Moved files to branch that are only related to OMOP CDM v4 or the conversion of v4 to v5
This commit is contained in:
kan7003
parent
bf39b90e3b
commit
2c7847236d
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@ -1,15 +0,0 @@
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LOAD DATA INPATH '${VAR:OMOP_SYNPUF_PATH}/CDM_CARE_SITE.csv' OVERWRITE INTO TABLE care_site;
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LOAD DATA INPATH '${VAR:OMOP_SYNPUF_PATH}/CDM_CONDITION_OCCURRENCE.csv' OVERWRITE INTO TABLE condition_occurrence;
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LOAD DATA INPATH '${VAR:OMOP_SYNPUF_PATH}/CDM_DEATH.csv' OVERWRITE INTO TABLE death;
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LOAD DATA INPATH '${VAR:OMOP_SYNPUF_PATH}/CDM_DRUG_EXPOSURE.csv' OVERWRITE INTO TABLE drug_exposure;
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LOAD DATA INPATH '${VAR:OMOP_SYNPUF_PATH}/CDM_DEVICE_EXPOSURE.csv' OVERWRITE INTO TABLE device_exposure;
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LOAD DATA INPATH '${VAR:OMOP_SYNPUF_PATH}/CDM_LOCATION.csv' OVERWRITE INTO TABLE `location`;
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LOAD DATA INPATH '${VAR:OMOP_SYNPUF_PATH}/CDM_MEASUREMENT.csv' OVERWRITE INTO TABLE measurement;
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LOAD DATA INPATH '${VAR:OMOP_SYNPUF_PATH}/CDM_OBSERVATION.csv' OVERWRITE INTO TABLE observation;
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LOAD DATA INPATH '${VAR:OMOP_SYNPUF_PATH}/CDM_OBSERVATION_PERIOD.csv' OVERWRITE INTO TABLE observation_period;
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LOAD DATA INPATH '${VAR:OMOP_SYNPUF_PATH}/CDM_PERSON.csv' OVERWRITE INTO TABLE person;
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LOAD DATA INPATH '${VAR:OMOP_SYNPUF_PATH}/CDM_PROCEDURE_OCCURRENCE.csv' OVERWRITE INTO TABLE procedure_occurrence;
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LOAD DATA INPATH '${VAR:OMOP_SYNPUF_PATH}/CDM_PROVIDER.csv' OVERWRITE INTO TABLE provider;
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LOAD DATA INPATH '${VAR:OMOP_SYNPUF_PATH}/CDM_VISIT_OCCURRENCE.csv' OVERWRITE INTO TABLE visit_occurrence;
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LOAD DATA INPATH '${VAR:OMOP_SYNPUF_PATH}/CDM_DRUG_ERA.csv' OVERWRITE INTO TABLE drug_era;
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LOAD DATA INPATH '${VAR:OMOP_SYNPUF_PATH}/CDM_CONDITION_ERA.csv' OVERWRITE INTO TABLE condition_era;
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@ -1,763 +0,0 @@
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/*********************************************************************************
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# Copyright 2014-6 Observational Health Data Sciences and Informatics
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#
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#
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# Licensed under the Apache License, Version 2.0 (the "License");
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# you may not use this file except in compliance with the License.
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# You may obtain a copy of the License at
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#
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# http://www.apache.org/licenses/LICENSE-2.0
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#
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# Unless required by applicable law or agreed to in writing, software
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# distributed under the License is distributed on an "AS IS" BASIS,
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# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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# See the License for the specific language governing permissions and
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# limitations under the License.
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********************************************************************************/
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/************************
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####### # # ####### ###### ##### ###### # # #######
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# # ## ## # # # # # # # # ## ## # # #
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# # # # # # # # # # # # # # # # # # # #
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# # # # # # # ###### # # # # # # # # ######
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# # # # # # # # # # # # # # #
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# # # # # # # # # # # # # # # # #
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####### # # ####### # ##### ###### # # ## #####
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script to create OMOP common data model, version 5.0 for Hadoop (Hive/Impala) database
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Based on the PostgreSQL version, with the following changes:
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* NULL/NOT NULL is not used.
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* Dates are stored as VARCHAR(8). See http://stackoverflow.com/questions/33024309/convert-yyyymmdd-string-to-date-in-impala for how to treat date columns as dates.
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* PostgreSQL NUMERIC is stored as DOUBLE for amounts, and DECIMAL(19,4) for prices.
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* PostgreSQL TEXT is stored as STRING.
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*************************/
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/************************
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Standardized vocabulary
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************************/
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CREATE TABLE concept (
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concept_id INTEGER,
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concept_name VARCHAR(255),
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domain_id VARCHAR(20),
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vocabulary_id VARCHAR(20),
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concept_class_id VARCHAR(20),
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standard_concept VARCHAR(1),
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concept_code VARCHAR(50),
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valid_start_date VARCHAR(8), -- DATE
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valid_end_date VARCHAR(8), -- DATE
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invalid_reason VARCHAR(1)
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)
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ROW FORMAT DELIMITED FIELDS TERMINATED BY '\t'
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TBLPROPERTIES ("skip.header.line.count"="1")
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;
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CREATE TABLE vocabulary (
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vocabulary_id VARCHAR(20),
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vocabulary_name VARCHAR(255),
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vocabulary_reference VARCHAR(255),
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vocabulary_version VARCHAR(255),
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vocabulary_concept_id INTEGER
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)
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ROW FORMAT DELIMITED FIELDS TERMINATED BY '\t'
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TBLPROPERTIES ("skip.header.line.count"="1")
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;
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CREATE TABLE domain (
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domain_id VARCHAR(20),
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domain_name VARCHAR(255),
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domain_concept_id INTEGER
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)
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ROW FORMAT DELIMITED FIELDS TERMINATED BY '\t'
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TBLPROPERTIES ("skip.header.line.count"="1")
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;
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CREATE TABLE concept_class (
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concept_class_id VARCHAR(20),
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concept_class_name VARCHAR(255),
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concept_class_concept_id INTEGER
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)
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ROW FORMAT DELIMITED FIELDS TERMINATED BY '\t'
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TBLPROPERTIES ("skip.header.line.count"="1")
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;
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CREATE TABLE concept_relationship (
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concept_id_1 INTEGER,
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concept_id_2 INTEGER,
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relationship_id VARCHAR(20),
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valid_start_date VARCHAR(8), -- DATE
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valid_end_date VARCHAR(8), -- DATE
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invalid_reason VARCHAR(1)
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)
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ROW FORMAT DELIMITED FIELDS TERMINATED BY '\t'
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TBLPROPERTIES ("skip.header.line.count"="1")
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;
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CREATE TABLE relationship (
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relationship_id VARCHAR(20),
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relationship_name VARCHAR(255),
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is_hierarchical VARCHAR(1),
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defines_ancestry VARCHAR(1),
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reverse_relationship_id VARCHAR(20),
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relationship_concept_id INTEGER
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)
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ROW FORMAT DELIMITED FIELDS TERMINATED BY '\t'
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TBLPROPERTIES ("skip.header.line.count"="1")
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;
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CREATE TABLE concept_synonym (
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concept_id INTEGER,
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concept_synonym_name VARCHAR(1000),
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language_concept_id INTEGER
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)
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ROW FORMAT DELIMITED FIELDS TERMINATED BY '\t'
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TBLPROPERTIES ("skip.header.line.count"="1")
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;
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CREATE TABLE concept_ancestor (
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ancestor_concept_id INTEGER,
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descendant_concept_id INTEGER,
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min_levels_of_separation INTEGER,
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max_levels_of_separation INTEGER
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)
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ROW FORMAT DELIMITED FIELDS TERMINATED BY '\t'
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TBLPROPERTIES ("skip.header.line.count"="1")
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;
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CREATE TABLE source_to_concept_map (
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source_code VARCHAR(50),
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source_concept_id INTEGER,
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source_vocabulary_id VARCHAR(20),
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source_code_description VARCHAR(255),
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target_concept_id INTEGER,
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target_vocabulary_id VARCHAR(20),
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valid_start_date VARCHAR(8), -- DATE
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valid_end_date VARCHAR(8), -- DATE
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invalid_reason VARCHAR(1)
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)
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ROW FORMAT DELIMITED FIELDS TERMINATED BY '\t'
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TBLPROPERTIES ("skip.header.line.count"="1")
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;
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CREATE TABLE drug_strength (
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drug_concept_id INTEGER,
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ingredient_concept_id INTEGER,
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amount_value DOUBLE, -- NUMERIC
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amount_unit_concept_id INTEGER,
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numerator_value DOUBLE, -- NUMERIC
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numerator_unit_concept_id INTEGER,
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denominator_value DOUBLE, -- NUMERIC
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denominator_unit_concept_id INTEGER,
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box_size INTEGER,
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valid_start_date VARCHAR(8), -- DATE
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valid_end_date VARCHAR(8), -- DATE
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invalid_reason VARCHAR(1)
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)
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ROW FORMAT DELIMITED FIELDS TERMINATED BY '\t'
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TBLPROPERTIES ("skip.header.line.count"="1")
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;
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CREATE TABLE cohort_definition (
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cohort_definition_id INTEGER,
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cohort_definition_name VARCHAR(255),
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cohort_definition_description STRING, -- TEXT
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definition_type_concept_id INTEGER,
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cohort_definition_syntax STRING, -- TEXT
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subject_concept_id INTEGER,
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cohort_initiation_date VARCHAR(8) -- DATE
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)
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;
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CREATE TABLE attribute_definition (
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attribute_definition_id INTEGER,
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attribute_name VARCHAR(255),
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attribute_description STRING, -- TEXT
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attribute_type_concept_id INTEGER,
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attribute_syntax STRING -- TEXT
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)
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;
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/**************************
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Standardized meta-data
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***************************/
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CREATE TABLE cdm_source
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(
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cdm_source_name VARCHAR(255),
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cdm_source_abbreviation VARCHAR(25),
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cdm_holder VARCHAR(255),
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source_description STRING, -- TEXT
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source_documentation_reference VARCHAR(255),
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cdm_etl_reference VARCHAR(255),
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source_release_date VARCHAR(8), -- DATE
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cdm_release_date VARCHAR(8), -- DATE
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cdm_version VARCHAR(10),
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vocabulary_version VARCHAR(20)
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)
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;
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/************************
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Standardized clinical data
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************************/
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CREATE TABLE person (
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person_id INTEGER,
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gender_concept_id INTEGER,
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year_of_birth INTEGER,
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month_of_birth INTEGER,
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day_of_birth INTEGER,
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time_of_birth VARCHAR(10),
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race_concept_id INTEGER,
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ethnicity_concept_id INTEGER,
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location_id INTEGER,
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provider_id INTEGER,
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care_site_id INTEGER,
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person_source_value VARCHAR(50),
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gender_source_value VARCHAR(50),
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gender_source_concept_id INTEGER,
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race_source_value VARCHAR(50),
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race_source_concept_id INTEGER,
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ethnicity_source_value VARCHAR(50),
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ethnicity_source_concept_id INTEGER
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)
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ROW FORMAT DELIMITED FIELDS TERMINATED BY ','
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TBLPROPERTIES ("skip.header.line.count"="1")
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;
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CREATE TABLE observation_period (
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observation_period_id INTEGER,
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person_id INTEGER,
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observation_period_start_date VARCHAR(8), -- DATE
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observation_period_end_date VARCHAR(8), -- DATE
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period_type_concept_id INTEGER
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)
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ROW FORMAT DELIMITED FIELDS TERMINATED BY ','
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TBLPROPERTIES ("skip.header.line.count"="1")
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;
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CREATE TABLE specimen (
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specimen_id INTEGER,
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person_id INTEGER,
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specimen_concept_id INTEGER,
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specimen_type_concept_id INTEGER,
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specimen_date VARCHAR(8), -- DATE
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specimen_time VARCHAR(10),
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quantity DOUBLE, -- NUMERIC
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unit_concept_id INTEGER,
