised: 15-November-2017 @@ -36,153 +36,6 @@ author: Patrick Ryan, Clair Blacketer *************************/ -/************************ -************************* -************************* -************************* - -Primary key constraints - -************************* -************************* -************************* -************************/ - - - -/************************ - -Standardized vocabulary - -************************/ - - - -ALTER TABLE concept ADD CONSTRAINT xpk_concept PRIMARY KEY (concept_id); - -ALTER TABLE vocabulary ADD CONSTRAINT xpk_vocabulary PRIMARY KEY (vocabulary_id); - -ALTER TABLE domain ADD CONSTRAINT xpk_domain PRIMARY KEY (domain_id); - -ALTER TABLE concept_class ADD CONSTRAINT xpk_concept_class PRIMARY KEY (concept_class_id); - -ALTER TABLE concept_relationship ADD CONSTRAINT xpk_concept_relationship PRIMARY KEY (concept_id_1,concept_id_2,relationship_id); - -ALTER TABLE relationship ADD CONSTRAINT xpk_relationship PRIMARY KEY (relationship_id); - -ALTER TABLE concept_ancestor ADD CONSTRAINT xpk_concept_ancestor PRIMARY KEY (ancestor_concept_id,descendant_concept_id); - -ALTER TABLE source_to_concept_map ADD CONSTRAINT xpk_source_to_concept_map PRIMARY KEY (source_vocabulary_id,target_concept_id,source_code,valid_end_date); - -ALTER TABLE drug_strength ADD CONSTRAINT xpk_drug_strength PRIMARY KEY (drug_concept_id, ingredient_concept_id); - -ALTER TABLE cohort_definition ADD CONSTRAINT xpk_cohort_definition PRIMARY KEY (cohort_definition_id); - -ALTER TABLE attribute_definition ADD CONSTRAINT xpk_attribute_definition PRIMARY KEY (attribute_definition_id); - - -/************************** - -Standardized meta-data - -***************************/ - - - - - - - - - -/************************ - -Standardized clinical data - -************************/ - - -/**PRIMARY KEY NONCLUSTERED constraints**/ - -ALTER TABLE person ADD CONSTRAINT xpk_person PRIMARY KEY ( person_id ) ; - -ALTER TABLE observation_period ADD CONSTRAINT xpk_observation_period PRIMARY KEY ( observation_period_id ) ; - -ALTER TABLE specimen ADD CONSTRAINT xpk_specimen PRIMARY KEY ( specimen_id ) ; - -ALTER TABLE death ADD CONSTRAINT xpk_death PRIMARY KEY ( person_id ) ; - -ALTER TABLE visit_occurrence ADD CONSTRAINT xpk_visit_occurrence PRIMARY KEY ( visit_occurrence_id ) ; - -ALTER TABLE procedure_occurrence ADD CONSTRAINT xpk_procedure_occurrence PRIMARY KEY ( procedure_occurrence_id ) ; - -ALTER TABLE drug_exposure ADD CONSTRAINT xpk_drug_exposure PRIMARY KEY ( drug_exposure_id ) ; - -ALTER TABLE device_exposure ADD CONSTRAINT xpk_device_exposure PRIMARY KEY ( device_exposure_id ) ; - -ALTER TABLE condition_occurrence ADD CONSTRAINT xpk_condition_occurrence PRIMARY KEY ( condition_occurrence_id ) ; - -ALTER TABLE measurement ADD CONSTRAINT xpk_measurement PRIMARY KEY ( measurement_id ) ; - -ALTER TABLE note ADD CONSTRAINT xpk_note PRIMARY KEY ( note_id ) ; - -ALTER TABLE note_nlp ADD CONSTRAINT xpk_note_nlp PRIMARY KEY ( note_nlp_id ) ; - -ALTER TABLE observation ADD CONSTRAINT xpk_observation PRIMARY KEY ( observation_id ) ; - - - - -/************************ - -Standardized health system data - -************************/ - - -ALTER TABLE location ADD CONSTRAINT xpk_location PRIMARY KEY ( location_id ) ; - -ALTER TABLE care_site ADD CONSTRAINT xpk_care_site PRIMARY KEY ( care_site_id ) ; - -ALTER TABLE provider ADD CONSTRAINT xpk_provider PRIMARY KEY ( provider_id ) ; - - - -/************************ - -Standardized health economics - -************************/ - - -ALTER TABLE payer_plan_period ADD CONSTRAINT xpk_payer_plan_period PRIMARY KEY ( payer_plan_period_id ) ; - -ALTER TABLE cost ADD CONSTRAINT xpk_visit_cost PRIMARY KEY ( cost_id ) ; - - -/************************ - -Standardized derived elements - -************************/ - -ALTER TABLE cohort ADD CONSTRAINT xpk_cohort PRIMARY KEY ( cohort_definition_id, subject_id, cohort_start_date, cohort_end_date ) ; - -ALTER TABLE cohort_attribute ADD CONSTRAINT xpk_cohort_attribute PRIMARY KEY ( 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 ( drug_era_id ) ; - -ALTER TABLE dose_era ADD CONSTRAINT xpk_dose_era PRIMARY KEY ( dose_era_id ) ; - -ALTER TABLE condition_era ADD CONSTRAINT xpk_condition_era PRIMARY KEY ( condition_era_id ) ; - - - - - - - - /************************ ************************* ************************* @@ -328,6 +181,31 @@ ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_admitting_s FOREIGN KEY (a ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_discharge FOREIGN KEY (discharge_to_concept_id) REFERENCES concept (concept_id); +ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_preceding FOREIGN KEY (preceding_visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id); + + +ALTER TABLE visit_detail ADD CONSTRAINT fpk_v_detail_person FOREIGN KEY (person_id) REFERENCES person (person_id); + +ALTER TABLE visit_detail ADD CONSTRAINT fpk_v_detail_concept FOREIGN KEY (visit_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE visit_detail ADD CONSTRAINT fpk_v_detail_type_concept FOREIGN KEY (visit_type_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE visit_detail ADD CONSTRAINT fpk_v_detail_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id); + +ALTER TABLE visit_detail ADD CONSTRAINT fpk_v_detail_care_site FOREIGN KEY (care_site_id) REFERENCES care_site (care_site_id); + +ALTER TABLE visit_detail ADD CONSTRAINT fpk_v_detail_concept_s FOREIGN KEY (visit_source_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE visit_detail ADD CONSTRAINT fpk_v_detail_admitting_s FOREIGN KEY (admitting_source_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE visit_detail ADD CONSTRAINT fpk_v_detail_discharge FOREIGN KEY (discharge_to_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE visit_detail ADD CONSTRAINT fpk_v_detail_preceding FOREIGN KEY (preceding_visit_detail_id) REFERENCES visit_detail (visit_detail_id); + +ALTER TABLE visit_detail ADD CONSTRAINT fpk_v_detail_parent FOREIGN KEY (visit_detail_parent_id) REFERENCES visit_detail (visit_detail_id); + +ALTER TABLE visit_detail ADD CONSTRAINT fpd_v_detail_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id); + ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_person FOREIGN KEY (person_id) REFERENCES person (person_id); @@ -526,3 +404,18 @@ ALTER TABLE dose_era ADD CONSTRAINT fpk_dose_era_unit_concept FOREIGN KEY (unit_ ALTER TABLE condition_era ADD CONSTRAINT fpk_condition_era_person FOREIGN KEY (person_id) REFERENCES person (person_id); ALTER TABLE condition_era ADD CONSTRAINT fpk_condition_era_concept FOREIGN KEY (condition_concept_id) REFERENCES concept (concept_id); + + +/************************ +************************* +************************* +************************* + +Unique constraints + +************************* +************************* +************************* +************************/ + +ALTER TABLE concept_synonym ADD CONSTRAINT uq_concept_synonym UNIQUE (concept_id, concept_synonym_name, language_concept_id); diff --git a/DDLGeneratr/output/oracle/OMOP CDM oracle indexes.txt b/DDLGeneratr/output/oracle/OMOP CDM oracle indexes.txt index 5e9c417..1e8d22c 100644 --- a/DDLGeneratr/output/oracle/OMOP CDM oracle indexes.txt +++ b/DDLGeneratr/output/oracle/OMOP CDM oracle indexes.txt @@ -1,13 +1,13 @@ /********************************************************************************* # 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. @@ -17,26 +17,175 @@ /************************ - ####### # # ####### ###### ##### ###### # # ####### ##### ### - # # ## ## # # # # # # # # ## ## # # # # # # # # ##### ###### # # ###### #### - # # # # # # # # # # # # # # # # # # # # # # ## # # # # # # # # - # # # # # # # ###### # # # # # # # # ###### ##### # # # # # # ##### ## ##### #### - # # # # # # # # # # # # # # # ### # # # # # # # # ## # # - # # # # # # # # # # # # # # # # # ### # # # # ## # # # # # # # # - ####### # # ####### # ##### ###### # # ## ##### ### ##### ### # # ##### ###### # # ###### #### - + ####### # # ####### ###### ##### ###### # # ####### ##### ### + # # ## ## # # # # # # # # ## ## # # # # # # # # ##### ###### # # ###### #### + # # # # # # # # # # # # # # # # # # # # # # ## # # # # # # # # + # # # # # # # ###### # # # # # # # # ###### ##### # # # # # # ##### ## ##### #### + # # # # # # # # # # # # # # # ### # # # # # # # # ## # # + # # # # # # # # # # # # # # # # # ### # # # # ## # # # # # # # # + ####### # # ####### # ##### ###### # # ## ##### ### ##### ### # # ##### ###### # # ###### #### -oracle script to create the required indexes within OMOP common data model, version 5.3 + +oracle script to create the required indexes within OMOP common data model, version 5.3 last revised: 14-November-2017 author: Patrick Ryan, Clair Blacketer -description: These indices are considered a minimal requirement to ensure adequate performance of analyses. +description: These primary keys and indices are considered a minimal requirement to ensure adequate performance of analyses. *************************/ +/************************ +************************* +************************* +************************* + +Primary key constraints + +************************* +************************* +************************* +************************/ + + + +/************************ + +Standardized vocabulary + +************************/ + + + +ALTER TABLE concept ADD CONSTRAINT xpk_concept PRIMARY KEY (concept_id); + +ALTER TABLE vocabulary ADD CONSTRAINT xpk_vocabulary PRIMARY KEY (vocabulary_id); + +ALTER TABLE domain ADD CONSTRAINT xpk_domain PRIMARY KEY (domain_id); + +ALTER TABLE concept_class ADD CONSTRAINT xpk_concept_class PRIMARY KEY (concept_class_id); + +ALTER TABLE concept_relationship ADD CONSTRAINT xpk_concept_relationship PRIMARY KEY (concept_id_1,concept_id_2,relationship_id); + +ALTER TABLE relationship ADD CONSTRAINT xpk_relationship PRIMARY KEY (relationship_id); + +ALTER TABLE concept_ancestor ADD CONSTRAINT xpk_concept_ancestor PRIMARY KEY (ancestor_concept_id,descendant_concept_id); + +ALTER TABLE source_to_concept_map ADD CONSTRAINT xpk_source_to_concept_map PRIMARY KEY (source_vocabulary_id,target_concept_id,source_code,valid_end_date); + +ALTER TABLE drug_strength ADD CONSTRAINT xpk_drug_strength PRIMARY KEY (drug_concept_id, ingredient_concept_id); + +ALTER TABLE cohort_definition ADD CONSTRAINT xpk_cohort_definition PRIMARY KEY (cohort_definition_id); + +ALTER TABLE attribute_definition ADD CONSTRAINT xpk_attribute_definition PRIMARY KEY (attribute_definition_id); + + +/************************** + +Standardized meta-data + +***************************/ + + + +/************************ + +Standardized clinical data + +************************/ + + +/**PRIMARY KEY NONCLUSTERED constraints**/ + +ALTER TABLE person ADD CONSTRAINT xpk_person PRIMARY KEY ( person_id ) ; + +ALTER TABLE observation_period ADD CONSTRAINT xpk_observation_period PRIMARY KEY ( observation_period_id ) ; + +ALTER TABLE specimen ADD CONSTRAINT xpk_specimen PRIMARY KEY ( specimen_id ) ; + +ALTER TABLE death ADD CONSTRAINT xpk_death PRIMARY KEY ( person_id ) ; + +ALTER TABLE visit_occurrence ADD CONSTRAINT xpk_visit_occurrence PRIMARY KEY ( visit_occurrence_id ) ; + +ALTER TABLE visit_detail ADD CONSTRAINT xpk_visit_detail PRIMARY KEY ( visit_detail_id ) ; + +ALTER TABLE procedure_occurrence ADD CONSTRAINT xpk_procedure_occurrence PRIMARY KEY ( procedure_occurrence_id ) ; + +ALTER TABLE drug_exposure ADD CONSTRAINT xpk_drug_exposure PRIMARY KEY ( drug_exposure_id ) ; + +ALTER TABLE device_exposure ADD CONSTRAINT xpk_device_exposure PRIMARY KEY ( device_exposure_id ) ; + +ALTER TABLE condition_occurrence ADD CONSTRAINT xpk_condition_occurrence PRIMARY KEY ( condition_occurrence_id ) ; + +ALTER TABLE measurement ADD CONSTRAINT xpk_measurement PRIMARY KEY ( measurement_id ) ; + +ALTER TABLE note ADD CONSTRAINT xpk_note PRIMARY KEY ( note_id ) ; + +ALTER TABLE note_nlp ADD CONSTRAINT xpk_note_nlp PRIMARY KEY ( note_nlp_id ) ; + +ALTER TABLE observation ADD CONSTRAINT xpk_observation PRIMARY KEY ( observation_id ) ; + + + + +/************************ + +Standardized health system data + +************************/ + + +ALTER TABLE location ADD CONSTRAINT xpk_location PRIMARY KEY ( location_id ) ; + +ALTER TABLE care_site ADD CONSTRAINT xpk_care_site PRIMARY KEY ( care_site_id ) ; + +ALTER TABLE provider ADD CONSTRAINT xpk_provider PRIMARY KEY ( provider_id ) ; + + + +/************************ + +Standardized health economics + +************************/ + + +ALTER TABLE payer_plan_period ADD CONSTRAINT xpk_payer_plan_period PRIMARY KEY ( payer_plan_period_id ) ; + +ALTER TABLE cost ADD CONSTRAINT xpk_visit_cost PRIMARY KEY ( cost_id ) ; + + +/************************ + +Standardized derived elements + +************************/ + +ALTER TABLE cohort ADD CONSTRAINT xpk_cohort PRIMARY KEY ( cohort_definition_id, subject_id, cohort_start_date, cohort_end_date ) ; + +ALTER TABLE cohort_attribute ADD CONSTRAINT xpk_cohort_attribute PRIMARY KEY ( 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 ( drug_era_id ) ; + +ALTER TABLE dose_era ADD CONSTRAINT xpk_dose_era PRIMARY KEY ( dose_era_id ) ; + +ALTER TABLE condition_era ADD CONSTRAINT xpk_condition_era PRIMARY KEY ( condition_era_id ) ; + + +/************************ +************************* +************************* +************************* + +Indices + +************************* +************************* +************************* +************************/ + /************************ Standardized vocabulary @@ -83,9 +232,9 @@ EXCEPTION END IF; END; -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 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); BEGIN EXECUTE IMMEDIATE 'CREATE UNIQUE INDEX idx_relationship_rel_id ON relationship (relationship_id ASC)'; @@ -149,6 +298,9 @@ CREATE INDEX idx_death_person_id ON death (person_id ASC); CREATE 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 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 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); diff --git a/DDLGeneratr/output/pdw/OMOP CDM pdw constraints.txt b/DDLGeneratr/output/pdw/OMOP CDM pdw constraints.txt new file mode 100644 index 0000000..a96d34c --- /dev/null +++ b/DDLGeneratr/output/pdw/OMOP CDM pdw constraints.txt @@ -0,0 +1,421 @@ +/********************************************************************************* +# 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. +********************************************************************************/ + +/************************ + + ####### # # ####### ###### ##### ###### # # ####### ##### ##### + # # ## ## # # # # # # # # ## ## # # # # # # # #### # # #### ##### ##### ## # # # ##### #### + # # # # # # # # # # # # # # # # # # # # # # # # ## # # # # # # # # ## # # # + # # # # # # # ###### # # # # # # # # ###### ##### # # # # # # #### # # # # # # # # # # #### + # # # # # # # # # # # # # # # ### # # # # # # # # # ##### ###### # # # # # # + # # # # # # # # # # # # # # # # # ### # # # # # # # ## # # # # # # # # # ## # # # + ####### # # ####### # ##### ###### # # ## ##### ### ##### ##### #### # # #### # # # # # # # # # #### + + +pdw script to create foreign key constraints within OMOP common data model, version 5.3.0 + +last revised: 15-November-2017 + +author: Patrick Ryan, Clair Blacketer + + +*************************/ + + +/************************ +************************* +************************* +************************* + +Foreign key constraints + +************************* +************************* +************************* +************************/ + + +/************************ + +Standardized vocabulary + +************************/ + + +ALTER TABLE concept ADD CONSTRAINT fpk_concept_domain FOREIGN KEY (domain_id) REFERENCES domain (domain_id); + +ALTER TABLE concept ADD CONSTRAINT fpk_concept_class FOREIGN KEY (concept_class_id) REFERENCES concept_class (concept_class_id); + +ALTER TABLE concept ADD CONSTRAINT fpk_concept_vocabulary FOREIGN KEY (vocabulary_id) REFERENCES vocabulary (vocabulary_id); + +ALTER TABLE vocabulary ADD CONSTRAINT fpk_vocabulary_concept FOREIGN KEY (vocabulary_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE domain ADD CONSTRAINT fpk_domain_concept FOREIGN KEY (domain_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE concept_class ADD CONSTRAINT fpk_concept_class_concept FOREIGN KEY (concept_class_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE concept_relationship ADD CONSTRAINT fpk_concept_relationship_c_1 FOREIGN KEY (concept_id_1) REFERENCES concept (concept_id); + +ALTER TABLE concept_relationship ADD CONSTRAINT fpk_concept_relationship_c_2 FOREIGN KEY (concept_id_2) REFERENCES concept (concept_id); + +ALTER TABLE concept_relationship ADD CONSTRAINT fpk_concept_relationship_id FOREIGN KEY (relationship_id) REFERENCES relationship (relationship_id); + +ALTER TABLE relationship ADD CONSTRAINT fpk_relationship_concept FOREIGN KEY (relationship_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE relationship ADD CONSTRAINT fpk_relationship_reverse FOREIGN KEY (reverse_relationship_id) REFERENCES relationship (relationship_id); + +ALTER TABLE concept_synonym ADD CONSTRAINT fpk_concept_synonym_concept FOREIGN KEY (concept_id) REFERENCES concept (concept_id); + +ALTER TABLE concept_ancestor ADD CONSTRAINT fpk_concept_ancestor_concept_1 FOREIGN KEY (ancestor_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE concept_ancestor ADD CONSTRAINT fpk_concept_ancestor_concept_2 FOREIGN KEY (descendant_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE source_to_concept_map ADD CONSTRAINT fpk_source_to_concept_map_v_1 FOREIGN KEY (source_vocabulary_id) REFERENCES vocabulary (vocabulary_id); + +ALTER TABLE source_to_concept_map ADD CONSTRAINT fpk_source_to_concept_map_v_2 FOREIGN KEY (target_vocabulary_id) REFERENCES vocabulary (vocabulary_id); + +ALTER TABLE source_to_concept_map ADD CONSTRAINT fpk_source_to_concept_map_c_1 FOREIGN KEY (target_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE drug_strength ADD CONSTRAINT fpk_drug_strength_concept_1 FOREIGN KEY (drug_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE drug_strength ADD CONSTRAINT fpk_drug_strength_concept_2 FOREIGN KEY (ingredient_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE drug_strength ADD CONSTRAINT fpk_drug_strength_unit_1 FOREIGN KEY (amount_unit_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE drug_strength ADD CONSTRAINT fpk_drug_strength_unit_2 FOREIGN KEY (numerator_unit_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE drug_strength ADD CONSTRAINT fpk_drug_strength_unit_3 FOREIGN KEY (denominator_unit_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE cohort_definition ADD CONSTRAINT fpk_cohort_definition_concept FOREIGN KEY (definition_type_concept_id) REFERENCES concept (concept_id); + + +/************************** + +Standardized meta-data + +***************************/ + + + + + +/************************ + +Standardized clinical data + +************************/ + +ALTER TABLE person ADD CONSTRAINT fpk_person_gender_concept FOREIGN KEY (gender_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE person ADD CONSTRAINT fpk_person_race_concept FOREIGN KEY (race_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE person ADD CONSTRAINT fpk_person_ethnicity_concept FOREIGN KEY (ethnicity_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE person ADD CONSTRAINT fpk_person_gender_concept_s FOREIGN KEY (gender_source_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE person ADD CONSTRAINT fpk_person_race_concept_s FOREIGN KEY (race_source_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE person ADD CONSTRAINT fpk_person_ethnicity_concept_s FOREIGN KEY (ethnicity_source_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE person ADD CONSTRAINT fpk_person_location FOREIGN KEY (location_id) REFERENCES location (location_id); + +ALTER TABLE person ADD CONSTRAINT fpk_person_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id); + +ALTER TABLE person ADD CONSTRAINT fpk_person_care_site FOREIGN KEY (care_site_id) REFERENCES care_site (care_site_id); + + +ALTER TABLE observation_period ADD CONSTRAINT fpk_observation_period_person FOREIGN KEY (person_id) REFERENCES person (person_id); + +ALTER TABLE observation_period ADD CONSTRAINT fpk_observation_period_concept FOREIGN KEY (period_type_concept_id) REFERENCES concept (concept_id); + + +ALTER TABLE specimen ADD CONSTRAINT fpk_specimen_person FOREIGN KEY (person_id) REFERENCES person (person_id); + +ALTER TABLE specimen ADD CONSTRAINT fpk_specimen_concept FOREIGN KEY (specimen_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE specimen ADD CONSTRAINT fpk_specimen_type_concept FOREIGN KEY (specimen_type_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE specimen ADD CONSTRAINT fpk_specimen_unit_concept FOREIGN KEY (unit_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE specimen ADD CONSTRAINT fpk_specimen_site_concept FOREIGN KEY (anatomic_site_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE specimen ADD CONSTRAINT fpk_specimen_status_concept FOREIGN KEY (disease_status_concept_id) REFERENCES concept (concept_id); + + +ALTER TABLE death ADD CONSTRAINT fpk_death_person FOREIGN KEY (person_id) REFERENCES person (person_id); + +ALTER TABLE death ADD CONSTRAINT fpk_death_type_concept FOREIGN KEY (death_type_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE death ADD CONSTRAINT fpk_death_cause_concept FOREIGN KEY (cause_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE death ADD CONSTRAINT fpk_death_cause_concept_s FOREIGN KEY (cause_source_concept_id) REFERENCES concept (concept_id); + + +ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_person FOREIGN KEY (person_id) REFERENCES person (person_id); + +ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_concept FOREIGN KEY (visit_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_type_concept FOREIGN KEY (visit_type_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id); + +ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_care_site FOREIGN KEY (care_site_id) REFERENCES care_site (care_site_id); + +ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_concept_s FOREIGN KEY (visit_source_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_admitting_s FOREIGN KEY (admitting_source_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_discharge FOREIGN KEY (discharge_to_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_preceding FOREIGN KEY (preceding_visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id); + + +ALTER TABLE visit_detail ADD CONSTRAINT fpk_v_detail_person FOREIGN KEY (person_id) REFERENCES person (person_id); + +ALTER TABLE visit_detail ADD CONSTRAINT fpk_v_detail_concept FOREIGN KEY (visit_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE visit_detail ADD CONSTRAINT fpk_v_detail_type_concept FOREIGN KEY (visit_type_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE visit_detail ADD CONSTRAINT fpk_v_detail_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id); + +ALTER TABLE visit_detail ADD CONSTRAINT fpk_v_detail_care_site FOREIGN KEY (care_site_id) REFERENCES care_site (care_site_id); + +ALTER TABLE visit_detail ADD CONSTRAINT fpk_v_detail_concept_s FOREIGN KEY (visit_source_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE visit_detail ADD CONSTRAINT fpk_v_detail_admitting_s FOREIGN KEY (admitting_source_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE visit_detail ADD CONSTRAINT fpk_v_detail_discharge FOREIGN KEY (discharge_to_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE visit_detail ADD CONSTRAINT fpk_v_detail_preceding FOREIGN KEY (preceding_visit_detail_id) REFERENCES visit_detail (visit_detail_id); + +ALTER TABLE visit_detail ADD CONSTRAINT fpk_v_detail_parent FOREIGN KEY (visit_detail_parent_id) REFERENCES visit_detail (visit_detail_id); + +ALTER TABLE visit_detail ADD CONSTRAINT fpd_v_detail_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id); + + +ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_person FOREIGN KEY (person_id) REFERENCES person (person_id); + +ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_concept FOREIGN KEY (procedure_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_type_concept FOREIGN KEY (procedure_type_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_modifier FOREIGN KEY (modifier_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id); + +ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id); + +ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_concept_s FOREIGN KEY (procedure_source_concept_id) REFERENCES concept (concept_id); + + +ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_person FOREIGN KEY (person_id) REFERENCES person (person_id); + +ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_concept FOREIGN KEY (drug_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_type_concept FOREIGN KEY (drug_type_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_route_concept FOREIGN KEY (route_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id); + +ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id); + +ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_concept_s FOREIGN KEY (drug_source_concept_id) REFERENCES concept (concept_id); + + +ALTER TABLE device_exposure ADD CONSTRAINT fpk_device_person FOREIGN KEY (person_id) REFERENCES person (person_id); + +ALTER TABLE device_exposure ADD CONSTRAINT fpk_device_concept FOREIGN KEY (device_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE device_exposure ADD CONSTRAINT fpk_device_type_concept FOREIGN KEY (device_type_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE device_exposure ADD CONSTRAINT