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anatomic_site_concept_id INTEGER,
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disease_status_concept_id INTEGER,
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specimen_source_id VARCHAR(50),
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specimen_source_value VARCHAR(50),
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unit_source_value VARCHAR(50),
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anatomic_site_source_value VARCHAR(50),
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disease_status_source_value VARCHAR(50)
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)
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;
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CREATE TABLE death (
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person_id INTEGER,
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death_date VARCHAR(8), -- DATE
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death_type_concept_id INTEGER,
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cause_concept_id INTEGER,
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cause_source_value VARCHAR(50),
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cause_source_concept_id INTEGER
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)
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ROW FORMAT DELIMITED FIELDS TERMINATED BY ','
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TBLPROPERTIES ("skip.header.line.count"="1")
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;
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CREATE TABLE visit_occurrence (
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visit_occurrence_id INTEGER,
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person_id INTEGER,
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visit_concept_id INTEGER,
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visit_start_date VARCHAR(8), -- DATE
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visit_start_time VARCHAR(10),
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visit_end_date VARCHAR(8), -- DATE
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visit_end_time VARCHAR(10),
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visit_type_concept_id INTEGER,
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provider_id INTEGER,
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care_site_id INTEGER,
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visit_source_value VARCHAR(50),
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visit_source_concept_id INTEGER
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)
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ROW FORMAT DELIMITED FIELDS TERMINATED BY ','
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TBLPROPERTIES ("skip.header.line.count"="1")
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;
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CREATE TABLE procedure_occurrence (
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procedure_occurrence_id INTEGER,
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person_id INTEGER,
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procedure_concept_id INTEGER,
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procedure_date VARCHAR(8), -- DATE
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procedure_type_concept_id INTEGER,
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modifier_concept_id INTEGER,
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quantity INTEGER,
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provider_id INTEGER,
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visit_occurrence_id INTEGER,
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procedure_source_value VARCHAR(50),
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procedure_source_concept_id INTEGER,
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qualifier_source_value VARCHAR(50)
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)
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ROW FORMAT DELIMITED FIELDS TERMINATED BY ','
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TBLPROPERTIES ("skip.header.line.count"="1")
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;
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CREATE TABLE drug_exposure (
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drug_exposure_id INTEGER,
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person_id INTEGER,
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drug_concept_id INTEGER,
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drug_exposure_start_date VARCHAR(8), -- DATE
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drug_exposure_end_date VARCHAR(8), -- DATE
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drug_type_concept_id INTEGER,
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stop_reason VARCHAR(20),
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refills INTEGER,
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quantity DOUBLE, -- NUMERIC
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days_supply INTEGER,
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sig STRING, -- TEXT
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route_concept_id INTEGER,
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effective_drug_dose DOUBLE, -- NUMERIC
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dose_unit_concept_id INTEGER,
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lot_number VARCHAR(50),
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provider_id INTEGER,
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visit_occurrence_id INTEGER,
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drug_source_value VARCHAR(50),
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drug_source_concept_id INTEGER,
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route_source_value VARCHAR(50),
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dose_unit_source_value VARCHAR(50)
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)
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ROW FORMAT DELIMITED FIELDS TERMINATED BY ','
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TBLPROPERTIES ("skip.header.line.count"="1")
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;
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CREATE TABLE device_exposure (
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device_exposure_id INTEGER,
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person_id INTEGER,
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device_concept_id INTEGER,
|
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device_exposure_start_date VARCHAR(8), -- DATE
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device_exposure_end_date VARCHAR(8), -- DATE
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device_type_concept_id INTEGER,
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unique_device_id VARCHAR(50),
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quantity INTEGER,
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provider_id INTEGER,
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visit_occurrence_id INTEGER,
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device_source_value VARCHAR(100),
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device_source_concept_id INTEGER
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)
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ROW FORMAT DELIMITED FIELDS TERMINATED BY ','
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TBLPROPERTIES ("skip.header.line.count"="1")
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;
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CREATE TABLE condition_occurrence (
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condition_occurrence_id INTEGER,
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person_id INTEGER,
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condition_concept_id INTEGER,
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condition_start_date VARCHAR(8), -- DATE
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condition_end_date VARCHAR(8), -- DATE
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condition_type_concept_id INTEGER,
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stop_reason VARCHAR(20),
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provider_id INTEGER,
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visit_occurrence_id INTEGER,
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condition_source_value VARCHAR(50),
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condition_source_concept_id INTEGER
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)
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ROW FORMAT DELIMITED FIELDS TERMINATED BY ','
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TBLPROPERTIES ("skip.header.line.count"="1")
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;
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|
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|
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CREATE TABLE measurement (
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measurement_id INTEGER,
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person_id INTEGER,
|
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measurement_concept_id INTEGER,
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measurement_date VARCHAR(8), -- DATE
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measurement_time VARCHAR(10),
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measurement_type_concept_id INTEGER,
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operator_concept_id INTEGER,
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value_as_number DOUBLE, -- NUMERIC
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value_as_concept_id INTEGER,
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unit_concept_id INTEGER,
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range_low DOUBLE, -- NUMERIC
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range_high DOUBLE, -- NUMERIC
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provider_id INTEGER,
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visit_occurrence_id INTEGER,
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measurement_source_value VARCHAR(50),
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measurement_source_concept_id INTEGER,
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unit_source_value VARCHAR(50),
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value_source_value VARCHAR(50)
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)
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ROW FORMAT DELIMITED FIELDS TERMINATED BY ','
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TBLPROPERTIES ("skip.header.line.count"="1")
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;
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|
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CREATE TABLE note (
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note_id INTEGER,
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person_id INTEGER,
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note_date VARCHAR(8), -- DATE
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note_time VARCHAR(10),
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note_type_concept_id INTEGER,
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note_text STRING, -- TEXT
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||||
provider_id INTEGER,
|
||||
visit_occurrence_id INTEGER,
|
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note_source_value VARCHAR(50)
|
||||
)
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;
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|
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|
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|
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CREATE TABLE observation (
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observation_id INTEGER,
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person_id INTEGER,
|
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observation_concept_id INTEGER,
|
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observation_date VARCHAR(8), -- DATE
|
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observation_time VARCHAR(10),
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||||
observation_type_concept_id INTEGER,
|
||||
value_as_number DOUBLE, -- NUMERIC
|
||||
value_as_string VARCHAR(60),
|
||||
value_as_concept_id INTEGER,
|
||||
qualifier_concept_id INTEGER,
|
||||
unit_concept_id INTEGER,
|
||||
provider_id INTEGER,
|
||||
visit_occurrence_id INTEGER,
|
||||
observation_source_value VARCHAR(50),
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||||
observation_source_concept_id INTEGER,
|
||||
unit_source_value VARCHAR(50),
|
||||
qualifier_source_value VARCHAR(50)
|
||||
)
|
||||
ROW FORMAT DELIMITED FIELDS TERMINATED BY ','
|
||||
TBLPROPERTIES ("skip.header.line.count"="1")
|
||||
;
|
||||
|
||||
|
||||
|
||||
CREATE TABLE fact_relationship (
|
||||
domain_concept_id_1 INTEGER,
|
||||
fact_id_1 INTEGER,
|
||||
domain_concept_id_2 INTEGER,
|
||||
fact_id_2 INTEGER,
|
||||
relationship_concept_id INTEGER
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
|
||||
/************************
|
||||
|
||||
Standardized health system data
|
||||
|
||||
************************/
|
||||
|
||||
|
||||
|
||||
CREATE TABLE `location` (
|
||||
location_id INTEGER,
|
||||
address_1 VARCHAR(50),
|
||||
address_2 VARCHAR(50),
|
||||
city VARCHAR(50),
|
||||
state VARCHAR(2),
|
||||
zip VARCHAR(9),
|
||||
county VARCHAR(20),
|
||||
location_source_value VARCHAR(50)
|
||||
)
|
||||
ROW FORMAT DELIMITED FIELDS TERMINATED BY ','
|
||||
TBLPROPERTIES ("skip.header.line.count"="1")
|
||||
;
|
||||
|
||||
|
||||
|
||||
CREATE TABLE care_site (
|
||||
care_site_id INTEGER,
|
||||
care_site_name VARCHAR(255),
|
||||
place_of_service_concept_id INTEGER,
|
||||
location_id INTEGER,
|
||||
care_site_source_value VARCHAR(50),
|
||||
place_of_service_source_value VARCHAR(50)
|
||||
)
|
||||
ROW FORMAT DELIMITED FIELDS TERMINATED BY ','
|
||||
TBLPROPERTIES ("skip.header.line.count"="1")
|
||||
;
|
||||
|
||||
|
||||
|
||||
CREATE TABLE provider (
|
||||
provider_id INTEGER,
|
||||
provider_name VARCHAR(255),
|
||||
NPI VARCHAR(20),
|
||||
DEA VARCHAR(20),
|
||||
specialty_concept_id INTEGER,
|
||||
care_site_id INTEGER,
|
||||
year_of_birth INTEGER,
|
||||
gender_concept_id INTEGER,
|
||||
provider_source_value VARCHAR(50),
|
||||
specialty_source_value VARCHAR(50),
|
||||
specialty_source_concept_id INTEGER,
|
||||
gender_source_value VARCHAR(50),
|
||||
gender_source_concept_id INTEGER
|
||||
)
|
||||
ROW FORMAT DELIMITED FIELDS TERMINATED BY ','
|
||||
TBLPROPERTIES ("skip.header.line.count"="1")
|
||||
;
|
||||
|
||||
|
||||
|
||||
|
||||
/************************
|
||||
|
||||
Standardized health economics
|
||||
|
||||
************************/
|
||||
|
||||
|
||||
CREATE TABLE payer_plan_period (
|
||||
payer_plan_period_id INTEGER,
|
||||
person_id INTEGER,
|
||||
payer_plan_period_start_date VARCHAR(8), -- DATE
|
||||
payer_plan_period_end_date VARCHAR(8), -- DATE
|
||||
payer_source_value VARCHAR (50),
|
||||
plan_source_value VARCHAR (50),
|
||||
family_source_value VARCHAR (50)
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
/* The individual cost tables are being phased out and will disappear soon
|
||||
|
||||
CREATE TABLE visit_cost (
|
||||
visit_cost_id INTEGER,
|
||||
visit_occurrence_id INTEGER,
|
||||
currency_concept_id INTEGER,
|
||||
paid_copay DECIMAL(19,4), -- NUMERIC
|
||||
paid_coinsurance DECIMAL(19,4), -- NUMERIC
|
||||
paid_toward_deductible DECIMAL(19,4), -- NUMERIC
|
||||
paid_by_payer DECIMAL(19,4), -- NUMERIC
|
||||
paid_by_coordination_benefits DECIMAL(19,4), -- NUMERIC
|
||||
total_out_of_pocket DECIMAL(19,4), -- NUMERIC
|
||||
total_paid DECIMAL(19,4), -- NUMERIC
|
||||
payer_plan_period_id INTEGER
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
CREATE TABLE procedure_cost (
|
||||
procedure_cost_id INTEGER,
|
||||
procedure_occurrence_id INTEGER,
|
||||
currency_concept_id INTEGER,
|
||||
paid_copay DECIMAL(19,4), -- NUMERIC
|
||||
paid_coinsurance DECIMAL(19,4), -- NUMERIC
|
||||
paid_toward_deductible DECIMAL(19,4), -- NUMERIC
|
||||
paid_by_payer DECIMAL(19,4), -- NUMERIC
|
||||
paid_by_coordination_benefits DECIMAL(19,4), -- NUMERIC
|
||||
total_out_of_pocket DECIMAL(19,4), -- NUMERIC
|
||||
total_paid DECIMAL(19,4), -- NUMERIC
|
||||
revenue_code_concept_id INTEGER,
|
||||
payer_plan_period_id INTEGER,
|
||||
revenue_code_source_value VARCHAR(50)
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
CREATE TABLE drug_cost (
|
||||
drug_cost_id INTEGER,
|
||||
drug_exposure_id INTEGER,
|
||||
currency_concept_id INTEGER,
|
||||
paid_copay DECIMAL(19,4), -- NUMERIC
|
||||
paid_coinsurance DECIMAL(19,4), -- NUMERIC
|
||||
paid_toward_deductible DECIMAL(19,4), -- NUMERIC
|
||||
paid_by_payer DECIMAL(19,4), -- NUMERIC
|
||||
paid_by_coordination_benefits DECIMAL(19,4), -- NUMERIC
|
||||
total_out_of_pocket DECIMAL(19,4), -- NUMERIC
|
||||
total_paid DECIMAL(19,4), -- NUMERIC
|
||||
ingredient_cost DECIMAL(19,4), -- NUMERIC
|
||||
dispensing_fee DECIMAL(19,4), -- NUMERIC
|
||||
average_wholesale_price DECIMAL(19,4), -- NUMERIC
|
||||
payer_plan_period_id INTEGER
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
CREATE TABLE device_cost (
|
||||
device_cost_id INTEGER,
|
||||
device_exposure_id INTEGER,
|
||||
currency_concept_id INTEGER,
|
||||
paid_copay DECIMAL(19,4), -- NUMERIC
|
||||
paid_coinsurance DECIMAL(19,4), -- NUMERIC
|
||||
paid_toward_deductible DECIMAL(19,4), -- NUMERIC
|
||||
paid_by_payer DECIMAL(19,4), -- NUMERIC
|
||||
paid_by_coordination_benefits DECIMAL(19,4), -- NUMERIC
|
||||
total_out_of_pocket DECIMAL(19,4), -- NUMERIC
|
||||
total_paid DECIMAL(19,4), -- NUMERIC
|
||||
payer_plan_period_id INTEGER
|
||||
)
|
||||
;
|
||||
*/
|
||||
|
||||
|
||||
CREATE TABLE cost (
|
||||
cost_id INTEGER,
|
||||
cost_event_id INTEGER,
|
||||
cost_domain_id VARCHAR(20),
|
||||
cost_type_concept_id INTEGER,
|
||||
currency_concept_id INTEGER,
|
||||
total_charge DECIMAL(19,4), -- NUMERIC
|
||||
total_cost DECIMAL(19,4), -- NUMERIC
|
||||
total_paid DECIMAL(19,4), -- NUMERIC
|
||||
paid_by_payer DECIMAL(19,4), -- NUMERIC
|
||||
paid_by_patient DECIMAL(19,4), -- NUMERIC
|
||||
paid_patient_copay DECIMAL(19,4), -- NUMERIC
|
||||
paid_patient_coinsurance DECIMAL(19,4), -- NUMERIC
|
||||
paid_patient_deductible DECIMAL(19,4), -- NUMERIC
|
||||
paid_by_primary DECIMAL(19,4), -- NUMERIC
|
||||
paid_ingredient_cost DECIMAL(19,4), -- NUMERIC
|
||||
paid_dispensing_fee DECIMAL(19,4), -- NUMERIC
|
||||
payer_plan_period_id INTEGER,
|
||||
amount_allowed DECIMAL(19,4), -- NUMERIC
|
||||
revenue_code_concept_id INTEGER,
|
||||
reveue_code_source_value VARCHAR(50)
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
/************************
|
||||
|
||||
Standardized derived elements
|
||||
|
||||
************************/
|
||||
|
||||
CREATE TABLE cohort (
|
||||
cohort_definition_id INTEGER,
|
||||
subject_id INTEGER,
|
||||
cohort_start_date VARCHAR(8), -- DATE
|
||||
cohort_end_date VARCHAR(8) -- DATE
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
CREATE TABLE cohort_attribute (
|
||||
cohort_definition_id INTEGER,
|
||||
cohort_start_date VARCHAR(8), -- DATE
|
||||
cohort_end_date VARCHAR(8), -- DATE
|
||||
subject_id INTEGER,
|
||||
attribute_definition_id INTEGER,
|
||||
value_as_number DOUBLE, -- NUMERIC
|
||||
value_as_concept_id INTEGER
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
|
||||
CREATE TABLE drug_era (
|
||||
drug_era_id INTEGER,
|
||||
person_id INTEGER,
|
||||
drug_concept_id INTEGER,
|
||||
drug_era_start_date VARCHAR(8), -- DATE
|
||||
drug_era_end_date VARCHAR(8), -- DATE
|
||||
drug_exposure_count INTEGER,
|
||||
gap_days INTEGER
|
||||
)
|
||||
ROW FORMAT DELIMITED FIELDS TERMINATED BY ','
|
||||
TBLPROPERTIES ("skip.header.line.count"="1")
|
||||
;
|
||||
|
||||
|
||||
CREATE TABLE dose_era (
|
||||
dose_era_id INTEGER,
|
||||
person_id INTEGER,
|
||||
drug_concept_id INTEGER,
|
||||
unit_concept_id INTEGER,
|
||||
dose_value DOUBLE, -- NUMERIC
|
||||
dose_era_start_date VARCHAR(8), -- DATE
|
||||
dose_era_end_date VARCHAR(8) -- DATE
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
|
||||
CREATE TABLE condition_era (
|
||||
condition_era_id INTEGER,
|
||||
person_id INTEGER,
|
||||
condition_concept_id INTEGER,
|
||||
condition_era_start_date VARCHAR(8), -- DATE
|
||||
condition_era_end_date VARCHAR(8), -- DATE
|
||||
condition_occurrence_count INTEGER
|
||||
)
|
||||
ROW FORMAT DELIMITED FIELDS TERMINATED BY ','
|
||||
TBLPROPERTIES ("skip.header.line.count"="1")
|
||||
;
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
|
@ -1,51 +0,0 @@
|
|||
Common-Data-Model / Impala
|
||||
=================
|
||||
|
||||
This folder contains the SQL scripts for Impala.
|
||||
|
||||
In order to create your instantiation of the Common Data Model, we recommend following these steps:
|
||||
|
||||
1. Create an empty schema.
|
||||
|
||||
```bash
|
||||
impala-shell -q 'CREATE DATABASE omop_cdm'
|
||||
```
|
||||
|
||||
2. Execute the script `OMOP_CDM_ddl_Impala.sql` to create the tables and fields.
|
||||
|
||||
```bash
|
||||
impala-shell -d omop_cdm -f OMOP_CDM_ddl_Impala.sql
|
||||
```
|
||||
|
||||
3. Load your data into the schema.
|
||||
|
||||
a. Load the vocabulary tables.
|
||||
|
||||
First, download the data from
|
||||
[http://www.ohdsi.org/web/athena/](http://www.ohdsi.org/web/athena/)
|
||||
and unzip into a _cdmv5vocab_ directory, then run
|
||||
|
||||
```bash
|
||||
hadoop fs -put cdmv5vocab cdmv5vocab
|
||||
hadoop fs -chmod +w cdmv5vocab
|
||||
impala-shell -d omop_cdm -f VocabImport/OMOP_CDM_vocabulary_load_Impala.sql --var=OMOP_VOCAB_PATH=/user/$USER/cdmv5vocab
|
||||
```
|
||||
|
||||
b. Load the patient data.
|
||||
|
||||
For example, download the 1000 person sample of simulated CMS SynPUF patient data from
|
||||
[http://www.ltscomputingllc.com/downloads/](http://www.ltscomputingllc.com/downloads/)
|
||||
and unzip into a _synpuf_ directory, then run
|
||||
|
||||
```bash
|
||||
hadoop fs -put synpuf synpuf
|
||||
hadoop fs -chmod +w synpuf
|
||||
impala-shell -d omop_cdm -f DataImport/OMOP_CDM_synpuf_load_Impala.sql --var=OMOP_SYNPUF_PATH=/user/$USER/synpuf
|
||||
```
|
||||
|
||||
4. Run simple queries to sanity check.
|
||||
|
||||
```bash
|
||||
impala-shell -d omop_cdm -q 'SELECT COUNT(1) FROM concept'
|
||||
impala-shell -d omop_cdm -q 'SELECT COUNT(1) FROM person'
|
||||
```
|
||||
|
|
@ -1,9 +0,0 @@
|
|||
LOAD DATA INPATH '${VAR:OMOP_VOCAB_PATH}/CONCEPT.csv' OVERWRITE INTO TABLE concept;
|
||||
LOAD DATA INPATH '${VAR:OMOP_VOCAB_PATH}/VOCABULARY.csv' OVERWRITE INTO TABLE vocabulary;
|
||||
LOAD DATA INPATH '${VAR:OMOP_VOCAB_PATH}/DOMAIN.csv' OVERWRITE INTO TABLE domain;
|
||||
LOAD DATA INPATH '${VAR:OMOP_VOCAB_PATH}/CONCEPT_CLASS.csv' OVERWRITE INTO TABLE concept_class;
|
||||
LOAD DATA INPATH '${VAR:OMOP_VOCAB_PATH}/CONCEPT_RELATIONSHIP.csv' OVERWRITE INTO TABLE concept_relationship;
|
||||
LOAD DATA INPATH '${VAR:OMOP_VOCAB_PATH}/RELATIONSHIP.csv' OVERWRITE INTO TABLE relationship;
|
||||
LOAD DATA INPATH '${VAR:OMOP_VOCAB_PATH}/CONCEPT_SYNONYM.csv' OVERWRITE INTO TABLE concept_synonym;
|
||||
LOAD DATA INPATH '${VAR:OMOP_VOCAB_PATH}/CONCEPT_ANCESTOR.csv' OVERWRITE INTO TABLE concept_ancestor;
|
||||
LOAD DATA INPATH '${VAR:OMOP_VOCAB_PATH}/DRUG_STRENGTH.csv' OVERWRITE INTO TABLE drug_strength;
|
||||
|
|
@ -1,544 +0,0 @@
|
|||
/*********************************************************************************
|
||||
# Copyright 2014 Observational Health Data Sciences and Informatics
|
||||
#
|
||||
#
|
||||
# Licensed under the Apache License, Version 2.0 (the "License");
|
||||
# you may not use this file except in compliance with the License.
|
||||
# You may obtain a copy of the License at
|
||||
#
|
||||
# http://www.apache.org/licenses/LICENSE-2.0
|
||||
#
|
||||
# Unless required by applicable law or agreed to in writing, software
|
||||
# distributed under the License is distributed on an "AS IS" BASIS,
|
||||
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
|
||||
# See the License for the specific language governing permissions and
|
||||
# limitations under the License.
|
||||
********************************************************************************/
|
||||
|
||||
/************************
|
||||
|
||||
####### # # ####### ###### ##### ###### # # ####### #####
|
||||
# # ## ## # # # # # # # # ## ## # # # # # #### # # #### ##### ##### ## # # # ##### ####
|
||||
# # # # # # # # # # # # # # # # # # # # # # # ## # # # # # # # # ## # # #
|
||||
# # # # # # # ###### # # # # # # # # ###### # # # # # # #### # # # # # # # # # # ####
|
||||
# # # # # # # # # # # # # # # # # # # # # # # ##### ###### # # # # # #
|
||||
# # # # # # # # # # # # # # # # # # # # # # ## # # # # # # # # # ## # # #
|
||||
####### # # ####### # ##### ###### # # ## ##### ##### #### # # #### # # # # # # # # # ####
|
||||
|
||||
|
||||
script to create constraints within OMOP common data model, version 5.0 for Oracle database
|
||||
|
||||
last revised: 12 Oct 2014
|
||||
|
||||
author: Patrick Ryan
|
||||
|
||||
*************************/
|
||||
|
||||
|
||||
/************************
|
||||
*************************
|
||||
*************************
|
||||
*************************
|
||||
|
||||
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 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 visit_cost ADD CONSTRAINT xpk_visit_cost PRIMARY KEY ( visit_cost_id ) ;
|
||||
|
||||
ALTER TABLE procedure_cost ADD CONSTRAINT xpk_procedure_cost PRIMARY KEY ( procedure_cost_id ) ;
|
||||
|
||||
ALTER TABLE drug_cost ADD CONSTRAINT xpk_drug_cost PRIMARY KEY ( drug_cost_id ) ;
|
||||
|
||||
ALTER TABLE device_cost ADD CONSTRAINT xpk_device_cost PRIMARY KEY ( device_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 ) ;
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
/************************
|
||||
*************************
|
||||
*************************
|
||||
*************************
|
||||
|
||||
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 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_dose_unit_concept FOREIGN KEY (dose_unit_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 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_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 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 visit_cost ADD CONSTRAINT fpk_visit_cost_id FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id);
|
||||
|
||||
ALTER TABLE visit_cost ADD CONSTRAINT fpk_visit_cost_currency FOREIGN KEY (currency_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE visit_cost ADD CONSTRAINT fpk_visit_cost_period FOREIGN KEY (payer_plan_period_id) REFERENCES payer_plan_period (payer_plan_period_id);
|
||||
|
||||
|
||||
ALTER TABLE procedure_cost ADD CONSTRAINT fpk_procedure_cost_id FOREIGN KEY (procedure_occurrence_id) REFERENCES procedure_occurrence (procedure_occurrence_id);
|
||||
|
||||
ALTER TABLE procedure_cost ADD CONSTRAINT fpk_procedure_cost_currency FOREIGN KEY (currency_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE procedure_cost ADD CONSTRAINT fpk_procedure_cost_period FOREIGN KEY (payer_plan_period_id) REFERENCES payer_plan_period (payer_plan_period_id);
|
||||
|
||||
ALTER TABLE procedure_cost ADD CONSTRAINT fpk_procedure_cost_revenue FOREIGN KEY (revenue_code_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
|
||||
ALTER TABLE drug_cost ADD CONSTRAINT fpk_drug_cost_id FOREIGN KEY (drug_exposure_id) REFERENCES drug_exposure (drug_exposure_id);
|
||||
|
||||
ALTER TABLE drug_cost ADD CONSTRAINT fpk_drug_cost_currency FOREIGN KEY (currency_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE drug_cost ADD CONSTRAINT fpk_drug_cost_period FOREIGN KEY (payer_plan_period_id) REFERENCES payer_plan_period (payer_plan_period_id);
|
||||
|
||||
|
||||
ALTER TABLE device_cost ADD CONSTRAINT fpk_device_cost_id FOREIGN KEY (device_exposure_id) REFERENCES device_exposure (device_exposure_id);
|
||||
|
||||
ALTER TABLE device_cost ADD CONSTRAINT fpk_device_cost_currency FOREIGN KEY (currency_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE device_cost ADD CONSTRAINT fpk_device_cost_period FOREIGN KEY (payer_plan_period_id) REFERENCES payer_plan_period (payer_plan_period_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);
|
||||
|
||||
|
|
@ -1,740 +0,0 @@
|
|||
/*********************************************************************************