fpk_device_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id); + +ALTER TABLE device_exposure ADD CONSTRAINT fpk_device_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id); + +ALTER TABLE device_exposure ADD CONSTRAINT fpk_device_concept_s FOREIGN KEY (device_source_concept_id) REFERENCES concept (concept_id); + + +ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_person FOREIGN KEY (person_id) REFERENCES person (person_id); + +ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_concept FOREIGN KEY (condition_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_type_concept FOREIGN KEY (condition_type_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id); + +ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id); + +ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_concept_s FOREIGN KEY (condition_source_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_status_concept FOREIGN KEY (condition_status_concept_id) REFERENCES concept (concept_id); + + +ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_person FOREIGN KEY (person_id) REFERENCES person (person_id); + +ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_concept FOREIGN KEY (measurement_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_type_concept FOREIGN KEY (measurement_type_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_operator FOREIGN KEY (operator_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_value FOREIGN KEY (value_as_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_unit FOREIGN KEY (unit_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id); + +ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id); + +ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_concept_s FOREIGN KEY (measurement_source_concept_id) REFERENCES concept (concept_id); + + +ALTER TABLE note ADD CONSTRAINT fpk_note_person FOREIGN KEY (person_id) REFERENCES person (person_id); + +ALTER TABLE note ADD CONSTRAINT fpk_note_type_concept FOREIGN KEY (note_type_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE note ADD CONSTRAINT fpk_note_class_concept FOREIGN KEY (note_class_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE note ADD CONSTRAINT fpk_note_encoding_concept FOREIGN KEY (encoding_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE note ADD CONSTRAINT fpk_language_concept FOREIGN KEY (language_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE note ADD CONSTRAINT fpk_note_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id); + +ALTER TABLE note ADD CONSTRAINT fpk_note_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id); + + +ALTER TABLE note_nlp ADD CONSTRAINT fpk_note_nlp_note FOREIGN KEY (note_id) REFERENCES note (note_id); + +ALTER TABLE note_nlp ADD CONSTRAINT fpk_note_nlp_section_concept FOREIGN KEY (section_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE note_nlp ADD CONSTRAINT fpk_note_nlp_concept FOREIGN KEY (note_nlp_concept_id) REFERENCES concept (concept_id); + + + +ALTER TABLE observation ADD CONSTRAINT fpk_observation_person FOREIGN KEY (person_id) REFERENCES person (person_id); + +ALTER TABLE observation ADD CONSTRAINT fpk_observation_concept FOREIGN KEY (observation_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE observation ADD CONSTRAINT fpk_observation_type_concept FOREIGN KEY (observation_type_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE observation ADD CONSTRAINT fpk_observation_value FOREIGN KEY (value_as_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE observation ADD CONSTRAINT fpk_observation_qualifier FOREIGN KEY (qualifier_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE observation ADD CONSTRAINT fpk_observation_unit FOREIGN KEY (unit_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE observation ADD CONSTRAINT fpk_observation_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id); + +ALTER TABLE observation ADD CONSTRAINT fpk_observation_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id); + +ALTER TABLE observation ADD CONSTRAINT fpk_observation_concept_s FOREIGN KEY (observation_source_concept_id) REFERENCES concept (concept_id); + + +ALTER TABLE fact_relationship ADD CONSTRAINT fpk_fact_domain_1 FOREIGN KEY (domain_concept_id_1) REFERENCES concept (concept_id); + +ALTER TABLE fact_relationship ADD CONSTRAINT fpk_fact_domain_2 FOREIGN KEY (domain_concept_id_2) REFERENCES concept (concept_id); + +ALTER TABLE fact_relationship ADD CONSTRAINT fpk_fact_relationship FOREIGN KEY (relationship_concept_id) REFERENCES concept (concept_id); + + + +/************************ + +Standardized health system data + +************************/ + +ALTER TABLE care_site ADD CONSTRAINT fpk_care_site_location FOREIGN KEY (location_id) REFERENCES location (location_id); + +ALTER TABLE care_site ADD CONSTRAINT fpk_care_site_place FOREIGN KEY (place_of_service_concept_id) REFERENCES concept (concept_id); + + +ALTER TABLE provider ADD CONSTRAINT fpk_provider_specialty FOREIGN KEY (specialty_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE provider ADD CONSTRAINT fpk_provider_care_site FOREIGN KEY (care_site_id) REFERENCES care_site (care_site_id); + +ALTER TABLE provider ADD CONSTRAINT fpk_provider_gender FOREIGN KEY (gender_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE provider ADD CONSTRAINT fpk_provider_specialty_s FOREIGN KEY (specialty_source_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE provider ADD CONSTRAINT fpk_provider_gender_s FOREIGN KEY (gender_source_concept_id) REFERENCES concept (concept_id); + + + + +/************************ + +Standardized health economics + +************************/ + +ALTER TABLE payer_plan_period ADD CONSTRAINT fpk_payer_plan_period FOREIGN KEY (person_id) REFERENCES person (person_id); + +ALTER TABLE cost ADD CONSTRAINT fpk_visit_cost_currency FOREIGN KEY (currency_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE cost ADD CONSTRAINT fpk_visit_cost_period FOREIGN KEY (payer_plan_period_id) REFERENCES payer_plan_period (payer_plan_period_id); + +ALTER TABLE cost ADD CONSTRAINT fpk_drg_concept FOREIGN KEY (drg_concept_id) REFERENCES concept (concept_id); + +/************************ + +Standardized derived elements + +************************/ + + +ALTER TABLE cohort ADD CONSTRAINT fpk_cohort_definition FOREIGN KEY (cohort_definition_id) REFERENCES cohort_definition (cohort_definition_id); + + +ALTER TABLE cohort_attribute ADD CONSTRAINT fpk_ca_cohort_definition FOREIGN KEY (cohort_definition_id) REFERENCES cohort_definition (cohort_definition_id); + +ALTER TABLE cohort_attribute ADD CONSTRAINT fpk_ca_attribute_definition FOREIGN KEY (attribute_definition_id) REFERENCES attribute_definition (attribute_definition_id); + +ALTER TABLE cohort_attribute ADD CONSTRAINT fpk_ca_value FOREIGN KEY (value_as_concept_id) REFERENCES concept (concept_id); + + +ALTER TABLE drug_era ADD CONSTRAINT fpk_drug_era_person FOREIGN KEY (person_id) REFERENCES person (person_id); + +ALTER TABLE drug_era ADD CONSTRAINT fpk_drug_era_concept FOREIGN KEY (drug_concept_id) REFERENCES concept (concept_id); + + +ALTER TABLE dose_era ADD CONSTRAINT fpk_dose_era_person FOREIGN KEY (person_id) REFERENCES person (person_id); + +ALTER TABLE dose_era ADD CONSTRAINT fpk_dose_era_concept FOREIGN KEY (drug_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE dose_era ADD CONSTRAINT fpk_dose_era_unit_concept FOREIGN KEY (unit_concept_id) REFERENCES concept (concept_id); + + +ALTER TABLE condition_era ADD CONSTRAINT fpk_condition_era_person FOREIGN KEY (person_id) REFERENCES person (person_id); + +ALTER TABLE condition_era ADD CONSTRAINT fpk_condition_era_concept FOREIGN KEY (condition_concept_id) REFERENCES concept (concept_id); + + +/************************ +************************* +************************* +************************* + +Unique constraints + +************************* +************************* +************************* +************************/ + +ALTER TABLE concept_synonym ADD CONSTRAINT uq_concept_synonym UNIQUE (concept_id, concept_synonym_name, language_concept_id); diff --git a/DDLGeneratr/output/pdw/OMOP CDM pdw indexes.txt b/DDLGeneratr/output/pdw/OMOP CDM pdw indexes.txt new file mode 100644 index 0000000..3eb3a92 --- /dev/null +++ b/DDLGeneratr/output/pdw/OMOP CDM pdw indexes.txt @@ -0,0 +1,342 @@ +/********************************************************************************* +# 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. +********************************************************************************/ + +/************************ + + ####### # # ####### ###### ##### ###### # # ####### ##### ### + # # ## ## # # # # # # # # ## ## # # # # # # # # ##### ###### # # ###### #### + # # # # # # # # # # # # # # # # # # # # # # ## # # # # # # # # + # # # # # # # ###### # # # # # # # # ###### ##### # # # # # # ##### ## ##### #### + # # # # # # # # # # # # # # # ### # # # # # # # # ## # # + # # # # # # # # # # # # # # # # # ### # # # # ## # # # # # # # # + ####### # # ####### # ##### ###### # # ## ##### ### ##### ### # # ##### ###### # # ###### #### + + +pdw script to create the required indexes within OMOP common data model, version 5.3 + +last revised: 14-November-2017 + +author: Patrick Ryan, Clair Blacketer + +description: These primary keys and indices are considered a minimal requirement to ensure adequate performance of analyses. + +*************************/ + + +/************************ +************************* +************************* +************************* + +Primary key constraints + +************************* +************************* +************************* +************************/ + + + +/************************ + +Standardized vocabulary + +************************/ + + + +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); + + +/************************** + +Standardized meta-data + +***************************/ + + + +/************************ + +Standardized clinical data + +************************/ + + +/**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 ) ; + + + + +/************************ + +Standardized health system data + +************************/ + + +ALTER TABLE location ADD CONSTRAINT xpk_location PRIMARY KEY NONCLUSTERED ( location_id ) ; + +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 ) ; + + + +/************************ + +Standardized health economics + +************************/ + + +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 ) ; + + +/************************ + +Standardized derived elements + +************************/ + +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 ) ; + + +/************************ +************************* +************************* +************************* + +Indices + +************************* +************************* +************************* +************************/ + +/************************ + +Standardized vocabulary + +************************/ + +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); + + +/************************** + +Standardized meta-data + +***************************/ + + + + + +/************************ + +Standardized clinical data + +************************/ + +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 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); + + + +/************************ + +Standardized health system data + +************************/ + + + + + +/************************ + +Standardized health economics + +************************/ + +CREATE CLUSTERED INDEX idx_period_person_id ON payer_plan_period (person_id ASC); + + + + + +/************************ + +Standardized derived elements + +************************/ + + +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); + diff --git a/DDLGeneratr/output/postgresql/OMOP CDM postgresql constraints.txt b/DDLGeneratr/output/postgresql/OMOP CDM postgresql constraints.txt new file mode 100644 index 0000000..075df5e --- /dev/null +++ b/DDLGeneratr/output/postgresql/OMOP CDM postgresql constraints.txt @@ -0,0 +1,421 @@ +/********************************************************************************* +# 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. +********************************************************************************/ + +/************************ + + ####### # # ####### ###### ##### ###### # # ####### ##### ##### + # # ## ## # # # # # # # # ## ## # # # # # # # #### # # #### ##### ##### ## # # # ##### #### + # # # # # # # # # # # # # # # # # # # # # # # # ## # # # # # # # # ## # # # + # # # # # # # ###### # # # # # # # # ###### ##### # # # # # # #### # # # # # # # # # # #### + # # # # # # # # # # # # # # # ### # # # # # # # # # ##### ###### # # # # # # + # # # # # # # # # # # # # # # # # ### # # # # # # # ## # # # # # # # # # ## # # # + ####### # # ####### # ##### ###### # # ## ##### ### ##### ##### #### # # #### # # # # # # # # # #### + + +postgresql script to create