|
||||
# Copyright 2014-6 Observational Health Data Sciences and Informatics
|
||||
#
|
||||
#
|
||||
# Licensed under the Apache License, Version 2.0 (the "License");
|
||||
# you may not use this file except in compliance with the License.
|
||||
# You may obtain a copy of the License at
|
||||
#
|
||||
# http://www.apache.org/licenses/LICENSE-2.0
|
||||
#
|
||||
# Unless required by applicable law or agreed to in writing, software
|
||||
# distributed under the License is distributed on an "AS IS" BASIS,
|
||||
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
|
||||
# See the License for the specific language governing permissions and
|
||||
# limitations under the License.
|
||||
********************************************************************************/
|
||||
|
||||
/************************
|
||||
|
||||
####### # # ####### ###### ##### ###### # # #######
|
||||
# # ## ## # # # # # # # # ## ## # # #
|
||||
# # # # # # # # # # # # # # # # # # # #
|
||||
# # # # # # # ###### # # # # # # # # ######
|
||||
# # # # # # # # # # # # # # #
|
||||
# # # # # # # # # # # # # # # # #
|
||||
####### # # ####### # ##### ###### # # ## #####
|
||||
|
||||
|
||||
script to create OMOP common data model, version 5.0 for Oracle database
|
||||
|
||||
last revised: 1-May-2016
|
||||
|
||||
Authors: Patrick Ryan, Christian Reich
|
||||
|
||||
|
||||
*************************/
|
||||
|
||||
|
||||
/************************
|
||||
|
||||
Standardized vocabulary
|
||||
|
||||
************************/
|
||||
|
||||
|
||||
CREATE TABLE concept (
|
||||
concept_id INTEGER NOT NULL,
|
||||
concept_name VARCHAR(255) NOT NULL,
|
||||
domain_id VARCHAR(20) NOT NULL,
|
||||
vocabulary_id VARCHAR(20) NOT NULL,
|
||||
concept_class_id VARCHAR(20) NOT NULL,
|
||||
standard_concept VARCHAR(1) NULL,
|
||||
concept_code VARCHAR(50) NOT NULL,
|
||||
valid_start_date DATE NOT NULL,
|
||||
valid_end_date DATE NOT NULL,
|
||||
invalid_reason VARCHAR(1) NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
|
||||
CREATE TABLE vocabulary (
|
||||
vocabulary_id VARCHAR(20) NOT NULL,
|
||||
vocabulary_name VARCHAR(255) NOT NULL,
|
||||
vocabulary_reference VARCHAR(255) NULL,
|
||||
vocabulary_version VARCHAR(255) NULL,
|
||||
vocabulary_concept_id INTEGER NOT NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
|
||||
CREATE TABLE domain (
|
||||
domain_id VARCHAR(20) NOT NULL,
|
||||
domain_name VARCHAR(255) NOT NULL,
|
||||
domain_concept_id INTEGER NOT NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
CREATE TABLE concept_class (
|
||||
concept_class_id VARCHAR(20) NOT NULL,
|
||||
concept_class_name VARCHAR(255) NOT NULL,
|
||||
concept_class_concept_id INTEGER NOT NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
|
||||
CREATE TABLE concept_relationship (
|
||||
concept_id_1 INTEGER NOT NULL,
|
||||
concept_id_2 INTEGER NOT NULL,
|
||||
relationship_id VARCHAR(20) NOT NULL,
|
||||
valid_start_date DATE NOT NULL,
|
||||
valid_end_date DATE NOT NULL,
|
||||
invalid_reason VARCHAR(1) NULL)
|
||||
;
|
||||
|
||||
|
||||
|
||||
CREATE TABLE relationship (
|
||||
relationship_id VARCHAR(20) NOT NULL,
|
||||
relationship_name VARCHAR(255) NOT NULL,
|
||||
is_hierarchical VARCHAR(1) NOT NULL,
|
||||
defines_ancestry VARCHAR(1) NOT NULL,
|
||||
reverse_relationship_id VARCHAR(20) NOT NULL,
|
||||
relationship_concept_id INTEGER NOT NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
CREATE TABLE concept_synonym (
|
||||
concept_id INTEGER NOT NULL,
|
||||
concept_synonym_name VARCHAR(1000) NOT NULL,
|
||||
language_concept_id INTEGER NOT NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
CREATE TABLE concept_ancestor (
|
||||
ancestor_concept_id INTEGER NOT NULL,
|
||||
descendant_concept_id INTEGER NOT NULL,
|
||||
min_levels_of_separation INTEGER NOT NULL,
|
||||
max_levels_of_separation INTEGER NOT NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
CREATE TABLE source_to_concept_map (
|
||||
source_code VARCHAR(50) NOT NULL,
|
||||
source_concept_id INTEGER NOT NULL,
|
||||
source_vocabulary_id VARCHAR(20) NOT NULL,
|
||||
source_code_description VARCHAR(255) NULL,
|
||||
target_concept_id INTEGER NOT NULL,
|
||||
target_vocabulary_id VARCHAR(20) NOT NULL,
|
||||
valid_start_date DATE NOT NULL,
|
||||
valid_end_date DATE NOT NULL,
|
||||
invalid_reason VARCHAR(1) NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
|
||||
CREATE TABLE drug_strength (
|
||||
drug_concept_id INTEGER NOT NULL,
|
||||
ingredient_concept_id INTEGER NOT NULL,
|
||||
amount_value FLOAT NULL,
|
||||
amount_unit_concept_id INTEGER NULL,
|
||||
numerator_value FLOAT NULL,
|
||||
numerator_unit_concept_id INTEGER NULL,
|
||||
denominator_value FLOAT NULL,
|
||||
denominator_unit_concept_id INTEGER NULL,
|
||||
box_size INTEGER NULL,
|
||||
valid_start_date DATE NOT NULL,
|
||||
valid_end_date DATE NOT NULL,
|
||||
invalid_reason VARCHAR(1) NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
CREATE TABLE cohort_definition (
|
||||
cohort_definition_id INTEGER NOT NULL,
|
||||
cohort_definition_name VARCHAR(255) NOT NULL,
|
||||
cohort_definition_description CLOB NULL,
|
||||
definition_type_concept_id INTEGER NOT NULL,
|
||||
cohort_definition_syntax CLOB NULL,
|
||||
subject_concept_id INTEGER NOT NULL,
|
||||
cohort_initiation_date DATE NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
CREATE TABLE attribute_definition (
|
||||
attribute_definition_id INTEGER NOT NULL,
|
||||
attribute_name VARCHAR(255) NOT NULL,
|
||||
attribute_description CLOB NULL,
|
||||
attribute_type_concept_id INTEGER NOT NULL,
|
||||
attribute_syntax CLOB NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
/**************************
|
||||
|
||||
Standardized meta-data
|
||||
|
||||
***************************/
|
||||
|
||||
|
||||
CREATE TABLE cdm_source
|
||||
(
|
||||
cdm_source_name VARCHAR(255) NOT NULL,
|
||||
cdm_source_abbreviation VARCHAR(25) NULL,
|
||||
cdm_holder VARCHAR(255) NULL,
|
||||
source_description CLOB NULL,
|
||||
source_documentation_reference VARCHAR(255) NULL,
|
||||
cdm_etl_reference VARCHAR(255) NULL,
|
||||
source_release_date DATE NULL,
|
||||
cdm_release_date DATE NULL,
|
||||
cdm_version VARCHAR(10) NULL,
|
||||
vocabulary_version VARCHAR(20) NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
/************************
|
||||
|
||||
Standardized clinical data
|
||||
|
||||
************************/
|
||||
|
||||
|
||||
CREATE TABLE person
|
||||
(
|
||||
person_id INTEGER NOT NULL ,
|
||||
gender_concept_id INTEGER NOT NULL ,
|
||||
year_of_birth INTEGER NOT NULL ,
|
||||
month_of_birth INTEGER NULL,
|
||||
day_of_birth INTEGER NULL,
|
||||
time_of_birth VARCHAR(10) NULL,
|
||||
race_concept_id INTEGER NOT NULL,
|
||||
ethnicity_concept_id INTEGER NOT NULL,
|
||||
location_id INTEGER NULL,
|
||||
provider_id INTEGER NULL,
|
||||
care_site_id INTEGER NULL,
|
||||
person_source_value VARCHAR(50) NULL,
|
||||
gender_source_value VARCHAR(50) NULL,
|
||||
gender_source_concept_id INTEGER NULL,
|
||||
race_source_value VARCHAR(50) NULL,
|
||||
race_source_concept_id INTEGER NULL,
|
||||
ethnicity_source_value VARCHAR(50) NULL,
|
||||
ethnicity_source_concept_id INTEGER NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
CREATE TABLE observation_period
|
||||
(
|
||||
observation_period_id INTEGER NOT NULL ,
|
||||
person_id INTEGER NOT NULL ,
|
||||
observation_period_start_date DATE NOT NULL ,
|
||||
observation_period_end_date DATE NOT NULL ,
|
||||
period_type_concept_id INTEGER NOT NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
CREATE TABLE specimen
|
||||
(
|
||||
specimen_id INTEGER NOT NULL ,
|
||||
person_id INTEGER NOT NULL ,
|
||||
specimen_concept_id INTEGER NOT NULL ,
|
||||
specimen_type_concept_id INTEGER NOT NULL ,
|
||||
specimen_date DATE NOT NULL ,
|
||||
specimen_time VARCHAR(10) NULL ,
|
||||
quantity FLOAT NULL ,
|
||||
unit_concept_id INTEGER NULL ,
|
||||
anatomic_site_concept_id INTEGER NULL ,
|
||||
disease_status_concept_id INTEGER NULL ,
|
||||
specimen_source_id VARCHAR(50) NULL ,
|
||||
specimen_source_value VARCHAR(50) NULL ,
|
||||
unit_source_value VARCHAR(50) NULL ,
|
||||
anatomic_site_source_value VARCHAR(50) NULL ,
|
||||
disease_status_source_value VARCHAR(50) NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
CREATE TABLE death
|
||||
(
|
||||
person_id INTEGER NOT NULL ,
|
||||
death_date DATE NOT NULL ,
|
||||
death_type_concept_id INTEGER NOT NULL ,
|
||||
cause_concept_id INTEGER NULL ,
|
||||
cause_source_value VARCHAR(50) NULL,
|
||||
cause_source_concept_id INTEGER NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
CREATE TABLE visit_occurrence
|
||||
(
|
||||
visit_occurrence_id INTEGER NOT NULL ,
|
||||
person_id INTEGER NOT NULL ,
|
||||
visit_concept_id INTEGER NOT NULL ,
|
||||
visit_start_date DATE NOT NULL ,
|
||||
visit_start_time VARCHAR(10) NULL ,
|
||||
visit_end_date DATE NOT NULL ,
|
||||
visit_end_time VARCHAR(10) NULL ,
|
||||
visit_type_concept_id INTEGER NOT NULL ,
|
||||
provider_id INTEGER NULL,
|
||||
care_site_id INTEGER NULL,
|
||||
visit_source_value VARCHAR(50) NULL,
|
||||
visit_source_concept_id INTEGER NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
CREATE TABLE procedure_occurrence
|
||||
(
|
||||
procedure_occurrence_id INTEGER NOT NULL ,
|
||||
person_id INTEGER NOT NULL ,
|
||||
procedure_concept_id INTEGER NOT NULL ,
|
||||
procedure_date DATE NOT NULL ,
|
||||
procedure_type_concept_id INTEGER NOT NULL ,
|
||||
modifier_concept_id INTEGER NULL ,
|
||||
quantity INTEGER NULL ,
|
||||
provider_id INTEGER NULL ,
|
||||
visit_occurrence_id INTEGER NULL ,
|
||||
procedure_source_value VARCHAR(50) NULL ,
|
||||
procedure_source_concept_id INTEGER NULL ,
|
||||
qualifier_source_value VARCHAR(50) NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
CREATE TABLE drug_exposure
|
||||
(
|
||||
drug_exposure_id INTEGER NOT NULL ,
|
||||
person_id INTEGER NOT NULL ,
|
||||
drug_concept_id INTEGER NOT NULL ,
|
||||
drug_exposure_start_date DATE NOT NULL ,
|
||||
drug_exposure_end_date DATE NULL ,
|
||||
drug_type_concept_id INTEGER NOT NULL ,
|
||||
stop_reason VARCHAR(20) NULL ,
|
||||
refills INTEGER NULL ,
|
||||
quantity FLOAT NULL ,
|
||||
days_supply INTEGER NULL ,
|
||||
sig CLOB NULL ,
|
||||
route_concept_id INTEGER NULL ,
|
||||
effective_drug_dose FLOAT NULL ,
|
||||
dose_unit_concept_id INTEGER NULL ,
|
||||
lot_number VARCHAR(50) NULL ,
|
||||
provider_id INTEGER NULL ,
|
||||
visit_occurrence_id INTEGER NULL ,
|
||||
drug_source_value VARCHAR(50) NULL ,
|
||||
drug_source_concept_id INTEGER NULL ,
|
||||
route_source_value VARCHAR(50) NULL ,
|
||||
dose_unit_source_value VARCHAR(50) NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
CREATE TABLE device_exposure
|
||||
(
|
||||
device_exposure_id INTEGER NOT NULL ,
|
||||
person_id INTEGER NOT NULL ,
|
||||
device_concept_id INTEGER NOT NULL ,
|
||||
device_exposure_start_date DATE NOT NULL ,
|
||||
device_exposure_end_date DATE NULL ,
|
||||
device_type_concept_id INTEGER NOT NULL ,
|
||||
unique_device_id VARCHAR(50) NULL ,
|
||||
quantity INTEGER NULL ,
|
||||
provider_id INTEGER NULL ,
|
||||
visit_occurrence_id INTEGER NULL ,
|
||||
device_source_value VARCHAR(100) NULL ,
|
||||
device_source_concept_id INTEGER NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
CREATE TABLE condition_occurrence
|
||||
(
|
||||
condition_occurrence_id INTEGER NOT NULL ,
|
||||
person_id INTEGER NOT NULL ,
|
||||
condition_concept_id INTEGER NOT NULL ,
|
||||
condition_start_date DATE NOT NULL ,
|
||||
condition_end_date DATE NULL ,
|
||||
condition_type_concept_id INTEGER NOT NULL ,
|
||||
stop_reason VARCHAR(20) NULL ,
|
||||
provider_id INTEGER NULL ,
|
||||
visit_occurrence_id INTEGER NULL ,
|
||||
condition_source_value VARCHAR(50) NULL ,
|
||||
condition_source_concept_id INTEGER NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
CREATE TABLE measurement
|
||||
(
|
||||
measurement_id INTEGER NOT NULL ,
|
||||
person_id INTEGER NOT NULL ,
|
||||
measurement_concept_id INTEGER NOT NULL ,
|
||||
measurement_date DATE NOT NULL ,
|
||||
measurement_time VARCHAR(10) NULL ,
|
||||
measurement_type_concept_id INTEGER NOT NULL ,
|
||||
operator_concept_id INTEGER NULL ,
|
||||
value_as_number FLOAT NULL ,
|
||||
value_as_concept_id INTEGER NULL ,
|
||||
unit_concept_id INTEGER NULL ,
|
||||
range_low FLOAT NULL ,
|
||||
range_high FLOAT NULL ,
|
||||
provider_id INTEGER NULL ,
|
||||
visit_occurrence_id INTEGER NULL ,
|
||||
measurement_source_value VARCHAR(50) NULL ,
|
||||
measurement_source_concept_id INTEGER NULL ,
|
||||
unit_source_value VARCHAR(50) NULL ,
|
||||
value_source_value VARCHAR(50) NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
CREATE TABLE note
|
||||
(
|
||||
note_id INTEGER NOT NULL ,
|
||||
person_id INTEGER NOT NULL ,
|
||||
note_date DATE NOT NULL ,
|
||||
note_time VARCHAR(10) NULL ,
|
||||
note_type_concept_id INTEGER NOT NULL ,
|
||||
note_text CLOB NOT NULL ,
|
||||
provider_id INTEGER NULL ,
|
||||
visit_occurrence_id INTEGER NULL ,
|
||||
note_source_value VARCHAR(50) NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
CREATE TABLE observation
|
||||
(
|
||||
observation_id INTEGER NOT NULL ,
|
||||
person_id INTEGER NOT NULL ,
|
||||
observation_concept_id INTEGER NOT NULL ,
|
||||
observation_date DATE NOT NULL ,
|
||||
observation_time VARCHAR(10) NULL ,
|
||||
observation_type_concept_id INTEGER NOT NULL ,
|
||||
value_as_number FLOAT NULL ,
|
||||
value_as_string VARCHAR(60) NULL ,
|
||||
value_as_concept_id INTEGER NULL ,
|
||||
qualifier_concept_id INTEGER NULL ,
|
||||
unit_concept_id INTEGER NULL ,
|
||||
provider_id INTEGER NULL ,
|
||||
visit_occurrence_id INTEGER NULL ,
|
||||
observation_source_value VARCHAR(50) NULL ,
|
||||
observation_source_concept_id INTEGER NULL ,
|
||||
unit_source_value VARCHAR(50) NULL ,
|
||||
qualifier_source_value VARCHAR(50) NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
CREATE TABLE fact_relationship
|
||||
(
|
||||
domain_concept_id_1 INTEGER NOT NULL ,
|
||||
fact_id_1 INTEGER NOT NULL ,
|
||||
domain_concept_id_2 INTEGER NOT NULL ,
|
||||
fact_id_2 INTEGER NOT NULL ,
|
||||
relationship_concept_id INTEGER NOT NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
|
||||
/************************
|
||||
|
||||
Standardized health system data
|
||||
|
||||
************************/
|
||||
|
||||
|
||||
|
||||
CREATE TABLE location
|
||||
(
|
||||
location_id INTEGER NOT NULL ,
|
||||
address_1 VARCHAR(50) NULL ,
|
||||
address_2 VARCHAR(50) NULL ,
|
||||
city VARCHAR(50) NULL ,
|
||||
state VARCHAR(2) NULL ,
|
||||
zip VARCHAR(9) NULL ,
|
||||
county VARCHAR(20) NULL ,
|
||||
location_source_value VARCHAR(50) NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
CREATE TABLE care_site
|
||||
(
|
||||
care_site_id INTEGER NOT NULL ,
|
||||
care_site_name VARCHAR(255) NULL ,
|
||||
place_of_service_concept_id INTEGER NULL ,
|
||||
location_id INTEGER NULL ,
|
||||
care_site_source_value VARCHAR(50) NULL ,
|
||||
place_of_service_source_value VARCHAR(50) NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
CREATE TABLE provider
|
||||
(
|
||||
provider_id INTEGER NOT NULL ,
|
||||
provider_name VARCHAR(255) NULL ,
|
||||
NPI VARCHAR(20) NULL ,
|
||||
DEA VARCHAR(20) NULL ,
|
||||
specialty_concept_id INTEGER NULL ,
|
||||
care_site_id INTEGER NULL ,
|
||||
year_of_birth INTEGER NULL ,
|
||||
gender_concept_id INTEGER NULL ,
|
||||
provider_source_value VARCHAR(50) NULL ,
|
||||
specialty_source_value VARCHAR(50) NULL ,
|
||||
specialty_source_concept_id INTEGER NULL ,
|
||||
gender_source_value VARCHAR(50) NULL ,
|
||||
gender_source_concept_id INTEGER NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
|
||||
/************************
|
||||
|
||||
Standardized health economics
|
||||
|
||||
************************/
|
||||
|
||||
|
||||
CREATE TABLE payer_plan_period
|
||||
(
|
||||
payer_plan_period_id INTEGER NOT NULL ,
|
||||
person_id INTEGER NOT NULL ,
|
||||
payer_plan_period_start_date DATE NOT NULL ,
|
||||
payer_plan_period_end_date DATE NOT NULL ,
|
||||
payer_source_value VARCHAR (50) NULL ,
|
||||
plan_source_value VARCHAR (50) NULL ,
|
||||
family_source_value VARCHAR (50) NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
-- The individual cost tables are phased out and will be removed
|
||||
/*
|
||||
CREATE TABLE visit_cost
|
||||
(
|
||||
visit_cost_id INTEGER NOT NULL ,
|
||||
visit_occurrence_id INTEGER NOT NULL ,
|
||||
currency_concept_id INTEGER NULL ,
|
||||
paid_copay FLOAT NULL ,
|
||||
paid_coinsurance FLOAT NULL ,
|
||||
paid_toward_deductible FLOAT NULL ,
|
||||
paid_by_payer FLOAT NULL ,
|
||||
paid_by_coordination_benefits FLOAT NULL ,
|
||||
total_out_of_pocket FLOAT NULL ,
|
||||
total_paid FLOAT NULL ,
|
||||
payer_plan_period_id INTEGER NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
CREATE TABLE procedure_cost
|
||||
(
|
||||
procedure_cost_id INTEGER NOT NULL ,
|
||||
procedure_occurrence_id INTEGER NOT NULL ,
|
||||
currency_concept_id INTEGER NULL ,
|
||||
paid_copay FLOAT NULL ,
|
||||
paid_coinsurance FLOAT NULL ,
|
||||
paid_toward_deductible FLOAT NULL ,
|
||||
paid_by_payer FLOAT NULL ,
|
||||
paid_by_coordination_benefits FLOAT NULL ,
|
||||
total_out_of_pocket FLOAT NULL ,
|
||||
total_paid FLOAT NULL ,
|
||||
revenue_code_concept_id INTEGER NULL ,
|
||||
payer_plan_period_id INTEGER NULL ,
|
||||
revenue_code_source_value VARCHAR(50) NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
CREATE TABLE drug_cost
|
||||
(
|
||||
drug_cost_id INTEGER NOT NULL ,
|
||||
drug_exposure_id INTEGER NOT NULL ,
|
||||
currency_concept_id INTEGER NULL ,
|
||||
paid_copay FLOAT NULL ,
|
||||
paid_coinsurance FLOAT NULL ,
|
||||
paid_toward_deductible FLOAT NULL ,
|
||||
paid_by_payer FLOAT NULL ,
|
||||
paid_by_coordination_benefits FLOAT NULL ,
|
||||
total_out_of_pocket FLOAT NULL ,
|
||||
total_paid FLOAT NULL ,
|
||||
ingredient_cost FLOAT NULL ,
|
||||
dispensing_fee FLOAT NULL ,
|
||||
average_wholesale_price FLOAT NULL ,
|
||||
payer_plan_period_id INTEGER NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
CREATE TABLE device_cost
|
||||
(
|
||||
device_cost_id INTEGER NOT NULL ,
|
||||
device_exposure_id INTEGER NOT NULL ,
|
||||
currency_concept_id INTEGER NULL ,
|
||||
paid_copay FLOAT NULL ,
|
||||
paid_coinsurance FLOAT NULL ,
|
||||
paid_toward_deductible FLOAT NULL ,
|
||||
paid_by_payer FLOAT NULL ,
|
||||
paid_by_coordination_benefits FLOAT NULL ,
|
||||
total_out_of_pocket FLOAT NULL ,
|
||||
total_paid FLOAT NULL ,
|
||||
payer_plan_period_id INTEGER NULL
|
||||
)
|
||||
;
|
||||
*/
|
||||
|
||||
|
||||
CREATE TABLE cost
|
||||
(
|
||||
cost_id INTEGER NOT NULL ,
|
||||
cost_event_id INTEGER NOT NULL ,
|
||||
cost_domain_id VARCHAR2(20) NOT NULL ,
|
||||
cost_type_concept_id INTEGER NOT NULL ,
|
||||
currency_concept_id INTEGER NULL ,
|
||||
total_charge FLOAT NULL ,
|
||||
total_cost FLOAT NULL ,
|
||||
total_paid FLOAT NULL ,
|
||||
paid_by_payer FLOAT NULL ,
|
||||
paid_by_patient FLOAT NULL ,
|
||||
paid_patient_copay FLOAT NULL ,
|
||||
paid_patient_coinsurance FLOAT NULL ,
|
||||
paid_patient_deductible FLOAT NULL ,
|
||||
paid_by_primary FLOAT NULL ,
|
||||
paid_ingredient_cost FLOAT NULL ,
|
||||
paid_dispensing_fee FLOAT NULL ,
|
||||
payer_plan_period_id INTEGER NULL ,
|
||||
amount_allowed FLOAT NULL ,
|
||||
revenue_code_concept_id INTEGER NULL ,
|
||||
reveue_code_source_value VARCHAR2(50) NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
/************************
|
||||
|
||||
Standardized derived elements
|
||||
|
||||
************************/
|
||||
|
||||
CREATE TABLE cohort
|
||||
(
|
||||
cohort_definition_id INTEGER NOT NULL ,
|
||||
subject_id INTEGER NOT NULL ,
|
||||
cohort_start_date DATE NOT NULL ,
|
||||
cohort_end_date DATE NOT NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
CREATE TABLE cohort_attribute
|
||||
(
|
||||
cohort_definition_id INTEGER NOT NULL ,
|
||||
cohort_start_date DATE NOT NULL ,
|
||||
cohort_end_date DATE NOT NULL ,
|
||||
subject_id INTEGER NOT NULL ,
|
||||
attribute_definition_id INTEGER NOT NULL ,
|
||||
value_as_number FLOAT NULL ,
|
||||
value_as_concept_id INTEGER NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
|
||||
CREATE TABLE drug_era
|
||||
(
|
||||
drug_era_id INTEGER NOT NULL ,
|
||||
person_id INTEGER NOT NULL ,
|
||||
drug_concept_id INTEGER NOT NULL ,
|
||||
drug_era_start_date DATE NOT NULL ,
|
||||
drug_era_end_date DATE NOT NULL ,
|
||||
drug_exposure_count INTEGER NULL ,
|
||||
gap_days INTEGER NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
CREATE TABLE dose_era
|
||||
(
|
||||
dose_era_id INTEGER NOT NULL ,
|
||||
person_id INTEGER NOT NULL ,
|
||||
drug_concept_id INTEGER NOT NULL ,
|
||||
unit_concept_id INTEGER NOT NULL ,
|
||||
dose_value FLOAT NOT NULL ,
|
||||
dose_era_start_date DATE NOT NULL ,
|
||||
dose_era_end_date DATE NOT NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
|
||||
CREATE TABLE condition_era
|
||||
(
|
||||
condition_era_id INTEGER NOT NULL ,
|
||||
person_id INTEGER NOT NULL ,
|
||||
condition_concept_id INTEGER NOT NULL ,
|
||||
condition_era_start_date DATE NOT NULL ,
|
||||
condition_era_end_date DATE NOT NULL ,
|
||||
condition_occurrence_count INTEGER NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
|
@ -1,168 +0,0 @@
|
|||
/*********************************************************************************
|
||||
# Copyright 2014 Observational Health Data Sciences and Informatics
|
||||
#
|
||||
#
|
||||
# Licensed under the Apache License, Version 2.0 (the "License");
|
||||
# you may not use this file except in compliance with the License.
|
||||
# You may obtain a copy of the License at
|
||||
#
|
||||
# http://www.apache.org/licenses/LICENSE-2.0
|
||||
#
|
||||
# Unless required by applicable law or agreed to in writing, software
|
||||
# distributed under the License is distributed on an "AS IS" BASIS,
|
||||
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
|
||||
# See the License for the specific language governing permissions and
|
||||
# limitations under the License.
|
||||
********************************************************************************/
|
||||
|
||||
/************************
|
||||
|
||||
####### # # ####### ###### ##### ###### # # ####### ###
|
||||
# # ## ## # # # # # # # # ## ## # # # # # # ##### ###### # # ###### ####
|
||||
# # # # # # # # # # # # # # # # # # # # # ## # # # # # # # #
|
||||
# # # # # # # ###### # # # # # # # # ###### # # # # # # ##### ## ##### ####
|
||||
# # # # # # # # # # # # # # # # # # # # # # ## # #
|
||||
# # # # # # # # # # # # # # # # # # # ## # # # # # # # #
|
||||
####### # # ####### # ##### ###### # # ## ##### ### # # ##### ###### # # ###### ####
|
||||
|
||||
|
||||
script to create the required indexes within OMOP common data model, version 5.0 for Oracle database
|
||||
|
||||
last revised: 12 Oct 2014
|
||||
|
||||
author: Patrick Ryan
|
||||
|
||||
description: These indices are considered a minimal requirement to ensure adequate performance of analyses.
|
||||
|
||||
*************************/
|
||||
|
||||
|
||||
/************************
|
||||
|
||||
Standardized vocabulary
|
||||
|
||||
************************/
|
||||
|
||||
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 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_synonym_id ON concept_synonym (concept_id ASC);
|
||||
|
||||
CREATE 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 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 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);
|
||||
|
||||
/**************************
|
||||
|
||||
Standardized meta-data
|
||||
|
||||
***************************/
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
/************************
|
||||
|
||||
Standardized clinical data
|
||||
|
||||
************************/
|
||||
|
||||
CREATE INDEX idx_observation_period_id ON observation_period (person_id ASC);
|
||||
|
||||
CREATE INDEX idx_specimen_person_id ON specimen (person_id ASC);
|
||||
CREATE INDEX idx_specimen_concept_id ON specimen (specimen_concept_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_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 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 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 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 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 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 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 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 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 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 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);
|
||||
|
||||
|
|
@ -1,188 +0,0 @@
|
|||
/*********************************************************************************
|
||||
# Copyright 2014 Observational Health Data Sciences and Informatics
|
||||
#
|
||||
#
|
||||
# Licensed under the Apache License, Version 2.0 (the "License");
|
||||
# you may not use this file except in compliance with the License.
|
||||
# You may obtain a copy of the License at
|
||||
#
|
||||
# http://www.apache.org/licenses/LICENSE-2.0
|
||||
#
|
||||
# Unless required by applicable law or agreed to in writing, software
|
||||
# distributed under the License is distributed on an "AS IS" BASIS,
|
||||
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
|
||||
# See the License for the specific language governing permissions and
|
||||
# limitations under the License.
|
||||
********************************************************************************/
|
||||
|
||||
/************************
|
||||
|
||||
####### # # ####### ###### ##### ###### # # ####### ###
|
||||
# # ## ## # # # # # # # # ## ## # # # # # # ##### ###### # # ###### ####
|
||||
# # # # # # # # # # # # # # # # # # # # # ## # # # # # # # #
|
||||
# # # # # # # ###### # # # # # # # # ###### # # # # # # ##### ## ##### ####
|
||||
# # # # # # # # # # # # # # # # # # # # # # ## # #
|
||||
# # # # # # # # # # # # # # # # # # # ## # # # # # # # #
|
||||
####### # # ####### # ##### ###### # # ## ##### ### # # ##### ###### # # ###### ####
|
||||
|
||||
|
||||
script to create the required indexes within OMOP common data model, version 5.0 for Oracle database
|
||||
|
||||
last revised: 12 Oct 2014
|
||||
|
||||
author: Patrick Ryan
|
||||
|
||||
description: These indices are considered a minimal requirement to ensure adequate performance of analyses.
|
||||
|
||||
*************************/
|
||||
|
||||
|
||||
/************************
|
||||
|
||||
Standardized vocabulary
|
||||
|
||||
************************/
|
||||
|
||||
CREATE UNIQUE 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 INDEX idx_vocabulary_vocabulary_id ON vocabulary (vocabulary_id ASC);
|
||||
|
||||
CREATE UNIQUE INDEX idx_domain_domain_id ON domain (domain_id ASC);
|
||||
|
||||
CREATE UNIQUE 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 INDEX idx_relationship_rel_id ON relationship (relationship_id ASC);
|
||||
|
||||
CREATE INDEX idx_concept_synonym_id ON concept_synonym (concept_id ASC);
|
||||
|
||||
CREATE 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 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 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 INDEX idx_cohort_definition_id ON cohort_definition (cohort_definition_id ASC);
|
||||
|
||||
CREATE INDEX idx_attribute_definition_id ON attribute_definition (attribute_definition_id ASC);
|
||||
|
||||
|
||||
/**************************
|
||||
|
||||
Standardized meta-data
|
||||
|
||||
***************************/
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
/************************
|
||||
|
||||
Standardized clinical data
|
||||
|
||||
************************/
|
||||
|
||||
CREATE UNIQUE INDEX idx_person_id ON person (person_id ASC);
|
||||
|
||||
CREATE INDEX idx_observation_period_id ON observation_period (person_id ASC);
|
||||
|
||||
CREATE INDEX idx_specimen_person_id ON specimen (person_id ASC);
|
||||
CREATE INDEX idx_specimen_concept_id ON specimen (specimen_concept_id ASC);
|
||||
|
||||
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_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 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 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 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 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 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 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 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 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 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 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);
|
||||
|
||||
|
|
@ -7,14 +7,8 @@ In order to create your instantiation of the Common Data Model, we recommend fol
|
|||
|
||||
1. Create an empty schema.
|
||||
|
||||
2. Execute the script `OMOP CDM ddl - Oracle.sql` to create the tables and fields.
|
||||
2. Execute the script `CDM V4 ddl.sql` to create the tables and fields.
|
||||
|
||||
3. Load your data into the schema.
|
||||
3. Load your data into the schema using the loading scripts in VocabImport
|
||||
|
||||
4. Execute the script `OMOP CDM constraints - Oracle.sql` to add the constraints (primary and foreign keys).
|
||||
|
||||
5. Execute the script `OMOP CDM indexes required - Oracle - With constraints.sql` to add the minimum set of indexes we recommend.