foreign key constraints within OMOP common data model, version 5.3.0 + +last revised: 15-November-2017 + +author: Patrick Ryan, Clair Blacketer + + +*************************/ + + +/************************ +************************* +************************* +************************* + +Foreign key constraints + +************************* +************************* +************************* +************************/ + + +/************************ + +Standardized vocabulary + +************************/ + + +ALTER TABLE concept ADD CONSTRAINT fpk_concept_domain FOREIGN KEY (domain_id) REFERENCES domain (domain_id); + +ALTER TABLE concept ADD CONSTRAINT fpk_concept_class FOREIGN KEY (concept_class_id) REFERENCES concept_class (concept_class_id); + +ALTER TABLE concept ADD CONSTRAINT fpk_concept_vocabulary FOREIGN KEY (vocabulary_id) REFERENCES vocabulary (vocabulary_id); + +ALTER TABLE vocabulary ADD CONSTRAINT fpk_vocabulary_concept FOREIGN KEY (vocabulary_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE domain ADD CONSTRAINT fpk_domain_concept FOREIGN KEY (domain_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE concept_class ADD CONSTRAINT fpk_concept_class_concept FOREIGN KEY (concept_class_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE concept_relationship ADD CONSTRAINT fpk_concept_relationship_c_1 FOREIGN KEY (concept_id_1) REFERENCES concept (concept_id); + +ALTER TABLE concept_relationship ADD CONSTRAINT fpk_concept_relationship_c_2 FOREIGN KEY (concept_id_2) REFERENCES concept (concept_id); + +ALTER TABLE concept_relationship ADD CONSTRAINT fpk_concept_relationship_id FOREIGN KEY (relationship_id) REFERENCES relationship (relationship_id); + +ALTER TABLE relationship ADD CONSTRAINT fpk_relationship_concept FOREIGN KEY (relationship_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE relationship ADD CONSTRAINT fpk_relationship_reverse FOREIGN KEY (reverse_relationship_id) REFERENCES relationship (relationship_id); + +ALTER TABLE concept_synonym ADD CONSTRAINT fpk_concept_synonym_concept FOREIGN KEY (concept_id) REFERENCES concept (concept_id); + +ALTER TABLE concept_ancestor ADD CONSTRAINT fpk_concept_ancestor_concept_1 FOREIGN KEY (ancestor_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE concept_ancestor ADD CONSTRAINT fpk_concept_ancestor_concept_2 FOREIGN KEY (descendant_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE source_to_concept_map ADD CONSTRAINT fpk_source_to_concept_map_v_1 FOREIGN KEY (source_vocabulary_id) REFERENCES vocabulary (vocabulary_id); + +ALTER TABLE source_to_concept_map ADD CONSTRAINT fpk_source_to_concept_map_v_2 FOREIGN KEY (target_vocabulary_id) REFERENCES vocabulary (vocabulary_id); + +ALTER TABLE source_to_concept_map ADD CONSTRAINT fpk_source_to_concept_map_c_1 FOREIGN KEY (target_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE drug_strength ADD CONSTRAINT fpk_drug_strength_concept_1 FOREIGN KEY (drug_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE drug_strength ADD CONSTRAINT fpk_drug_strength_concept_2 FOREIGN KEY (ingredient_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE drug_strength ADD CONSTRAINT fpk_drug_strength_unit_1 FOREIGN KEY (amount_unit_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE drug_strength ADD CONSTRAINT fpk_drug_strength_unit_2 FOREIGN KEY (numerator_unit_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE drug_strength ADD CONSTRAINT fpk_drug_strength_unit_3 FOREIGN KEY (denominator_unit_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE cohort_definition ADD CONSTRAINT fpk_cohort_definition_concept FOREIGN KEY (definition_type_concept_id) REFERENCES concept (concept_id); + + +/************************** + +Standardized meta-data + +***************************/ + + + + + +/************************ + +Standardized clinical data + +************************/ + +ALTER TABLE person ADD CONSTRAINT fpk_person_gender_concept FOREIGN KEY (gender_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE person ADD CONSTRAINT fpk_person_race_concept FOREIGN KEY (race_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE person ADD CONSTRAINT fpk_person_ethnicity_concept FOREIGN KEY (ethnicity_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE person ADD CONSTRAINT fpk_person_gender_concept_s FOREIGN KEY (gender_source_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE person ADD CONSTRAINT fpk_person_race_concept_s FOREIGN KEY (race_source_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE person ADD CONSTRAINT fpk_person_ethnicity_concept_s FOREIGN KEY (ethnicity_source_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE person ADD CONSTRAINT fpk_person_location FOREIGN KEY (location_id) REFERENCES location (location_id); + +ALTER TABLE person ADD CONSTRAINT fpk_person_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id); + +ALTER TABLE person ADD CONSTRAINT fpk_person_care_site FOREIGN KEY (care_site_id) REFERENCES care_site (care_site_id); + + +ALTER TABLE observation_period ADD CONSTRAINT fpk_observation_period_person FOREIGN KEY (person_id) REFERENCES person (person_id); + +ALTER TABLE observation_period ADD CONSTRAINT fpk_observation_period_concept FOREIGN KEY (period_type_concept_id) REFERENCES concept (concept_id); + + +ALTER TABLE specimen ADD CONSTRAINT fpk_specimen_person FOREIGN KEY (person_id) REFERENCES person (person_id); + +ALTER TABLE specimen ADD CONSTRAINT fpk_specimen_concept FOREIGN KEY (specimen_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE specimen ADD CONSTRAINT fpk_specimen_type_concept FOREIGN KEY (specimen_type_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE specimen ADD CONSTRAINT fpk_specimen_unit_concept FOREIGN KEY (unit_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE specimen ADD CONSTRAINT fpk_specimen_site_concept FOREIGN KEY (anatomic_site_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE specimen ADD CONSTRAINT fpk_specimen_status_concept FOREIGN KEY (disease_status_concept_id) REFERENCES concept (concept_id); + + +ALTER TABLE death ADD CONSTRAINT fpk_death_person FOREIGN KEY (person_id) REFERENCES person (person_id); + +ALTER TABLE death ADD CONSTRAINT fpk_death_type_concept FOREIGN KEY (death_type_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE death ADD CONSTRAINT fpk_death_cause_concept FOREIGN KEY (cause_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE death ADD CONSTRAINT fpk_death_cause_concept_s FOREIGN KEY (cause_source_concept_id) REFERENCES concept (concept_id); + + +ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_person FOREIGN KEY (person_id) REFERENCES person (person_id); + +ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_concept FOREIGN KEY (visit_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_type_concept FOREIGN KEY (visit_type_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id); + +ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_care_site FOREIGN KEY (care_site_id) REFERENCES care_site (care_site_id); + +ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_concept_s FOREIGN KEY (visit_source_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_admitting_s FOREIGN KEY (admitting_source_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_discharge FOREIGN KEY (discharge_to_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_preceding FOREIGN KEY (preceding_visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id); + + +ALTER TABLE visit_detail ADD CONSTRAINT fpk_v_detail_person FOREIGN KEY (person_id) REFERENCES person (person_id); + +ALTER TABLE visit_detail ADD CONSTRAINT fpk_v_detail_concept FOREIGN KEY (visit_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE visit_detail ADD CONSTRAINT fpk_v_detail_type_concept FOREIGN KEY (visit_type_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE visit_detail ADD CONSTRAINT fpk_v_detail_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id); + +ALTER TABLE visit_detail ADD CONSTRAINT fpk_v_detail_care_site FOREIGN KEY (care_site_id) REFERENCES care_site (care_site_id); + +ALTER TABLE visit_detail ADD CONSTRAINT fpk_v_detail_concept_s FOREIGN KEY (visit_source_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE visit_detail ADD CONSTRAINT fpk_v_detail_admitting_s FOREIGN KEY (admitting_source_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE visit_detail ADD CONSTRAINT fpk_v_detail_discharge FOREIGN KEY (discharge_to_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE visit_detail ADD CONSTRAINT fpk_v_detail_preceding FOREIGN KEY (preceding_visit_detail_id) REFERENCES visit_detail (visit_detail_id); + +ALTER TABLE visit_detail ADD CONSTRAINT fpk_v_detail_parent FOREIGN KEY (visit_detail_parent_id) REFERENCES visit_detail (visit_detail_id); + +ALTER TABLE visit_detail ADD CONSTRAINT fpd_v_detail_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id); + + +ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_person FOREIGN KEY (person_id) REFERENCES person (person_id); + +ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_concept FOREIGN KEY (procedure_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_type_concept FOREIGN KEY (procedure_type_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_modifier FOREIGN KEY (modifier_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id); + +ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id); + +ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_concept_s FOREIGN KEY (procedure_source_concept_id) REFERENCES concept (concept_id); + + +ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_person FOREIGN KEY (person_id) REFERENCES person (person_id); + +ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_concept FOREIGN KEY (drug_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_type_concept FOREIGN KEY (drug_type_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_route_concept FOREIGN KEY (route_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id); + +ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id); + +ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_concept_s FOREIGN KEY (drug_source_concept_id) REFERENCES concept (concept_id); + + +ALTER TABLE device_exposure ADD CONSTRAINT fpk_device_person FOREIGN KEY (person_id) REFERENCES person (person_id); + +ALTER TABLE device_exposure ADD CONSTRAINT fpk_device_concept FOREIGN KEY (device_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE device_exposure ADD CONSTRAINT fpk_device_type_concept FOREIGN KEY (device_type_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE device_exposure ADD CONSTRAINT fpk_device_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id); + +ALTER TABLE device_exposure ADD CONSTRAINT fpk_device_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id); + +ALTER TABLE device_exposure ADD CONSTRAINT fpk_device_concept_s FOREIGN KEY (device_source_concept_id) REFERENCES concept (concept_id); + + +ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_person FOREIGN KEY (person_id) REFERENCES person (person_id); + +ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_concept FOREIGN KEY (condition_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_type_concept FOREIGN KEY (condition_type_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id); + +ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id); + +ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_concept_s FOREIGN KEY (condition_source_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_status_concept FOREIGN KEY (condition_status_concept_id) REFERENCES concept (concept_id); + + +ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_person FOREIGN KEY (person_id) REFERENCES person (person_id); + +ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_concept FOREIGN KEY (measurement_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_type_concept FOREIGN KEY (measurement_type_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_operator FOREIGN KEY (operator_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_value FOREIGN KEY (value_as_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_unit FOREIGN KEY (unit_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id); + +ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id); + +ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_concept_s FOREIGN KEY (measurement_source_concept_id) REFERENCES concept (concept_id); + + +ALTER TABLE note ADD CONSTRAINT fpk_note_person FOREIGN KEY (person_id) REFERENCES person (person_id); + +ALTER TABLE note ADD CONSTRAINT fpk_note_type_concept FOREIGN KEY (note_type_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE note ADD CONSTRAINT fpk_note_class_concept FOREIGN KEY (note_class_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE note ADD CONSTRAINT fpk_note_encoding_concept FOREIGN KEY (encoding_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE note ADD CONSTRAINT fpk_language_concept