|
||||
|
||||
Note: you could also apply the constraints and/or the indexes before loading the data, but this will slow down the insertion of the data considerably.
|
||||
|
||||
Also note: you can apply the indexes without first applying the constraints, but then we recommend you use the script `OMOP CDM indexes required - Oracle - Without constraints.sql`. (This script will also create the indexes that would normally be automatically created by the primary key constraints.)
|
||||
Note: you could also apply the constraints and the indexes after loading the data, this will speed up the insertion of the data considerably.
|
||||
|
|
|
|||
|
|
@ -1,52 +1,51 @@
|
|||
REM *********************************************************************************
|
||||
REM Copyright 2014 Observational Health Data Sciences and Informatics
|
||||
REM
|
||||
REM
|
||||
REM Licensed under the Apache License, Version 2.0 (the "License");
|
||||
REM you may not use this file except in compliance with the License.
|
||||
REM You may obtain a copy of the License at
|
||||
REM
|
||||
REM http://www.apache.org/licenses/LICENSE-2.0
|
||||
REM
|
||||
REM Unless required by applicable law or agreed to in writing, software
|
||||
REM distributed under the License is distributed on an "AS IS" BASIS,
|
||||
REM WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
|
||||
REM See the License for the specific language governing permissions and
|
||||
REM limitations under the License.
|
||||
REM *******************************************************************************/
|
||||
/*********************************************************************************
|
||||
# Copyright 2015 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.4
|
||||
********************************************************************************/
|
||||
|
||||
REM ************************
|
||||
REM
|
||||
REM ####### # # ####### ###### ##### ###### # # #######
|
||||
REM # # ## ## # # # # # # # # ## ## # # #
|
||||
REM # # # # # # # # # # # # # # # # # # # #
|
||||
REM # # # # # # # ###### # # # # # # # # ######
|
||||
REM # # # # # # # # # # # # # # #
|
||||
REM # # # # # # # # # # # # # # # # #
|
||||
REM ####### # # ####### # ##### ###### # # ## #####
|
||||
REM
|
||||
REM
|
||||
REM Script to load the common data model, version 5.0 vocabulary tables for PostgreSQL database on Windows (MS-DOS style file paths)
|
||||
REM
|
||||
REM Notes
|
||||
REM
|
||||
REM 1) There is no data file load for the SOURCE_TO_CONCEPT_MAP table because that table is deprecated in CDM version 5.0
|
||||
REM 2) This script assumes the CDM version 5 vocabulary zip file has been unzipped into the "C:\CDMV5VOCAB" directory.
|
||||
REM 3) If you unzipped your CDM version 5 vocabulary files into a different directory then replace all file paths below, with your directory path.
|
||||
REM
|
||||
REM last revised: 26 Nov 2014
|
||||
REM
|
||||
REM author: Lee Evans
|
||||
REM
|
||||
REM
|
||||
REM *************************/
|
||||
/************************
|
||||
|
||||
sqlldr CDMV5/<password> CONTROL=CONCEPT.ctl LOG=C:\CDMV5VOCAB\CONCEPT.log BAD=C:\CDMV5VOCAB\CONCEPT.bad
|
||||
sqlldr CDMV5/<password> CONTROL=CONCEPT_ANCESTOR.ctl LOG=C:\CDMV5VOCAB\CONCEPT_ANCESTOR.log BAD=C:\CDMV5VOCAB\CONCEPT_ANCESTOR.bad
|
||||
sqlldr CDMV5/<password> CONTROL=CONCEPT_CLASS.ctl LOG=C:\CDMV5VOCAB\CONCEPT_CLASS.log BAD=C:\CDMV5VOCAB\CONCEPT_CLASS.bad
|
||||
sqlldr CDMV5/<password> CONTROL=CONCEPT_RELATIONSHIP.ctl LOG=C:\CDMV5VOCAB\CONCEPT_RELATIONSHIP.log BAD=C:\CDMV5VOCAB\CONCEPT_RELATIONSHIP.bad
|
||||
sqlldr CDMV5/<password> CONTROL=CONCEPT_SYNONYM.ctl LOG=C:\CDMV5VOCAB\CONCEPT_SYNONYM.log BAD=C:\CDMV5VOCAB\CONCEPT_SYNONYM.bad
|
||||
sqlldr CDMV5/<password> CONTROL=DOMAIN.ctl LOG=C:\CDMV5VOCAB\DOMAIN.log BAD=C:\CDMV5VOCAB\DOMAIN.bad
|
||||
sqlldr CDMV5/<password> CONTROL=DRUG_STRENGTH.ctl LOG=C:\CDMV5VOCAB\DRUG_STRENGTH.log BAD=C:\CDMV5VOCAB\DRUG_STRENGTH.bad
|
||||
sqlldr CDMV5/<password> CONTROL=RELATIONSHIP.ctl LOG=C:\CDMV5VOCAB\RELATIONSHIP.log BAD=C:\CDMV5VOCAB\RELATIONSHIP.bad
|
||||
sqlldr CDMV5/<password> CONTROL=VOCABULARY.ctl LOG=C:\CDMV5VOCAB\VOCABULARY.log BAD=C:\CDMV5VOCAB\VOCABULARY.bad
|
||||
####### # # ####### ###### ##### ###### # # ## #######
|
||||
# # ## ## # # # # # # # # ## ## # # # # #
|
||||
# # # # # # # # # # # # # # # # # # # # # #
|
||||
# # # # # # # ###### # # # # # # # # ####### #######
|
||||
# # # # # # # # # # # # # # # #
|
||||
# # # # # # # # # # # # # # # # # #
|
||||
####### # # ####### # ##### ###### # # ## # # #####
|
||||
|
||||
|
||||
script to load the Vocabulary related tables in the OMOP common data model, version 4.5 for Oracle database
|
||||
|
||||
last revised: 19 Mar 2015
|
||||
|
||||
author: Lee Evans
|
||||
|
||||
Notes
|
||||
|
||||
1) This script assumes the CDM version 4.5 vocabulary zip file has been unzipped into the "C:\CDM" directory.
|
||||
2) If you unzipped your CDM version 4.5 vocabulary files into a different directory then replace all file paths below, with your directory path.
|
||||
3) If you have existing data in your CDM vocabulary tables then backup that data (if needed) and truncate those tables before loading
|
||||
|
||||
|
||||
*************************/
|
||||
|
||||
sqlldr CDM/<password> CONTROL=CONCEPT.ctl LOG=C:\CDM\CONCEPT.log BAD=C:\CDM\CONCEPT.bad
|
||||
sqlldr CDM/<password> CONTROL=CONCEPT_ANCESTOR.ctl LOG=C:\CDM\CONCEPT_ANCESTOR.log BAD=C:\CDM\CONCEPT_ANCESTOR.bad
|
||||
sqlldr CDM/<password> CONTROL=CONCEPT_RELATIONSHIP.ctl LOG=C:\CDM\CONCEPT_RELATIONSHIP.log BAD=C:\CDM\CONCEPT_RELATIONSHIP.bad
|
||||
sqlldr CDM/<password> CONTROL=CONCEPT_SYNONYM.ctl LOG=C:\CDM\CONCEPT_SYNONYM.log BAD=C:\CDM\CONCEPT_SYNONYM.bad
|
||||
sqlldr CDM/<password> CONTROL=DRUG_STRENGTH.ctl LOG=C:\CDM\DRUG_STRENGTH.log BAD=C:\CDM\DRUG_STRENGTH.bad
|
||||
sqlldr CDM/<password> CONTROL=RELATIONSHIP.ctl LOG=C:\CDM\RELATIONSHIP.log BAD=C:\CDM\RELATIONSHIP.bad
|
||||
sqlldr CDM/<password> CONTROL=VOCABULARY.ctl LOG=C:\CDM\VOCABULARY.log BAD=C:\CDM\VOCABULARY.bad
|
||||
sqlldr CDM/<password> CONTROL=SOURCE_TO_CONCEPT_MAP.ctl LOG=C:\CDM\SOURCE_TO_CONCEPT_MAP.log BAD=C:\CDM\SOURCE_TO_CONCEPT_MAP.bad
|
||||
|
|
|
|||
|
|
@ -7,11 +7,10 @@ fields terminated by '\t'
|
|||
trailing nullcols
|
||||
(
|
||||
concept_id,
|
||||
concept_name,
|
||||
domain_id,
|
||||
concept_name CHAR(256),
|
||||
concept_level,
|
||||
concept_class,
|
||||
vocabulary_id,
|
||||
concept_class_id,
|
||||
standard_concept,
|
||||
concept_code,
|
||||
valid_start_date DATE 'YYYYMMDD',
|
||||
valid_end_date DATE 'YYYYMMDD',
|
||||
|
|
|
|||
|
|
@ -1,12 +0,0 @@
|
|||
options (skip=1)
|
||||
load data
|
||||
infile concept_class.csv
|
||||
into table concept_class
|
||||
replace
|
||||
fields terminated by '\t'
|
||||
trailing nullcols
|
||||
(
|
||||
concept_class_id,
|
||||
concept_class_name,
|
||||
concept_class_concept_id
|
||||
)
|
||||
|
|
@ -6,7 +6,7 @@ replace
|
|||
fields terminated by '\t'
|
||||
trailing nullcols
|
||||
(
|
||||
concept_synonym_id,
|
||||
concept_id,
|
||||
concept_synonym_name CHAR(1000),
|
||||
language_concept_id
|
||||
concept_synonym_name CHAR(1000)
|
||||
)
|
||||
|
|
@ -1,12 +0,0 @@
|
|||
options (skip=1)
|
||||
load data
|
||||
infile domain.csv
|
||||
into table domain
|
||||
replace
|
||||
fields terminated by '\t'
|
||||
trailing nullcols
|
||||
(
|
||||
domain_id,
|
||||
domain_name,
|
||||
domain_concept_id
|
||||
)
|
||||
|
|
@ -9,12 +9,10 @@ trailing nullcols
|
|||
drug_concept_id,
|
||||
ingredient_concept_id,
|
||||
amount_value,
|
||||
amount_unit_concept_id,
|
||||
numerator_value,
|
||||
numerator_unit_concept_id,
|
||||
denominator_value,
|
||||
denominator_unit_concept_id,
|
||||
box_size,
|
||||
amount_unit,
|
||||
concentration_value,
|
||||
concentration_enum_unit,
|
||||
concentration_denom_unit,
|
||||
valid_start_date DATE 'YYYYMMDD',
|
||||
valid_end_date DATE 'YYYYMMDD',
|
||||
invalid_reason
|
||||
|
|
|
|||
|
|
@ -10,6 +10,5 @@ trailing nullcols
|
|||
relationship_name,
|
||||
is_hierarchical,
|
||||
defines_ancestry,
|
||||
reverse_relationship_id,
|
||||
relationship_concept_id
|
||||
reverse_relationship
|
||||
)
|
||||
|
|
@ -7,8 +7,5 @@ fields terminated by '\t'
|
|||
trailing nullcols
|
||||
(
|
||||
vocabulary_id,
|
||||
vocabulary_name,
|
||||
vocabulary_reference,
|
||||
vocabulary_version,
|
||||
vocabulary_concept_id
|
||||
vocabulary_name
|
||||
)
|
||||
|
|
@ -1,545 +0,0 @@
|
|||
/*********************************************************************************
|
||||
# Copyright 2014 Observational Health Data Sciences and Informatics
|
||||
#
|
||||
#
|
||||
# Licensed under the Apache License, Version 2.0 (the "License");
|
||||
# you may not use this file except in compliance with the License.
|
||||
# You may obtain a copy of the License at
|
||||
#
|
||||
# http://www.apache.org/licenses/LICENSE-2.0
|
||||
#
|
||||
# Unless required by applicable law or agreed to in writing, software
|
||||
# distributed under the License is distributed on an "AS IS" BASIS,
|
||||
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
|
||||
# See the License for the specific language governing permissions and
|
||||
# limitations under the License.
|
||||
********************************************************************************/
|
||||
|
||||
/************************
|
||||
|
||||
####### # # ####### ###### ##### ###### # # ####### #####
|
||||
# # ## ## # # # # # # # # ## ## # # # # # #### # # #### ##### ##### ## # # # ##### ####
|
||||
# # # # # # # # # # # # # # # # # # # # # # # ## # # # # # # # # ## # # #
|
||||
# # # # # # # ###### # # # # # # # # ###### # # # # # # #### # # # # # # # # # # ####
|
||||
# # # # # # # # # # # # # # # # # # # # # # # ##### ###### # # # # # #
|
||||
# # # # # # # # # # # # # # # # # # # # # # ## # # # # # # # # # ## # # #
|
||||
####### # # ####### # ##### ###### # # ## ##### ##### #### # # #### # # # # # # # # # ####
|
||||
|
||||
|
||||
script to create constraints within OMOP common data model, version 5.0 for PostgreSQL database
|
||||
|
||||
last revised: 12 Oct 2014
|
||||
|
||||
author: Patrick Ryan
|
||||
|
||||
|
||||
*************************/
|
||||
|
||||
|
||||
/************************
|
||||
*************************
|
||||
*************************
|
||||
*************************
|
||||
|
||||
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 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 visit_cost ADD CONSTRAINT xpk_visit_cost PRIMARY KEY ( visit_cost_id ) ;
|
||||
|
||||
ALTER TABLE procedure_cost ADD CONSTRAINT xpk_procedure_cost PRIMARY KEY ( procedure_cost_id ) ;
|
||||
|
||||
ALTER TABLE drug_cost ADD CONSTRAINT xpk_drug_cost PRIMARY KEY ( drug_cost_id ) ;
|
||||
|
||||
ALTER TABLE device_cost ADD CONSTRAINT xpk_device_cost PRIMARY KEY ( device_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 ) ;
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
/************************
|
||||
*************************
|
||||
*************************
|
||||
*************************
|
||||
|
||||
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 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_dose_unit_concept FOREIGN KEY (dose_unit_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 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_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 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 visit_cost ADD CONSTRAINT fpk_visit_cost_id FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id);
|
||||
|
||||
ALTER TABLE visit_cost ADD CONSTRAINT fpk_visit_cost_currency FOREIGN KEY (currency_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE visit_cost ADD CONSTRAINT fpk_visit_cost_period FOREIGN KEY (payer_plan_period_id) REFERENCES payer_plan_period (payer_plan_period_id);
|
||||
|
||||
|
||||
ALTER TABLE procedure_cost ADD CONSTRAINT fpk_procedure_cost_id FOREIGN KEY (procedure_occurrence_id) REFERENCES procedure_occurrence (procedure_occurrence_id);
|
||||
|
||||
ALTER TABLE procedure_cost ADD CONSTRAINT fpk_procedure_cost_currency FOREIGN KEY (currency_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE procedure_cost ADD CONSTRAINT fpk_procedure_cost_period FOREIGN KEY (payer_plan_period_id) REFERENCES payer_plan_period (payer_plan_period_id);
|
||||
|
||||
ALTER TABLE procedure_cost ADD CONSTRAINT fpk_procedure_cost_revenue FOREIGN KEY (revenue_code_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
|
||||
ALTER TABLE drug_cost ADD CONSTRAINT fpk_drug_cost_id FOREIGN KEY (drug_exposure_id) REFERENCES drug_exposure (drug_exposure_id);
|
||||
|
||||
ALTER TABLE drug_cost ADD CONSTRAINT fpk_drug_cost_currency FOREIGN KEY (currency_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE drug_cost ADD CONSTRAINT fpk_drug_cost_period FOREIGN KEY (payer_plan_period_id) REFERENCES payer_plan_period (payer_plan_period_id);
|
||||
|
||||
|
||||
ALTER TABLE device_cost ADD CONSTRAINT fpk_device_cost_id FOREIGN KEY (device_exposure_id) REFERENCES device_exposure (device_exposure_id);
|
||||
|
||||
ALTER TABLE device_cost ADD CONSTRAINT fpk_device_cost_currency FOREIGN KEY (currency_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE device_cost ADD CONSTRAINT fpk_device_cost_period FOREIGN KEY (payer_plan_period_id) REFERENCES payer_plan_period (payer_plan_period_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);
|
||||
|
||||
|
|
@ -1,740 +0,0 @@
|
|||
/*********************************************************************************
|
||||
# Copyright 2014-6 Observational Health Data Sciences and Informatics
|
||||
#
|
||||
#
|
||||
# Licensed under the Apache License, Version 2.0 (the "License");
|
||||
# you may not use this file except in compliance with the License.
|
||||
# You may obtain a copy of the License at
|
||||
#
|
||||
# http://www.apache.org/licenses/LICENSE-2.0
|
||||
#
|
||||
# Unless required by applicable law or agreed to in writing, software
|
||||
# distributed under the License is distributed on an "AS IS" BASIS,
|
||||
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
|
||||
# See the License for the specific language governing permissions and
|
||||
# limitations under the License.
|
||||
********************************************************************************/
|
||||
|
||||
/************************
|
||||
|
||||
####### # # ####### ###### ##### ###### # # #######
|
||||
# # ## ## # # # # # # # # ## ## # # #
|
||||
# # # # # # # # # # # # # # # # # # # #
|
||||
# # # # # # # ###### # # # # # # # # ######
|
||||
# # # # # # # # # # # # # # #
|
||||
# # # # # # # # # # # # # # # # #
|
||||
####### # # ####### # ##### ###### # # ## #####
|
||||
|
||||
|
||||
script to create OMOP common data model, version 5.0 for PostgreSQL database
|
||||
|
||||
last revised: 1-May-2016
|
||||
|
||||
Authors: Patrick Ryan, Christian Reich
|
||||
|
||||
|
||||
*************************/
|
||||
|
||||
|
||||
/************************
|
||||
|
||||
Standardized vocabulary
|
||||
|
||||
************************/
|
||||
|
||||
|
||||
CREATE TABLE concept (
|
||||
concept_id INTEGER NOT NULL,
|
||||
concept_name VARCHAR(255) NOT NULL,
|
||||
domain_id VARCHAR(20) NOT NULL,
|
||||
vocabulary_id VARCHAR(20) NOT NULL,
|
||||
concept_class_id VARCHAR(20) NOT NULL,
|
||||
standard_concept VARCHAR(1) NULL,
|
||||
concept_code VARCHAR(50) NOT NULL,
|
||||
valid_start_date DATE NOT NULL,
|
||||
valid_end_date DATE NOT NULL,
|
||||
invalid_reason VARCHAR(1) NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
|
||||
CREATE TABLE vocabulary (
|
||||
vocabulary_id VARCHAR(20) NOT NULL,
|
||||
vocabulary_name VARCHAR(255) NOT NULL,
|
||||
vocabulary_reference VARCHAR(255) NULL,
|
||||
vocabulary_version VARCHAR(255) NULL,
|
||||
vocabulary_concept_id INTEGER NOT NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
|
||||
CREATE TABLE domain (
|
||||
domain_id VARCHAR(20) NOT NULL,
|
||||
domain_name VARCHAR(255) NOT NULL,
|
||||
domain_concept_id INTEGER NOT NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
CREATE TABLE concept_class (
|
||||
concept_class_id VARCHAR(20) NOT NULL,
|
||||
concept_class_name VARCHAR(255) NOT NULL,
|
||||
concept_class_concept_id INTEGER NOT NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
|
||||
CREATE TABLE concept_relationship (
|
||||
concept_id_1 INTEGER NOT NULL,
|
||||
concept_id_2 INTEGER NOT NULL,
|
||||
relationship_id VARCHAR(20) NOT NULL,
|
||||
valid_start_date DATE NOT NULL,
|
||||
valid_end_date DATE NOT NULL,
|
||||
invalid_reason VARCHAR(1) NULL)
|
||||
;
|
||||
|
||||
|
||||
|
||||
CREATE TABLE relationship (
|
||||
relationship_id VARCHAR(20) NOT NULL,
|
||||
relationship_name VARCHAR(255) NOT NULL,
|
||||
is_hierarchical VARCHAR(1) NOT NULL,
|
||||
defines_ancestry VARCHAR(1) NOT NULL,
|
||||
reverse_relationship_id VARCHAR(20) NOT NULL,
|
||||
relationship_concept_id INTEGER NOT NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
CREATE TABLE concept_synonym (
|
||||
concept_id INTEGER NOT NULL,
|
||||
concept_synonym_name VARCHAR(1000) NOT NULL,
|
||||
language_concept_id INTEGER NOT NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
CREATE TABLE concept_ancestor (
|
||||
ancestor_concept_id INTEGER NOT NULL,
|
||||
descendant_concept_id INTEGER NOT NULL,
|
||||
min_levels_of_separation INTEGER NOT NULL,
|
||||
max_levels_of_separation INTEGER NOT NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
CREATE TABLE source_to_concept_map (
|
||||
source_code VARCHAR(50) NOT NULL,
|
||||
source_concept_id INTEGER NOT NULL,
|
||||
source_vocabulary_id VARCHAR(20) NOT NULL,
|
||||
source_code_description VARCHAR(255) NULL,
|
||||
target_concept_id INTEGER NOT NULL,
|
||||
target_vocabulary_id VARCHAR(20) NOT NULL,
|
||||
valid_start_date DATE NOT NULL,
|
||||
valid_end_date DATE NOT NULL,
|
||||
invalid_reason VARCHAR(1) NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
|
||||
CREATE TABLE drug_strength (
|
||||
drug_concept_id INTEGER NOT NULL,
|
||||
ingredient_concept_id INTEGER NOT NULL,
|
||||
amount_value NUMERIC NULL,
|
||||
amount_unit_concept_id INTEGER NULL,
|
||||
numerator_value NUMERIC NULL,
|
||||
numerator_unit_concept_id INTEGER NULL,
|
||||
denominator_value NUMERIC NULL,
|
||||
denominator_unit_concept_id INTEGER NULL,
|
||||
box_size INTEGER NULL,
|
||||
valid_start_date DATE NOT NULL,
|
||||
valid_end_date DATE NOT NULL,
|
||||
invalid_reason VARCHAR(1) NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
CREATE TABLE cohort_definition (
|
||||
cohort_definition_id INTEGER NOT NULL,
|
||||
cohort_definition_name VARCHAR(255) NOT NULL,
|
||||
cohort_definition_description TEXT NULL,
|
||||
definition_type_concept_id INTEGER NOT NULL,
|
||||
cohort_definition_syntax TEXT NULL,
|
||||
subject_concept_id INTEGER NOT NULL,
|
||||
cohort_initiation_date DATE NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
CREATE TABLE attribute_definition (
|
||||
attribute_definition_id INTEGER NOT NULL,
|
||||
attribute_name VARCHAR(255) NOT NULL,
|
||||
attribute_description TEXT NULL,
|
||||
attribute_type_concept_id INTEGER NOT NULL,
|
||||
attribute_syntax TEXT NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
/**************************
|
||||
|
||||
Standardized meta-data
|
||||
|
||||
***************************/
|
||||
|
||||
|
||||
CREATE TABLE cdm_source
|
||||
(
|
||||
cdm_source_name VARCHAR(255) NOT NULL,
|
||||
cdm_source_abbreviation VARCHAR(25) NULL,
|
||||
cdm_holder VARCHAR(255) NULL,
|
||||
source_description TEXT NULL,
|
||||
source_documentation_reference VARCHAR(255) NULL,
|
||||
cdm_etl_reference VARCHAR(255) NULL,
|
||||
source_release_date DATE NULL,
|
||||
cdm_release_date DATE NULL,
|
||||
cdm_version VARCHAR(10) NULL,
|
||||
vocabulary_version VARCHAR(20) NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
/************************
|
||||
|
||||
Standardized clinical data
|
||||
|
||||
************************/
|
||||
|
||||
|
||||
CREATE TABLE person
|
||||
(
|
||||
person_id INTEGER NOT NULL ,
|
||||
gender_concept_id INTEGER NOT NULL ,
|
||||
year_of_birth INTEGER NOT NULL ,
|
||||
month_of_birth INTEGER NULL,
|
||||
day_of_birth INTEGER NULL,
|
||||
time_of_birth VARCHAR(10) NULL,
|
||||
race_concept_id INTEGER NOT NULL,
|
||||
ethnicity_concept_id INTEGER NOT NULL,
|
||||
location_id INTEGER NULL,
|
||||
provider_id INTEGER NULL,
|
||||
care_site_id INTEGER NULL,
|
||||
person_source_value VARCHAR(50) NULL,
|
||||
gender_source_value VARCHAR(50) NULL,
|
||||
gender_source_concept_id INTEGER NULL,
|
||||
race_source_value VARCHAR(50) NULL,
|
||||
race_source_concept_id INTEGER NULL,
|
||||
ethnicity_source_value VARCHAR(50) NULL,
|
||||
ethnicity_source_concept_id INTEGER NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
CREATE TABLE observation_period
|
||||
(
|
||||
observation_period_id INTEGER NOT NULL ,
|
||||
person_id INTEGER NOT NULL ,
|
||||
observation_period_start_date DATE NOT NULL ,
|
||||
observation_period_end_date DATE NOT NULL ,
|
||||
period_type_concept_id INTEGER NOT NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
CREATE TABLE specimen
|
||||
(
|
||||
specimen_id INTEGER NOT NULL ,
|
||||
person_id INTEGER NOT NULL ,
|
||||
specimen_concept_id INTEGER NOT NULL ,
|
||||
specimen_type_concept_id INTEGER NOT NULL ,
|
||||
specimen_date DATE NOT NULL ,
|
||||
specimen_time VARCHAR(10) NULL ,
|
||||
quantity NUMERIC NULL ,
|
||||
unit_concept_id INTEGER NULL ,
|
||||
anatomic_site_concept_id INTEGER NULL ,
|
||||
disease_status_concept_id INTEGER NULL ,
|
||||
specimen_source_id VARCHAR(50) NULL ,
|
||||
specimen_source_value VARCHAR(50) NULL ,
|
||||
unit_source_value VARCHAR(50) NULL ,
|
||||
anatomic_site_source_value VARCHAR(50) NULL ,
|
||||
disease_status_source_value VARCHAR(50) NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
CREATE TABLE death
|
||||
(
|
||||
person_id INTEGER NOT NULL ,
|
||||
death_date DATE NOT NULL ,
|
||||
death_type_concept_id INTEGER NOT NULL ,
|
||||
cause_concept_id INTEGER NULL ,
|
||||
cause_source_value VARCHAR(50) NULL,
|
||||
cause_source_concept_id INTEGER NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
CREATE TABLE visit_occurrence
|
||||
(
|
||||
visit_occurrence_id INTEGER NOT NULL ,
|
||||
person_id INTEGER NOT NULL ,
|
||||
visit_concept_id INTEGER NOT NULL ,
|
||||
visit_start_date DATE NOT NULL ,
|
||||
visit_start_time VARCHAR(10) NULL ,
|
||||
visit_end_date DATE NOT NULL ,
|
||||
visit_end_time VARCHAR(10) NULL ,
|
||||
visit_type_concept_id INTEGER NOT NULL ,
|
||||
provider_id INTEGER NULL,
|
||||
care_site_id INTEGER NULL,
|
||||
visit_source_value VARCHAR(50) NULL,
|
||||
visit_source_concept_id INTEGER NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
CREATE TABLE procedure_occurrence
|
||||
(
|
||||
procedure_occurrence_id INTEGER NOT NULL ,
|
||||
person_id INTEGER NOT NULL ,
|
||||
procedure_concept_id INTEGER NOT NULL ,
|
||||
procedure_date DATE NOT NULL ,
|
||||
procedure_type_concept_id INTEGER NOT NULL ,
|
||||
modifier_concept_id INTEGER NULL ,
|
||||
quantity INTEGER NULL ,
|
||||
provider_id INTEGER NULL ,
|
||||
visit_occurrence_id INTEGER NULL ,
|
||||
procedure_source_value VARCHAR(50) NULL ,
|
||||
procedure_source_concept_id INTEGER NULL ,
|
||||
qualifier_source_value VARCHAR(50) NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
CREATE TABLE drug_exposure
|
||||
(
|
||||
drug_exposure_id INTEGER NOT NULL ,
|
||||
person_id INTEGER NOT NULL ,
|
||||
drug_concept_id INTEGER NOT NULL ,
|
||||
drug_exposure_start_date DATE NOT NULL ,
|
||||
drug_exposure_end_date DATE NULL ,
|
||||
drug_type_concept_id INTEGER NOT NULL ,
|
||||
stop_reason VARCHAR(20) NULL ,
|
||||
refills INTEGER NULL ,
|
||||
quantity NUMERIC NULL ,
|
||||
days_supply INTEGER NULL ,
|
||||
sig TEXT NULL ,
|
||||
route_concept_id INTEGER NULL ,
|
||||
effective_drug_dose NUMERIC NULL ,
|
||||
dose_unit_concept_id INTEGER NULL ,
|
||||
lot_number VARCHAR(50) NULL ,
|
||||
provider_id INTEGER NULL ,
|
||||
visit_occurrence_id INTEGER NULL ,
|
||||
drug_source_value VARCHAR(50) NULL ,
|
||||
drug_source_concept_id INTEGER NULL ,
|
||||
route_source_value VARCHAR(50) NULL ,
|
||||
dose_unit_source_value VARCHAR(50) NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
CREATE TABLE device_exposure
|
||||
(
|