FOREIGN KEY (language_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE note ADD CONSTRAINT fpk_note_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id); + +ALTER TABLE note ADD CONSTRAINT fpk_note_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id); + + +ALTER TABLE note_nlp ADD CONSTRAINT fpk_note_nlp_note FOREIGN KEY (note_id) REFERENCES note (note_id); + +ALTER TABLE note_nlp ADD CONSTRAINT fpk_note_nlp_section_concept FOREIGN KEY (section_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE note_nlp ADD CONSTRAINT fpk_note_nlp_concept FOREIGN KEY (note_nlp_concept_id) REFERENCES concept (concept_id); + + + +ALTER TABLE observation ADD CONSTRAINT fpk_observation_person FOREIGN KEY (person_id) REFERENCES person (person_id); + +ALTER TABLE observation ADD CONSTRAINT fpk_observation_concept FOREIGN KEY (observation_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE observation ADD CONSTRAINT fpk_observation_type_concept FOREIGN KEY (observation_type_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE observation ADD CONSTRAINT fpk_observation_value FOREIGN KEY (value_as_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE observation ADD CONSTRAINT fpk_observation_qualifier FOREIGN KEY (qualifier_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE observation ADD CONSTRAINT fpk_observation_unit FOREIGN KEY (unit_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE observation ADD CONSTRAINT fpk_observation_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id); + +ALTER TABLE observation ADD CONSTRAINT fpk_observation_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id); + +ALTER TABLE observation ADD CONSTRAINT fpk_observation_concept_s FOREIGN KEY (observation_source_concept_id) REFERENCES concept (concept_id); + + +ALTER TABLE fact_relationship ADD CONSTRAINT fpk_fact_domain_1 FOREIGN KEY (domain_concept_id_1) REFERENCES concept (concept_id); + +ALTER TABLE fact_relationship ADD CONSTRAINT fpk_fact_domain_2 FOREIGN KEY (domain_concept_id_2) REFERENCES concept (concept_id); + +ALTER TABLE fact_relationship ADD CONSTRAINT fpk_fact_relationship FOREIGN KEY (relationship_concept_id) REFERENCES concept (concept_id); + + + +/************************ + +Standardized health system data + +************************/ + +ALTER TABLE care_site ADD CONSTRAINT fpk_care_site_location FOREIGN KEY (location_id) REFERENCES location (location_id); + +ALTER TABLE care_site ADD CONSTRAINT fpk_care_site_place FOREIGN KEY (place_of_service_concept_id) REFERENCES concept (concept_id); + + +ALTER TABLE provider ADD CONSTRAINT fpk_provider_specialty FOREIGN KEY (specialty_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE provider ADD CONSTRAINT fpk_provider_care_site FOREIGN KEY (care_site_id) REFERENCES care_site (care_site_id); + +ALTER TABLE provider ADD CONSTRAINT fpk_provider_gender FOREIGN KEY (gender_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE provider ADD CONSTRAINT fpk_provider_specialty_s FOREIGN KEY (specialty_source_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE provider ADD CONSTRAINT fpk_provider_gender_s FOREIGN KEY (gender_source_concept_id) REFERENCES concept (concept_id); + + + + +/************************ + +Standardized health economics + +************************/ + +ALTER TABLE payer_plan_period ADD CONSTRAINT fpk_payer_plan_period FOREIGN KEY (person_id) REFERENCES person (person_id); + +ALTER TABLE cost ADD CONSTRAINT fpk_visit_cost_currency FOREIGN KEY (currency_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE cost ADD CONSTRAINT fpk_visit_cost_period FOREIGN KEY (payer_plan_period_id) REFERENCES payer_plan_period (payer_plan_period_id); + +ALTER TABLE cost ADD CONSTRAINT fpk_drg_concept FOREIGN KEY (drg_concept_id) REFERENCES concept (concept_id); + +/************************ + +Standardized derived elements + +************************/ + + +ALTER TABLE cohort ADD CONSTRAINT fpk_cohort_definition FOREIGN KEY (cohort_definition_id) REFERENCES cohort_definition (cohort_definition_id); + + +ALTER TABLE cohort_attribute ADD CONSTRAINT fpk_ca_cohort_definition FOREIGN KEY (cohort_definition_id) REFERENCES cohort_definition (cohort_definition_id); + +ALTER TABLE cohort_attribute ADD CONSTRAINT fpk_ca_attribute_definition FOREIGN KEY (attribute_definition_id) REFERENCES attribute_definition (attribute_definition_id); + +ALTER TABLE cohort_attribute ADD CONSTRAINT fpk_ca_value FOREIGN KEY (value_as_concept_id) REFERENCES concept (concept_id); + + +ALTER TABLE drug_era ADD CONSTRAINT fpk_drug_era_person FOREIGN KEY (person_id) REFERENCES person (person_id); + +ALTER TABLE drug_era ADD CONSTRAINT fpk_drug_era_concept FOREIGN KEY (drug_concept_id) REFERENCES concept (concept_id); + + +ALTER TABLE dose_era ADD CONSTRAINT fpk_dose_era_person FOREIGN KEY (person_id) REFERENCES person (person_id); + +ALTER TABLE dose_era ADD CONSTRAINT fpk_dose_era_concept FOREIGN KEY (drug_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE dose_era ADD CONSTRAINT fpk_dose_era_unit_concept FOREIGN KEY (unit_concept_id) REFERENCES concept (concept_id); + + +ALTER TABLE condition_era ADD CONSTRAINT fpk_condition_era_person FOREIGN KEY (person_id) REFERENCES person (person_id); + +ALTER TABLE condition_era ADD CONSTRAINT fpk_condition_era_concept FOREIGN KEY (condition_concept_id) REFERENCES concept (concept_id); + + +/************************ +************************* +************************* +************************* + +Unique constraints + +************************* +************************* +************************* +************************/ + +ALTER TABLE concept_synonym ADD CONSTRAINT uq_concept_synonym UNIQUE (concept_id, concept_synonym_name, language_concept_id); diff --git a/DDLGeneratr/output/postgresql/OMOP CDM postgresql indexes.txt b/DDLGeneratr/output/postgresql/OMOP CDM postgresql indexes.txt new file mode 100644 index 0000000..9d27e1a --- /dev/null +++ b/DDLGeneratr/output/postgresql/OMOP CDM postgresql indexes.txt @@ -0,0 +1,371 @@ +/********************************************************************************* +# 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. +********************************************************************************/ + +/************************ + + ####### # # ####### ###### ##### ###### # # ####### ##### ### + # # ## ## # # # # # # # # ## ## # # # # # # # # ##### ###### # # ###### #### + # # # # # # # # # # # # # # # # # # # # # # ## # # # # # # # # + # # # # # # # ###### # # # # # # # # ###### ##### # # # # # # ##### ## ##### #### + # # # # # # # # # # # # # # # ### # # # # # # # # ## # # + # # # # # # # # # # # # # # # # # ### # # # # ## # # # # # # # # + ####### # # ####### # ##### ###### # # ## ##### ### ##### ### # # ##### ###### # # ###### #### + + +postgresql script to create the required indexes within OMOP common data model, version 5.3 + +last revised: 14-November-2017 + +author: Patrick Ryan, Clair Blacketer + +description: These primary keys and indices are considered a minimal requirement to ensure adequate performance of analyses. + +*************************/ + + +/************************ +************************* +************************* +************************* + +Primary key constraints + +************************* +************************* +************************* +************************/ + + + +/************************ + +Standardized vocabulary + +************************/ + + + +ALTER TABLE concept ADD CONSTRAINT xpk_concept PRIMARY KEY (concept_id); + +ALTER TABLE vocabulary ADD CONSTRAINT xpk_vocabulary PRIMARY KEY (vocabulary_id); + +ALTER TABLE domain ADD CONSTRAINT xpk_domain PRIMARY KEY (domain_id); + +ALTER TABLE concept_class ADD CONSTRAINT xpk_concept_class PRIMARY KEY (concept_class_id); + +ALTER TABLE concept_relationship ADD CONSTRAINT xpk_concept_relationship PRIMARY KEY (concept_id_1,concept_id_2,relationship_id); + +ALTER TABLE relationship ADD CONSTRAINT xpk_relationship PRIMARY KEY (relationship_id); + +ALTER TABLE concept_ancestor ADD CONSTRAINT xpk_concept_ancestor PRIMARY KEY (ancestor_concept_id,descendant_concept_id); + +ALTER TABLE source_to_concept_map ADD CONSTRAINT xpk_source_to_concept_map PRIMARY KEY (source_vocabulary_id,target_concept_id,source_code,valid_end_date); + +ALTER TABLE drug_strength ADD CONSTRAINT xpk_drug_strength PRIMARY KEY (drug_concept_id, ingredient_concept_id); + +ALTER TABLE cohort_definition ADD CONSTRAINT xpk_cohort_definition PRIMARY KEY (cohort_definition_id); + +ALTER TABLE attribute_definition ADD CONSTRAINT xpk_attribute_definition PRIMARY KEY (attribute_definition_id); + + +/************************** + +Standardized meta-data + +***************************/ + + + +/************************ + +Standardized clinical data + +************************/ + + +/**PRIMARY KEY NONCLUSTERED constraints**/ + +ALTER TABLE person ADD CONSTRAINT xpk_person PRIMARY KEY ( person_id ) ; + +ALTER TABLE observation_period ADD CONSTRAINT xpk_observation_period PRIMARY KEY ( observation_period_id ) ; + +ALTER TABLE specimen ADD CONSTRAINT xpk_specimen PRIMARY KEY ( specimen_id ) ; + +ALTER TABLE death ADD CONSTRAINT xpk_death PRIMARY KEY ( person_id ) ; + +ALTER TABLE visit_occurrence ADD CONSTRAINT xpk_visit_occurrence PRIMARY KEY ( visit_occurrence_id ) ; + +ALTER TABLE visit_detail ADD CONSTRAINT xpk_visit_detail PRIMARY KEY ( visit_detail_id ) ; + +ALTER TABLE procedure_occurrence ADD CONSTRAINT xpk_procedure_occurrence PRIMARY KEY ( procedure_occurrence_id ) ; + +ALTER TABLE drug_exposure ADD CONSTRAINT xpk_drug_exposure PRIMARY KEY ( drug_exposure_id ) ; + +ALTER TABLE device_exposure ADD CONSTRAINT xpk_device_exposure PRIMARY KEY ( device_exposure_id ) ; + +ALTER TABLE condition_occurrence ADD CONSTRAINT xpk_condition_occurrence PRIMARY KEY ( condition_occurrence_id ) ; + +ALTER TABLE measurement ADD CONSTRAINT xpk_measurement PRIMARY KEY ( measurement_id ) ; + +ALTER TABLE note ADD CONSTRAINT xpk_note PRIMARY KEY ( note_id ) ; + +ALTER TABLE note_nlp ADD CONSTRAINT xpk_note_nlp PRIMARY KEY ( note_nlp_id ) ; + +ALTER TABLE observation ADD CONSTRAINT xpk_observation PRIMARY KEY ( observation_id ) ; + + + + +/************************ + +Standardized health system data + +************************/ + + +ALTER TABLE location ADD CONSTRAINT xpk_location PRIMARY KEY ( location_id ) ; + +ALTER TABLE care_site ADD CONSTRAINT xpk_care_site PRIMARY KEY ( care_site_id ) ; + +ALTER TABLE provider ADD CONSTRAINT xpk_provider PRIMARY KEY ( provider_id ) ; + + + +/************************ + +Standardized health economics + +************************/ + + +ALTER TABLE payer_plan_period ADD CONSTRAINT xpk_payer_plan_period PRIMARY KEY ( payer_plan_period_id ) ; + +ALTER TABLE cost ADD CONSTRAINT xpk_visit_cost PRIMARY KEY ( cost_id ) ; + + +/************************ + +Standardized derived elements + +************************/ + +ALTER TABLE cohort ADD CONSTRAINT xpk_cohort PRIMARY KEY ( cohort_definition_id, subject_id, cohort_start_date, cohort_end_date ) ; + +ALTER TABLE cohort_attribute ADD CONSTRAINT xpk_cohort_attribute PRIMARY KEY ( 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 ( drug_era_id ) ; + +ALTER TABLE dose_era ADD CONSTRAINT xpk_dose_era PRIMARY KEY ( dose_era_id ) ; + +ALTER TABLE condition_era ADD CONSTRAINT xpk_condition_era PRIMARY KEY ( condition_era_id ) ; + + +/************************ +************************* +************************* +************************* + +Indices + +************************* +************************* +************************* +************************/ + +/************************ + +Standardized vocabulary + +************************/ + +CREATE UNIQUE INDEX idx_concept_concept_id ON concept (concept_id ASC); +CLUSTER concept USING idx_concept_concept_id ; +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 INDEX idx_vocabulary_vocabulary_id ON vocabulary (vocabulary_id ASC); +CLUSTER vocabulary USING idx_vocabulary_vocabulary_id ; + +CREATE UNIQUE INDEX idx_domain_domain_id ON domain (domain_id ASC); +CLUSTER domain USING idx_domain_domain_id ; + +CREATE UNIQUE INDEX idx_concept_class_class_id ON concept_class (concept_class_id ASC); +CLUSTER concept_class USING idx_concept_class_class_id ; + +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 INDEX idx_relationship_rel_id ON relationship (relationship_id ASC); +CLUSTER relationship USING idx_relationship_rel_id ; + +CREATE INDEX idx_concept_synonym_id ON concept_synonym (concept_id ASC); +CLUSTER concept_synonym USING idx_concept_synonym_id ; + +CREATE INDEX idx_concept_ancestor_id_1 ON concept_ancestor (ancestor_concept_id ASC); +CLUSTER concept_ancestor USING idx_concept_ancestor_id_1 ; +CREATE INDEX idx_concept_ancestor_id_2 ON concept_ancestor (descendant_concept_id ASC); + +CREATE INDEX idx_source_to_concept_map_id_3 ON source_to_concept_map (target_concept_id ASC); +CLUSTER source_to_concept_map USING idx_source_to_concept_map_id_3 ; +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 INDEX idx_drug_strength_id_1 ON drug_strength (drug_concept_id ASC); +CLUSTER drug_strength USING idx_drug_strength_id_1 ; +CREATE INDEX idx_drug_strength_id_2 ON drug_strength (ingredient_concept_id ASC); + +CREATE INDEX idx_cohort_definition_id ON cohort_definition (cohort_definition_id ASC); +CLUSTER cohort_definition USING idx_cohort_definition_id ; + +CREATE INDEX idx_attribute_definition_id ON attribute_definition (attribute_definition_id ASC); +CLUSTER attribute_definition USING idx_attribute_definition_id ; + + +/************************** + +Standardized meta-data + +***************************/ + + + + + +/************************ + +Standardized clinical data + +************************/ + +CREATE UNIQUE INDEX idx_person_id ON person (person_id ASC); +CLUSTER person USING idx_person_id ; + +CREATE INDEX idx_observation_period_id ON observation_period (person_id ASC); +CLUSTER observation_period USING idx_observation_period_id ; + +CREATE INDEX idx_specimen_person_id ON specimen (person_id ASC); +CLUSTER specimen USING idx_specimen_person_id ; +CREATE INDEX idx_specimen_concept_id ON specimen (specimen_concept_id ASC); + +CREATE INDEX idx_death_person_id ON death (person_id ASC); +CLUSTER death USING idx_death_person_id ; + +CREATE INDEX idx_visit_person_id ON visit_occurrence (person_id ASC); +CLUSTER visit_occurrence USING idx_visit_person_id ; +CREATE INDEX idx_visit_concept_id ON visit_occurrence (visit_concept_id ASC); + +CREATE INDEX idx_visit_detail_person_id ON visit_detail (person_id ASC); +CLUSTER visit_detail USING idx_visit_detail_person_id ; +CREATE INDEX idx_visit_detail_concept_id ON visit_detail (visit_detail_concept_id ASC); + +CREATE INDEX idx_procedure_person_id ON procedure_occurrence (person_id ASC); +CLUSTER procedure_occurrence USING idx_procedure_person_id ; +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 INDEX idx_drug_person_id ON drug_exposure (person_id ASC); +CLUSTER drug_exposure USING idx_drug_person_id ; +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 INDEX idx_device_person_id ON device_exposure (person_id ASC); +CLUSTER device_exposure USING idx_device_person_id ; +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 INDEX idx_condition_person_id ON condition_occurrence (person_id ASC); +CLUSTER condition_occurrence USING idx_condition_person_id ; +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 INDEX idx_measurement_person_id ON measurement (person_id ASC); +CLUSTER measurement USING idx_measurement_person_id ; +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 INDEX idx_note_person_id ON note (person_id ASC); +CLUSTER note USING idx_note_person_id ; +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 INDEX idx_note_nlp_note_id ON note_nlp (note_id ASC); +CLUSTER note_nlp USING idx_note_nlp_note_id ; +CREATE INDEX idx_note_nlp_concept_id ON note_nlp (note_nlp_concept_id ASC); + +CREATE INDEX idx_observation_person_id ON observation (person_id ASC); +CLUSTER observation USING idx_observation_person_id ; +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 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); + + + +/************************ + +Standardized health system data + +************************/ + + + + + +/************************ + +Standardized health economics + +************************/ + +CREATE INDEX idx_period_person_id ON payer_plan_period (person_id ASC); +CLUSTER payer_plan_period USING idx_period_person_id ; + + + + + +/************************ + +Standardized derived elements + +************************/ + + +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 INDEX idx_drug_era_person_id ON drug_era (person_id ASC); +CLUSTER drug_era USING idx_drug_era_person_id ; +CREATE INDEX idx_drug_era_concept_id ON drug_era (drug_concept_id ASC); + +CREATE INDEX idx_dose_era_person_id ON dose_era (person_id ASC); +CLUSTER dose_era USING idx_dose_era_person_id ; +CREATE INDEX idx_dose_era_concept_id ON dose_era (drug_concept_id ASC); + +CREATE INDEX idx_condition_era_person_id ON condition_era (person_id ASC); +CLUSTER condition_era USING idx_condition_era_person_id ; +CREATE INDEX idx_condition_era_concept_id ON condition_era (condition_concept_id ASC); + diff --git a/DDLGeneratr/output/sql server/OMOP CDM sql server constraints.txt b/DDLGeneratr/output/sql server/OMOP CDM sql server constraints.txt new file mode 100644 index 0000000..470bd94 --- /dev/null +++ b/DDLGeneratr/output/sql server/OMOP CDM sql server constraints.txt @@ -0,0 +1,421 @@ +/********************************************************************************* +# 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. +********************************************************************************/ + +/************************ + + ####### # # ####### ###### ##### ###### # # ####### ##### ##### + # # ## ## # # # # # # # # ## ## # # # # # # # #### # # #### ##### ##### ## # # # ##### #### + # # # # # # # # # # # # # # # # # # # # # # # # ## # # # # # # # # ## # # # + # # # # # # # ###### # # # # # # # # ###### ##### # # # # # # #### # # # # # # # # # # #### + # # # # # # # # # # # # # # # ### # # # # # # # # # ##### ###### # # # # # # + # # # # # # # # # # # # # # # # # ### # # # # # # # ## # # # # # # # # # ## # # # + ####### # # ####### # ##### ###### # # ## ##### ### ##### ##### #### # # #### # # # # # # # # # #### + + +sql server script to create foreign key constraints within OMOP common data model, version 5.3.0 + +last revised: 15-November-2017 + +author: Patrick Ryan, Clair Blacketer + + +*************************/ + + +/************************ +************************* +************************* +************************* + +Foreign key constraints + +************************* +************************* +************************* +************************/ + + +/************************ + +Standardized vocabulary + +************************/ + + +ALTER TABLE concept ADD CONSTRAINT fpk_concept_domain FOREIGN KEY (domain_id) REFERENCES domain (domain_id); + +ALTER TABLE concept ADD CONSTRAINT fpk_concept_class FOREIGN KEY (concept_class_id) REFERENCES concept_class (concept_class_id); + +ALTER TABLE concept ADD CONSTRAINT fpk_concept_vocabulary FOREIGN KEY (vocabulary_id) REFERENCES vocabulary (vocabulary_id); + +ALTER TABLE vocabulary ADD CONSTRAINT fpk_vocabulary_concept FOREIGN KEY (vocabulary_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE domain ADD CONSTRAINT fpk_domain_concept FOREIGN KEY (domain_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE concept_class ADD CONSTRAINT fpk_concept_class_concept FOREIGN KEY (concept_class_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE concept_relationship ADD CONSTRAINT fpk_concept_relationship_c_1 FOREIGN KEY (concept_id_1) REFERENCES concept (concept_id); + +ALTER TABLE concept_relationship ADD CONSTRAINT fpk_concept_relationship_c_2 FOREIGN KEY (concept_id_2) REFERENCES concept (concept_id); + +ALTER TABLE concept_relationship ADD CONSTRAINT fpk_concept_relationship_id FOREIGN KEY (relationship_id) REFERENCES relationship (relationship_id); + +ALTER TABLE relationship ADD CONSTRAINT fpk_relationship_concept FOREIGN KEY (relationship_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE relationship ADD CONSTRAINT fpk_relationship_reverse FOREIGN KEY (reverse_relationship_id) REFERENCES relationship (relationship_id); + +ALTER TABLE concept_synonym ADD CONSTRAINT fpk_concept_synonym_concept FOREIGN KEY (concept_id) REFERENCES concept (concept_id); + +ALTER TABLE concept_ancestor ADD CONSTRAINT fpk_concept_ancestor_concept_1 FOREIGN KEY (ancestor_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE concept_ancestor ADD CONSTRAINT fpk_concept_ancestor_concept_2 FOREIGN KEY (descendant_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE source_to_concept_map ADD CONSTRAINT fpk_source_to_concept_map_v_1 FOREIGN KEY (source_vocabulary_id) REFERENCES vocabulary (vocabulary_id); + +ALTER TABLE source_to_concept_map ADD CONSTRAINT fpk_source_to_concept_map_v_2 FOREIGN KEY (target_vocabulary_id) REFERENCES vocabulary (vocabulary_id); + +ALTER TABLE source_to_concept_map ADD CONSTRAINT fpk_source_to_concept_map_c_1 FOREIGN KEY (target_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE drug_strength ADD CONSTRAINT fpk_drug_strength_concept_1 FOREIGN KEY (drug_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE drug_strength ADD CONSTRAINT fpk_drug_strength_concept_2 FOREIGN KEY (ingredient_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE drug_strength ADD CONSTRAINT fpk_drug_strength_unit_1 FOREIGN KEY (amount_unit_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE drug_strength ADD CONSTRAINT fpk_drug_strength_unit_2 FOREIGN KEY (numerator_unit_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE drug_strength ADD CONSTRAINT fpk_drug_strength_unit_3 FOREIGN KEY (denominator_unit_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE cohort_definition ADD CONSTRAINT fpk_cohort_definition_concept FOREIGN KEY (definition_type_concept_id) REFERENCES concept (concept_id); + + +/************************** + +Standardized meta-data + +***************************/ + + + + + +/************************ + +Standardized clinical data + +************************/ + +ALTER TABLE person ADD CONSTRAINT fpk_person_gender_concept FOREIGN KEY (gender_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE person ADD CONSTRAINT fpk_person_race_concept FOREIGN KEY (race_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE person ADD CONSTRAINT fpk_person_ethnicity_concept FOREIGN KEY (ethnicity_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE person ADD CONSTRAINT fpk_person_gender_concept_s FOREIGN KEY (gender_source_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE person ADD CONSTRAINT fpk_person_race_concept_s FOREIGN KEY (race_source_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE person ADD CONSTRAINT fpk_person_ethnicity_concept_s FOREIGN KEY (ethnicity_source_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE person ADD CONSTRAINT fpk_person_location FOREIGN KEY (location_id) REFERENCES location (location_id); + +ALTER TABLE person ADD CONSTRAINT fpk_person_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id); + +ALTER TABLE person ADD CONSTRAINT fpk_person_care_site FOREIGN KEY (care_site_id) REFERENCES care_site (care_site_id); + + +ALTER TABLE observation_period ADD CONSTRAINT fpk_observation_period_person FOREIGN KEY (person_id) REFERENCES person (person_id); + +ALTER TABLE observation_period ADD CONSTRAINT fpk_observation_period_concept FOREIGN KEY (period_type_concept_id) REFERENCES concept (concept_id); + + +ALTER TABLE specimen ADD CONSTRAINT fpk_specimen_person FOREIGN KEY (person_id) REFERENCES person (person_id); + +ALTER TABLE specimen ADD CONSTRAINT fpk_specimen_concept FOREIGN KEY (specimen_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE specimen ADD CONSTRAINT fpk_specimen_type_concept FOREIGN KEY (specimen_type_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE specimen ADD CONSTRAINT fpk_specimen_unit_concept FOREIGN KEY (unit_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE specimen ADD CONSTRAINT fpk_specimen_site_concept FOREIGN KEY (anatomic_site_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE specimen ADD CONSTRAINT fpk_specimen_status_concept FOREIGN KEY (disease_status_concept_id) REFERENCES concept (concept_id); + + +ALTER TABLE death ADD CONSTRAINT fpk_death_person FOREIGN KEY (person_id) REFERENCES person (person_id); + +ALTER TABLE death ADD CONSTRAINT fpk_death_type_concept FOREIGN KEY (death_type_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE death ADD CONSTRAINT fpk_death_cause_concept FOREIGN KEY (cause_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE death ADD CONSTRAINT fpk_death_cause_concept_s FOREIGN KEY (cause_source_concept_id) REFERENCES concept (concept_id); + + +ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_person FOREIGN KEY (person_id) REFERENCES person (person_id); + +ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_concept FOREIGN KEY (visit_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_type_concept FOREIGN KEY (visit_type_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id); + +ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_care_site FOREIGN KEY (care_site_id) REFERENCES care_site (care_site_id); + +ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_concept_s FOREIGN KEY (visit_source_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_admitting_s FOREIGN KEY (admitting_source_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_discharge FOREIGN KEY (discharge_to_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_preceding FOREIGN KEY (preceding_visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id); + + +ALTER TABLE visit_detail ADD CONSTRAINT fpk_v_detail_person FOREIGN KEY (person_id) REFERENCES person (person_id); + +ALTER TABLE visit_detail ADD CONSTRAINT fpk_v_detail_concept FOREIGN KEY (visit_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE visit_detail ADD CONSTRAINT fpk_v_detail_type_concept FOREIGN KEY (visit_type_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE visit_detail ADD CONSTRAINT fpk_v_detail_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id); + +ALTER TABLE visit_detail ADD CONSTRAINT fpk_v_detail_care_site FOREIGN KEY (care_site_id) REFERENCES care_site (care_site_id); + +ALTER TABLE visit_detail ADD CONSTRAINT fpk_v_detail_concept_s FOREIGN KEY (visit_source_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE visit_detail ADD CONSTRAINT fpk_v_detail_admitting_s FOREIGN KEY (admitting_source_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE visit_detail ADD CONSTRAINT fpk_v_detail_discharge FOREIGN KEY (discharge_to_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE visit_detail ADD CONSTRAINT fpk_v_detail_preceding FOREIGN KEY (preceding_visit_detail_id) REFERENCES visit_detail (visit_detail_id); + +ALTER TABLE visit_detail ADD CONSTRAINT fpk_v_detail_parent FOREIGN KEY (visit_detail_parent_id) REFERENCES visit_detail (visit_detail_id); + +ALTER TABLE visit_detail ADD CONSTRAINT fpd_v_detail_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id); + + +ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_person FOREIGN KEY (person_id) REFERENCES person (person_id); + +ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_concept FOREIGN KEY (procedure_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_type_concept FOREIGN KEY (procedure_type_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_modifier FOREIGN KEY (modifier_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id); + +ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id); + +ALTER TABLE procedure_occurrence ADD CONSTRAINT fpk_procedure_concept_s FOREIGN KEY (procedure_source_concept_id) REFERENCES concept (concept_id); + + +ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_person FOREIGN KEY (person_id) REFERENCES person (person_id); + +ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_concept FOREIGN KEY (drug_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_type_concept FOREIGN KEY (drug_type_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_route_concept FOREIGN KEY (route_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id); + +ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id); + +ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_concept_s FOREIGN KEY (drug_source_concept_id) REFERENCES concept (concept_id); + + +ALTER TABLE device_exposure ADD CONSTRAINT fpk_device_person FOREIGN KEY (person_id) REFERENCES person (person_id); + +ALTER TABLE device_exposure ADD CONSTRAINT fpk_device_concept FOREIGN KEY (device_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE device_exposure ADD CONSTRAINT fpk_device_type_concept FOREIGN KEY (device_type_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE device_exposure ADD CONSTRAINT fpk_device_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id); + +ALTER TABLE device_exposure ADD CONSTRAINT fpk_device_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id); + +ALTER TABLE device_exposure ADD CONSTRAINT fpk_device_concept_s FOREIGN KEY (device_source_concept_id) REFERENCES concept (concept_id); + + +ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_person FOREIGN KEY (person_id) REFERENCES person (person_id); + +ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_concept FOREIGN KEY (condition_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_type_concept FOREIGN KEY (condition_type_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id); + +ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id); + +ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_concept_s FOREIGN KEY (condition_source_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE condition_occurrence ADD CONSTRAINT fpk_condition_status_concept FOREIGN KEY (condition_status_concept_id) REFERENCES concept (concept_id); + + +ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_person FOREIGN KEY (person_id) REFERENCES person (person_id); + +ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_concept FOREIGN KEY (measurement_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_type_concept FOREIGN KEY (measurement_type_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_operator FOREIGN KEY (operator_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_value FOREIGN KEY (value_as_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_unit FOREIGN KEY (unit_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id); + +ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id); + +ALTER TABLE measurement ADD CONSTRAINT fpk_measurement_concept_s FOREIGN KEY (measurement_source_concept_id) REFERENCES concept (concept_id); + + +ALTER TABLE note ADD CONSTRAINT fpk_note_person FOREIGN KEY (person_id) REFERENCES person (person_id); + +ALTER TABLE note ADD CONSTRAINT fpk_note_type_concept FOREIGN KEY (note_type_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE note ADD CONSTRAINT fpk_note_class_concept FOREIGN KEY (note_class_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE note ADD CONSTRAINT fpk_note_encoding_concept FOREIGN KEY (encoding_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE note ADD CONSTRAINT fpk_language_concept FOREIGN KEY (language_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE note ADD CONSTRAINT fpk_note_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id); + +ALTER TABLE note ADD CONSTRAINT fpk_note_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id); + + +ALTER TABLE note_nlp ADD CONSTRAINT fpk_note_nlp_note FOREIGN KEY (note_id) REFERENCES note (note_id); + +ALTER TABLE note_nlp ADD CONSTRAINT fpk_note_nlp_section_concept FOREIGN KEY (section_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE note_nlp ADD CONSTRAINT fpk_note_nlp_concept FOREIGN KEY (note_nlp_concept_id) REFERENCES concept (concept_id); + + + +ALTER TABLE observation ADD CONSTRAINT fpk_observation_person FOREIGN KEY (person_id) REFERENCES person (person_id); + +ALTER TABLE observation ADD CONSTRAINT fpk_observation_concept FOREIGN KEY (observation_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE observation ADD CONSTRAINT fpk_observation_type_concept FOREIGN KEY (observation_type_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE observation ADD CONSTRAINT fpk_observation_value FOREIGN KEY (value_as_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE observation ADD CONSTRAINT fpk_observation_qualifier FOREIGN KEY (qualifier_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE observation ADD CONSTRAINT fpk_observation_unit FOREIGN KEY (unit_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE observation ADD CONSTRAINT fpk_observation_provider FOREIGN KEY (provider_id) REFERENCES provider (provider_id); + +ALTER TABLE observation ADD CONSTRAINT fpk_observation_visit FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id); + +ALTER TABLE observation ADD CONSTRAINT fpk_observation_concept_s FOREIGN KEY (observation_source_concept_id) REFERENCES concept (concept_id); + + +ALTER TABLE fact_relationship ADD CONSTRAINT fpk_fact_domain_1 FOREIGN KEY (domain_concept_id_1) REFERENCES concept (concept_id); + +ALTER TABLE fact_relationship ADD CONSTRAINT fpk_fact_domain_2 FOREIGN KEY (domain_concept_id_2) REFERENCES concept (concept_id); + +ALTER TABLE fact_relationship ADD CONSTRAINT fpk_fact_relationship FOREIGN KEY (relationship_concept_id) REFERENCES concept (concept_id); + + + +/************************ + +Standardized health system data + +************************/ + +ALTER TABLE care_site ADD CONSTRAINT fpk_care_site_location FOREIGN KEY (location_id) REFERENCES location (location_id); + +ALTER TABLE care_site ADD CONSTRAINT fpk_care_site_place FOREIGN KEY (place_of_service_concept_id) REFERENCES concept (concept_id); + + +ALTER TABLE provider ADD CONSTRAINT fpk_provider_specialty FOREIGN KEY (specialty_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE provider ADD CONSTRAINT fpk_provider_care_site FOREIGN KEY (care_site_id) REFERENCES care_site (care_site_id); + +ALTER TABLE provider ADD CONSTRAINT fpk_provider_gender FOREIGN KEY (gender_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE provider ADD CONSTRAINT fpk_provider_specialty_s FOREIGN KEY (specialty_source_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE provider ADD CONSTRAINT fpk_provider_gender_s FOREIGN KEY (gender_source_concept_id) REFERENCES concept (concept_id); + + + + +/************************ + +Standardized health economics + +************************/ + +ALTER TABLE payer_plan_period ADD CONSTRAINT fpk_payer_plan_period FOREIGN KEY (person_id) REFERENCES person (person_id); + +ALTER TABLE cost ADD CONSTRAINT fpk_visit_cost_currency FOREIGN KEY (currency_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE cost ADD CONSTRAINT fpk_visit_cost_period FOREIGN KEY (payer_plan_period_id) REFERENCES payer_plan_period (payer_plan_period_id); + +ALTER TABLE cost ADD CONSTRAINT fpk_drg_concept FOREIGN KEY (drg_concept_id) REFERENCES concept (concept_id); + +/************************ + +Standardized derived elements + +************************/ + + +ALTER TABLE cohort ADD CONSTRAINT fpk_cohort_definition FOREIGN KEY (cohort_definition_id) REFERENCES cohort_definition (cohort_definition_id); + + +ALTER TABLE cohort_attribute ADD CONSTRAINT fpk_ca_cohort_definition FOREIGN KEY (cohort_definition_id) REFERENCES cohort_definition (cohort_definition_id); + +ALTER TABLE cohort_attribute ADD CONSTRAINT fpk_ca_attribute_definition FOREIGN KEY (attribute_definition_id) REFERENCES attribute_definition (attribute_definition_id); + +ALTER TABLE cohort_attribute ADD CONSTRAINT fpk_ca_value FOREIGN KEY (value_as_concept_id) REFERENCES concept (concept_id); + + +ALTER TABLE drug_era ADD CONSTRAINT fpk_drug_era_person FOREIGN KEY (person_id) REFERENCES person (person_id); + +ALTER TABLE drug_era ADD CONSTRAINT fpk_drug_era_concept FOREIGN KEY (drug_concept_id) REFERENCES concept (concept_id); + + +ALTER TABLE dose_era ADD CONSTRAINT fpk_dose_era_person FOREIGN KEY (person_id) REFERENCES person (person_id); + +ALTER TABLE dose_era ADD CONSTRAINT fpk_dose_era_concept FOREIGN KEY (drug_concept_id) REFERENCES concept (concept_id); + +ALTER TABLE dose_era ADD CONSTRAINT fpk_dose_era_unit_concept FOREIGN KEY (unit_concept_id) REFERENCES concept (concept_id); + + +ALTER TABLE condition_era ADD CONSTRAINT fpk_condition_era_person FOREIGN KEY (person_id) REFERENCES person (person_id); + +ALTER TABLE condition_era ADD CONSTRAINT fpk_condition_era_concept FOREIGN KEY (condition_concept_id) REFERENCES concept (concept_id); + + +/************************ +************************* +************************* +************************* + +Unique constraints + +************************* +************************* +************************* +************************/ + +ALTER TABLE concept_synonym ADD CONSTRAINT uq_concept_synonym UNIQUE (concept_id, concept_synonym_name, language_concept_id); diff --git a/DDLGeneratr/output/sql server/OMOP CDM sql server indexes.txt b/DDLGeneratr/output/sql server/OMOP CDM sql server indexes.txt new file mode 100644 index 0000000..8c4a798 --- /dev/null +++ b/DDLGeneratr/output/sql server/OMOP CDM sql server indexes.txt @@ -0,0 +1,342 @@ +/********************************************************************************* +# 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. +********************************************************************************/ + +/************************ + + ####### # # ####### ###### ##### ###### # # ####### ##### ### + # # ## ## # # # # # # # # ## ## # # # # # # # # ##### ###### # # ###### #### + # # # # # # # # # # # # # # # # # # # # # # ## # # # # # # # # + # # # # # # # ###### # # # # # # # # ###### ##### # # # # # # ##### ## ##### #### + # # # # # # # # # # # # # # # ### # # # # # # # # ## # # + # # # # # # # # # # # # # # # # # ### # # # # ## # # # # # # # # + ####### # # ####### # ##### ###### # # ## ##### ### ##### ### # # ##### ###### # # ###### #### + + +sql server script to create the required indexes within OMOP common data model, version 5.3 + +last revised: 14-November-2017 + +author: Patrick Ryan, Clair Blacketer + +description: These primary keys and indices are considered a minimal requirement to ensure adequate performance of analyses. + +*************************/ + + +/************************ +************************* +************************* +************************* + +Primary key constraints + +************************* +************************* +************************* +************************/ + + + +/************************ + +Standardized vocabulary + +************************/ + + + +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); + + +/************************** + +Standardized meta-data + +***************************/ + + + +/************************ + +Standardized clinical data + +************************/ + + +/**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 ) ; + + + + +/************************ + +Standardized health system data + +************************/ + + +ALTER TABLE location ADD CONSTRAINT xpk_location PRIMARY KEY NONCLUSTERED ( location_id ) ; + +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 ) ; + + + +/************************ + +Standardized health economics + +************************/ + + +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 ) ; + + +/************************ + +Standardized derived elements + +************************/ + +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 ) ; + + +/************************ +************************* +************************* +************************* + +Indices + +************************* +************************* +************************* +************************/ + +/************************ + +Standardized vocabulary + +************************/ + +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); + + +/************************** + +Standardized meta-data + +***************************/ + + + + + +/************************ + +Standardized clinical data + +************************/ + +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 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); + + + +/************************ + +Standardized health system data + +************************/ + + + + + +/************************ + +Standardized health economics + +************************/ + +CREATE CLUSTERED INDEX idx_period_person_id ON payer_plan_period (person_id ASC); + + + + + +/************************ + +Standardized derived elements + +************************/ + + +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); + diff --git a/DDLGeneratr/reports/OMOP_CDM_PDF.Rmd b/DDLGeneratr/reports/OMOP_CDM_PDF.Rmd index 0061d2d..f4ae247 100644 --- a/DDLGeneratr/reports/OMOP_CDM_PDF.Rmd +++ b/DDLGeneratr/reports/OMOP_CDM_PDF.Rmd @@ -2,6 +2,8 @@ title: "OMOP Common Data Model Specifications" author: "Christian Reich, Patrick Ryan, Rimma Belenkaya, Karthik Natarajan and Clair Blacketer" date: "`r Sys.Date()`" +params: + mdFilesLocation:"../../Documentation/CommonDataModel_Wiki_Files" output: pdf_document: number_sections: yes @@ -10,198 +12,197 @@ linkcolor: blue --- # License - -```{r child = '../CommonDataModel_Wiki_Files/License.md'} +```{r child = paste0(params$mdFilesLocation,'/License.md')} ``` # Background -```{r child = '../CommonDataModel_Wiki_Files/Background/Background.md'} +```{r child = '@mdFilesLocation/Background/Background.md'} ``` ## The Role of the Common Data Model -```{r child = '../CommonDataModel_Wiki_Files/Background/The-Role-of-the-Common-Data-Model.md'} +```{r child = '@mdFilesLocation/Background/The-Role-of-the-Common-Data-Model.md'} ``` ## Design Principles -```{r child = '../CommonDataModel_Wiki_Files/Background/Design-Principles.md'} +```{r child = '@mdFilesLocation/Background/Design-Principles.md'} ``` ## Data Model Conventions -```{r child = '../CommonDataModel_Wiki_Files/Background/Data-Model-Conventions.md'} +```{r child = '@mdFilesLocation/Background/Data-Model-Conventions.md'} ``` # Glossary of Terms -```{r child = '../CommonDataModel_Wiki_Files/Glossary-of-Terms.md'} +```{r child = '@mdFilesLocation/Glossary-of-Terms.md'} ``` # Standardized Vocabularies -```{r child = '../CommonDataModel_Wiki_Files/StandardizedVocabularies/Standardized-Vocabularies.md'} +```{r child = '@mdFilesLocation/StandardizedVocabularies/Standardized-Vocabularies.md'} ``` ## CONCEPT -```{r child = '../CommonDataModel_Wiki_Files/StandardizedVocabularies/CONCEPT.md'} +```{r child = '@mdFilesLocation/StandardizedVocabularies/CONCEPT.md'} ``` ## VOCABULARY -```{r child = '../CommonDataModel_Wiki_Files/StandardizedVocabularies/VOCABULARY.md'} +```{r child = '@mdFilesLocation/StandardizedVocabularies/VOCABULARY.md'} ``` ## DOMAIN -```{r child = '../CommonDataModel_Wiki_Files/StandardizedVocabularies/DOMAIN.md'} +```{r child = '@mdFilesLocation/StandardizedVocabularies/DOMAIN.md'} ``` ## CONCEPT_CLASS -```{r child = '../CommonDataModel_Wiki_Files/StandardizedVocabularies/CONCEPT_CLASS.md'} +```{r child = '@mdFilesLocation/StandardizedVocabularies/CONCEPT_CLASS.md'} ``` ## CONCEPT_RELATIONSHIP -```{r child = '../CommonDataModel_Wiki_Files/StandardizedVocabularies/CONCEPT_RELATIONSHIP.md'} +```{r child = '@mdFilesLocation/StandardizedVocabularies/CONCEPT_RELATIONSHIP.md'} ``` ## RELATIONSHIP -```{r child = '../CommonDataModel_Wiki_Files/StandardizedVocabularies/RELATIONSHIP.md'} +```{r child = '@mdFilesLocation/StandardizedVocabularies/RELATIONSHIP.md'} ``` ## CONCEPT_SYNONYM -```{r child = '../CommonDataModel_Wiki_Files/StandardizedVocabularies/CONCEPT_SYNONYM.md'} +```{r child = '@mdFilesLocation/StandardizedVocabularies/CONCEPT_SYNONYM.md'} ``` ## CONCEPT_ANCESTOR -```{r child = '../CommonDataModel_Wiki_Files/StandardizedVocabularies/CONCEPT_ANCESTOR.md'} +```{r child = '@mdFilesLocation/StandardizedVocabularies/CONCEPT_ANCESTOR.md'} ``` ## SOURCE_TO_CONCEPT_MAP -```{r child = '../CommonDataModel_Wiki_Files/StandardizedVocabularies/SOURCE_TO_CONCEPT_MAP.md'} +```{r child = '@mdFilesLocation/StandardizedVocabularies/SOURCE_TO_CONCEPT_MAP.md'} ``` ## DRUG_STRENGTH -```{r child = '../CommonDataModel_Wiki_Files/StandardizedVocabularies/DRUG_STRENGTH.md'} +```{r child = '@mdFilesLocation/StandardizedVocabularies/DRUG_STRENGTH.md'} ``` ## COHORT_DEFINITION -```{r child = '../CommonDataModel_Wiki_Files/StandardizedVocabularies/COHORT_DEFINITION.md'} +```{r child = '@mdFilesLocation/StandardizedVocabularies/COHORT_DEFINITION.md'} ``` ## ATTRIBUTE_DEFINITION -```{r child = '../CommonDataModel_Wiki_Files/StandardizedVocabularies/ATTRIBUTE_DEFINITION.md'} +```{r child = '@mdFilesLocation/StandardizedVocabularies/ATTRIBUTE_DEFINITION.md'} ``` # Standardized Metadata -```{r child = '../CommonDataModel_Wiki_Files/StandardizedMetadata/Standardized-Metadata.md'} +```{r child = '@mdFilesLocation/StandardizedMetadata/Standardized-Metadata.md'} ``` ## CDM_SOURCE -```{r child = '../CommonDataModel_Wiki_Files/StandardizedMetadata/CDM_SOURCE.md'} +```{r child = '@mdFilesLocation/StandardizedMetadata/CDM_SOURCE.md'} ``` # Standardized Clinical Data Tables -```{r child = '../CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/Standardized-clinical-Data-Tables.md'} +```{r child = '@mdFilesLocation/StandardizedclinicalDataTables/Standardized-clinical-Data-Tables.md'} ``` ## PERSON -```{r child = '../CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/PERSON.md'} +```{r child = '@mdFilesLocation/StandardizedclinicalDataTables/PERSON.md'} ``` ## OBSERVATION_PERIOD -```{r child = '../CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/OBSERVATION_PERIOD.md'} +```{r child = '@mdFilesLocation/StandardizedclinicalDataTables/OBSERVATION_PERIOD.md'} ``` ## SPECIMEN -```{r child = '../CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/SPECIMEN.md'} +```{r child = '@mdFilesLocation/StandardizedclinicalDataTables/SPECIMEN.md'} ``` ## DEATH -```{r child = '../CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/DEATH.md'} +```{r child = '@mdFilesLocation/StandardizedclinicalDataTables/DEATH.md'} ``` ## VISIT_OCCURRENCE -```{r child = '../CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/VISIT_OCCURRENCE.md'} +```{r child = '@mdFilesLocation/StandardizedclinicalDataTables/VISIT_OCCURRENCE.md'} ``` ## PROCEDURE_OCCURRENCE -```{r child = '../CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/PROCEDURE_OCCURRENCE.md'} +```{r child = '@mdFilesLocation/StandardizedclinicalDataTables/PROCEDURE_OCCURRENCE.md'} ``` ## DRUG_EXPOSURE -```{r child = '../CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/DRUG_EXPOSURE.md'} +```{r child = '@mdFilesLocation/StandardizedclinicalDataTables/DRUG_EXPOSURE.md'} ``` ## DEVICE_EXPOSURE -```{r child = '../CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/DEVICE_EXPOSURE.md'} +```{r child = '@mdFilesLocation/StandardizedclinicalDataTables/DEVICE_EXPOSURE.md'} ``` ## CONDITION_OCCURRENCE -```{r child = '../CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/CONDITION_OCCURRENCE.md'} +```{r child = '@mdFilesLocation/StandardizedclinicalDataTables/CONDITION_OCCURRENCE.md'} ``` ## MEASUREMENT -```{r child = '../CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/MEASUREMENT.md'} +```{r child = '@mdFilesLocation/StandardizedclinicalDataTables/MEASUREMENT.md'} ``` ## NOTE -```{r child = '../CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/NOTE.md'} +```{r child = '@mdFilesLocation/StandardizedclinicalDataTables/NOTE.md'} ``` ## NOTE_NLP -```{r child = '../CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/NOTE_NLP.md'} +```{r child = '@mdFilesLocation/StandardizedclinicalDataTables/NOTE_NLP.md'} ``` ## OBSERVATION -```{r child = '../CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/OBSERVATION.md'} +```{r child = '@mdFilesLocation/StandardizedclinicalDataTables/OBSERVATION.md'} ``` ## FACT_RELATIONSHIP -```{r child = '../CommonDataModel_Wiki_Files/StandardizedclinicalDataTables/FACT_RELATIONSHIP.md'} +```{r child = '@mdFilesLocation/StandardizedclinicalDataTables/FACT_RELATIONSHIP.md'} ``` # Standardized Health System Data Tables -```{r child = '../CommonDataModel_Wiki_Files/StandardizedHealthSystemDataTables/Standardized-Health-System-Data-Tables.md'} +```{r child = '@mdFilesLocation/StandardizedHealthSystemDataTables/Standardized-Health-System-Data-Tables.md'} ``` ## LOCATION -```{r child = '../CommonDataModel_Wiki_Files/StandardizedHealthSystemDataTables/LOCATION.md'} +```{r child = '@mdFilesLocation/StandardizedHealthSystemDataTables/LOCATION.md'} ``` ## CARE_SITE -```{r child = '../CommonDataModel_Wiki_Files/StandardizedHealthSystemDataTables/CARE_SITE.md'} +```{r child = '@mdFilesLocation/StandardizedHealthSystemDataTables/CARE_SITE.md'} ``` ## PROVIDER -```{r child = '../CommonDataModel_Wiki_Files/StandardizedHealthSystemDataTables/PROVIDER.md'} +```{r child = '@mdFilesLocation/StandardizedHealthSystemDataTables/PROVIDER.md'} ``` # Standardized Health Economics Data Tables -```{r child = '../CommonDataModel_Wiki_Files/StandardizedHealthEconomicsDataTables/Standardized-Health-Economics-Data-Tables.md'} +```{r child = '@mdFilesLocation/StandardizedHealthEconomicsDataTables/Standardized-Health-Economics-Data-Tables.md'} ``` ## PAYER_PLAN_PERIOD -```{r child = '../CommonDataModel_Wiki_Files/StandardizedHealthEconomicsDataTables/PAYER_PLAN_PERIOD.md'} +```{r child = '@mdFilesLocation/StandardizedHealthEconomicsDataTables/PAYER_PLAN_PERIOD.md'} ``` ## COST -```{r child = '../CommonDataModel_Wiki_Files/StandardizedHealthEconomicsDataTables/COST.md'} +```{r child = '@mdFilesLocation/StandardizedHealthEconomicsDataTables/COST.md'} ``` # Standardized Derived Elements -```{r child = '../CommonDataModel_Wiki_Files/StandardizedDerivedElements/Standardized-Derived-Elements.md'} +```{r child = '@mdFilesLocation/StandardizedDerivedElements/Standardized-Derived-Elements.md'} ``` ## COHORT -```{r child = '../CommonDataModel_Wiki_Files/StandardizedDerivedElements/COHORT.md'} +```{r child = '@mdFilesLocation/StandardizedDerivedElements/COHORT.md'} ``` ## COHORT_ATTRIBUTE -```{r child = '../CommonDataModel_Wiki_Files/StandardizedDerivedElements/COHORT_ATTRIBUTE.md'} +```{r child = '@mdFilesLocation/StandardizedDerivedElements/COHORT_ATTRIBUTE.md'} ``` ## DRUG_ERA -```{r child = '../CommonDataModel_Wiki_Files/StandardizedDerivedElements/DRUG_ERA.md'} +```{r child = '@mdFilesLocation/StandardizedDerivedElements/DRUG_ERA.md'} ``` ## DOSE_ERA -```{r child = '../CommonDataModel_Wiki_Files/StandardizedDerivedElements/DOSE_ERA.md'} +```{r child = '@mdFilesLocation/StandardizedDerivedElements/DOSE_ERA.md'} ``` ## CONDITION_ERA -```{r child = '../CommonDataModel_Wiki_Files/StandardizedDerivedElements/CONDITION_ERA.md'} +```{r child = '@mdFilesLocation/StandardizedDerivedElements/CONDITION_ERA.md'} ``` diff --git a/DDLGeneratr/reports/OMOP_CDM_v5_3.pdf b/DDLGeneratr/reports/OMOP_CDM_v5_3.pdf index 9161315..6e9bfdc 100644 --- a/DDLGeneratr/reports/OMOP_CDM_v5_3.pdf +++ b/DDLGeneratr/reports/OMOP_CDM_v5_3.pdf @@ -304,12 +304,12 @@ endobj >> stream x[]SH}_cj`x]R@fRLDeT*oCHb@ǹ{PԠv ǃӗCdkcEDm@nkѹ} gby֟wty2{N&ߐIJe/h6c8LaaKӑmؘќE\q6 舟$\}aZm<\f e &6.nu/VWi@L_*gi> stream -xZKs8WPE{nIL^GsؚL(CKP:~ gD Џζ3w;}t_ܼ~"x?섁'z2uO˫Q}5zR/*?ك?r_kBߺ)a7)%'FLS7҃\̮"QqN4-@lS;LB䄾2q"oY8]a3ry~7;JOOۮ[+4 ܛ77+iwŁŒPVk5 ȉOwcMTIJWlΠKVgo@\CnES5{gS;i 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