||||
device_exposure_id INTEGER NOT NULL ,
|
||||
person_id INTEGER NOT NULL ,
|
||||
device_concept_id INTEGER NOT NULL ,
|
||||
device_exposure_start_date DATE NOT NULL ,
|
||||
device_exposure_end_date DATE NULL ,
|
||||
device_type_concept_id INTEGER NOT NULL ,
|
||||
unique_device_id VARCHAR(50) NULL ,
|
||||
quantity INTEGER NULL ,
|
||||
provider_id INTEGER NULL ,
|
||||
visit_occurrence_id INTEGER NULL ,
|
||||
device_source_value VARCHAR(100) NULL ,
|
||||
device_source_concept_id INTEGER NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
CREATE TABLE condition_occurrence
|
||||
(
|
||||
condition_occurrence_id INTEGER NOT NULL ,
|
||||
person_id INTEGER NOT NULL ,
|
||||
condition_concept_id INTEGER NOT NULL ,
|
||||
condition_start_date DATE NOT NULL ,
|
||||
condition_end_date DATE NULL ,
|
||||
condition_type_concept_id INTEGER NOT NULL ,
|
||||
stop_reason VARCHAR(20) NULL ,
|
||||
provider_id INTEGER NULL ,
|
||||
visit_occurrence_id INTEGER NULL ,
|
||||
condition_source_value VARCHAR(50) NULL ,
|
||||
condition_source_concept_id INTEGER NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
CREATE TABLE measurement
|
||||
(
|
||||
measurement_id INTEGER NOT NULL ,
|
||||
person_id INTEGER NOT NULL ,
|
||||
measurement_concept_id INTEGER NOT NULL ,
|
||||
measurement_date DATE NOT NULL ,
|
||||
measurement_time VARCHAR(10) NULL ,
|
||||
measurement_type_concept_id INTEGER NOT NULL ,
|
||||
operator_concept_id INTEGER NULL ,
|
||||
value_as_number NUMERIC NULL ,
|
||||
value_as_concept_id INTEGER NULL ,
|
||||
unit_concept_id INTEGER NULL ,
|
||||
range_low NUMERIC NULL ,
|
||||
range_high NUMERIC NULL ,
|
||||
provider_id INTEGER NULL ,
|
||||
visit_occurrence_id INTEGER NULL ,
|
||||
measurement_source_value VARCHAR(50) NULL ,
|
||||
measurement_source_concept_id INTEGER NULL ,
|
||||
unit_source_value VARCHAR(50) NULL ,
|
||||
value_source_value VARCHAR(50) NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
CREATE TABLE note
|
||||
(
|
||||
note_id INTEGER NOT NULL ,
|
||||
person_id INTEGER NOT NULL ,
|
||||
note_date DATE NOT NULL ,
|
||||
note_time VARCHAR(10) NULL ,
|
||||
note_type_concept_id INTEGER NOT NULL ,
|
||||
note_text TEXT NOT NULL ,
|
||||
provider_id INTEGER NULL ,
|
||||
visit_occurrence_id INTEGER NULL ,
|
||||
note_source_value VARCHAR(50) NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
CREATE TABLE observation
|
||||
(
|
||||
observation_id INTEGER NOT NULL ,
|
||||
person_id INTEGER NOT NULL ,
|
||||
observation_concept_id INTEGER NOT NULL ,
|
||||
observation_date DATE NOT NULL ,
|
||||
observation_time VARCHAR(10) NULL ,
|
||||
observation_type_concept_id INTEGER NOT NULL ,
|
||||
value_as_number NUMERIC NULL ,
|
||||
value_as_string VARCHAR(60) NULL ,
|
||||
value_as_concept_id INTEGER NULL ,
|
||||
qualifier_concept_id INTEGER NULL ,
|
||||
unit_concept_id INTEGER NULL ,
|
||||
provider_id INTEGER NULL ,
|
||||
visit_occurrence_id INTEGER NULL ,
|
||||
observation_source_value VARCHAR(50) NULL ,
|
||||
observation_source_concept_id INTEGER NULL ,
|
||||
unit_source_value VARCHAR(50) NULL ,
|
||||
qualifier_source_value VARCHAR(50) NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
CREATE TABLE fact_relationship
|
||||
(
|
||||
domain_concept_id_1 INTEGER NOT NULL ,
|
||||
fact_id_1 INTEGER NOT NULL ,
|
||||
domain_concept_id_2 INTEGER NOT NULL ,
|
||||
fact_id_2 INTEGER NOT NULL ,
|
||||
relationship_concept_id INTEGER NOT NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
|
||||
/************************
|
||||
|
||||
Standardized health system data
|
||||
|
||||
************************/
|
||||
|
||||
|
||||
|
||||
CREATE TABLE location
|
||||
(
|
||||
location_id INTEGER NOT NULL ,
|
||||
address_1 VARCHAR(50) NULL ,
|
||||
address_2 VARCHAR(50) NULL ,
|
||||
city VARCHAR(50) NULL ,
|
||||
state VARCHAR(2) NULL ,
|
||||
zip VARCHAR(9) NULL ,
|
||||
county VARCHAR(20) NULL ,
|
||||
location_source_value VARCHAR(50) NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
CREATE TABLE care_site
|
||||
(
|
||||
care_site_id INTEGER NOT NULL ,
|
||||
care_site_name VARCHAR(255) NULL ,
|
||||
place_of_service_concept_id INTEGER NULL ,
|
||||
location_id INTEGER NULL ,
|
||||
care_site_source_value VARCHAR(50) NULL ,
|
||||
place_of_service_source_value VARCHAR(50) NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
CREATE TABLE provider
|
||||
(
|
||||
provider_id INTEGER NOT NULL ,
|
||||
provider_name VARCHAR(255) NULL ,
|
||||
NPI VARCHAR(20) NULL ,
|
||||
DEA VARCHAR(20) NULL ,
|
||||
specialty_concept_id INTEGER NULL ,
|
||||
care_site_id INTEGER NULL ,
|
||||
year_of_birth INTEGER NULL ,
|
||||
gender_concept_id INTEGER NULL ,
|
||||
provider_source_value VARCHAR(50) NULL ,
|
||||
specialty_source_value VARCHAR(50) NULL ,
|
||||
specialty_source_concept_id INTEGER NULL ,
|
||||
gender_source_value VARCHAR(50) NULL ,
|
||||
gender_source_concept_id INTEGER NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
|
||||
/************************
|
||||
|
||||
Standardized health economics
|
||||
|
||||
************************/
|
||||
|
||||
|
||||
CREATE TABLE payer_plan_period
|
||||
(
|
||||
payer_plan_period_id INTEGER NOT NULL ,
|
||||
person_id INTEGER NOT NULL ,
|
||||
payer_plan_period_start_date DATE NOT NULL ,
|
||||
payer_plan_period_end_date DATE NOT NULL ,
|
||||
payer_source_value VARCHAR (50) NULL ,
|
||||
plan_source_value VARCHAR (50) NULL ,
|
||||
family_source_value VARCHAR (50) NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
/* The individual cost tables are being phased out and will disappear soon
|
||||
|
||||
CREATE TABLE visit_cost
|
||||
(
|
||||
visit_cost_id INTEGER NOT NULL ,
|
||||
visit_occurrence_id INTEGER NOT NULL ,
|
||||
currency_concept_id INTEGER NULL ,
|
||||
paid_copay NUMERIC NULL ,
|
||||
paid_coinsurance NUMERIC NULL ,
|
||||
paid_toward_deductible NUMERIC NULL ,
|
||||
paid_by_payer NUMERIC NULL ,
|
||||
paid_by_coordination_benefits NUMERIC NULL ,
|
||||
total_out_of_pocket NUMERIC NULL ,
|
||||
total_paid NUMERIC NULL ,
|
||||
payer_plan_period_id INTEGER NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
CREATE TABLE procedure_cost
|
||||
(
|
||||
procedure_cost_id INTEGER NOT NULL ,
|
||||
procedure_occurrence_id INTEGER NOT NULL ,
|
||||
currency_concept_id INTEGER NULL ,
|
||||
paid_copay NUMERIC NULL ,
|
||||
paid_coinsurance NUMERIC NULL ,
|
||||
paid_toward_deductible NUMERIC NULL ,
|
||||
paid_by_payer NUMERIC NULL ,
|
||||
paid_by_coordination_benefits NUMERIC NULL ,
|
||||
total_out_of_pocket NUMERIC NULL ,
|
||||
total_paid NUMERIC NULL ,
|
||||
revenue_code_concept_id INTEGER NULL ,
|
||||
payer_plan_period_id INTEGER NULL ,
|
||||
revenue_code_source_value VARCHAR(50) NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
CREATE TABLE drug_cost
|
||||
(
|
||||
drug_cost_id INTEGER NOT NULL ,
|
||||
drug_exposure_id INTEGER NOT NULL ,
|
||||
currency_concept_id INTEGER NULL ,
|
||||
paid_copay NUMERIC NULL ,
|
||||
paid_coinsurance NUMERIC NULL ,
|
||||
paid_toward_deductible NUMERIC NULL ,
|
||||
paid_by_payer NUMERIC NULL ,
|
||||
paid_by_coordination_benefits NUMERIC NULL ,
|
||||
total_out_of_pocket NUMERIC NULL ,
|
||||
total_paid NUMERIC NULL ,
|
||||
ingredient_cost NUMERIC NULL ,
|
||||
dispensing_fee NUMERIC NULL ,
|
||||
average_wholesale_price NUMERIC NULL ,
|
||||
payer_plan_period_id INTEGER NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
CREATE TABLE device_cost
|
||||
(
|
||||
device_cost_id INTEGER NOT NULL ,
|
||||
device_exposure_id INTEGER NOT NULL ,
|
||||
currency_concept_id INTEGER NULL ,
|
||||
paid_copay NUMERIC NULL ,
|
||||
paid_coinsurance NUMERIC NULL ,
|
||||
paid_toward_deductible NUMERIC NULL ,
|
||||
paid_by_payer NUMERIC NULL ,
|
||||
paid_by_coordination_benefits NUMERIC NULL ,
|
||||
total_out_of_pocket NUMERIC NULL ,
|
||||
total_paid NUMERIC NULL ,
|
||||
payer_plan_period_id INTEGER NULL
|
||||
)
|
||||
;
|
||||
*/
|
||||
|
||||
|
||||
CREATE TABLE cost
|
||||
(
|
||||
cost_id INTEGER NOT NULL ,
|
||||
cost_event_id INTEGER NOT NULL ,
|
||||
cost_domain_id VARCHAR(20) NOT NULL ,
|
||||
cost_type_concept_id INTEGER NOT NULL ,
|
||||
currency_concept_id INTEGER NULL ,
|
||||
total_charge NUMERIC NULL ,
|
||||
total_cost NUMERIC NULL ,
|
||||
total_paid NUMERIC NULL ,
|
||||
paid_by_payer NUMERIC NULL ,
|
||||
paid_by_patient NUMERIC NULL ,
|
||||
paid_patient_copay NUMERIC NULL ,
|
||||
paid_patient_coinsurance NUMERIC NULL ,
|
||||
paid_patient_deductible NUMERIC NULL ,
|
||||
paid_by_primary NUMERIC NULL ,
|
||||
paid_ingredient_cost NUMERIC NULL ,
|
||||
paid_dispensing_fee NUMERIC NULL ,
|
||||
payer_plan_period_id INTEGER NULL ,
|
||||
amount_allowed NUMERIC NULL ,
|
||||
revenue_code_concept_id INTEGER NULL ,
|
||||
reveue_code_source_value VARCHAR(50) NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
/************************
|
||||
|
||||
Standardized derived elements
|
||||
|
||||
************************/
|
||||
|
||||
CREATE TABLE cohort
|
||||
(
|
||||
cohort_definition_id INTEGER NOT NULL ,
|
||||
subject_id INTEGER NOT NULL ,
|
||||
cohort_start_date DATE NOT NULL ,
|
||||
cohort_end_date DATE NOT NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
CREATE TABLE cohort_attribute
|
||||
(
|
||||
cohort_definition_id INTEGER NOT NULL ,
|
||||
cohort_start_date DATE NOT NULL ,
|
||||
cohort_end_date DATE NOT NULL ,
|
||||
subject_id INTEGER NOT NULL ,
|
||||
attribute_definition_id INTEGER NOT NULL ,
|
||||
value_as_number NUMERIC NULL ,
|
||||
value_as_concept_id INTEGER NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
|
||||
CREATE TABLE drug_era
|
||||
(
|
||||
drug_era_id INTEGER NOT NULL ,
|
||||
person_id INTEGER NOT NULL ,
|
||||
drug_concept_id INTEGER NOT NULL ,
|
||||
drug_era_start_date DATE NOT NULL ,
|
||||
drug_era_end_date DATE NOT NULL ,
|
||||
drug_exposure_count INTEGER NULL ,
|
||||
gap_days INTEGER NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
CREATE TABLE dose_era
|
||||
(
|
||||
dose_era_id INTEGER NOT NULL ,
|
||||
person_id INTEGER NOT NULL ,
|
||||
drug_concept_id INTEGER NOT NULL ,
|
||||
unit_concept_id INTEGER NOT NULL ,
|
||||
dose_value NUMERIC NOT NULL ,
|
||||
dose_era_start_date DATE NOT NULL ,
|
||||
dose_era_end_date DATE NOT NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
|
||||
CREATE TABLE condition_era
|
||||
(
|
||||
condition_era_id INTEGER NOT NULL ,
|
||||
person_id INTEGER NOT NULL ,
|
||||
condition_concept_id INTEGER NOT NULL ,
|
||||
condition_era_start_date DATE NOT NULL ,
|
||||
condition_era_end_date DATE NOT NULL ,
|
||||
condition_occurrence_count INTEGER NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
|
@ -1,214 +0,0 @@
|
|||
/*********************************************************************************
|
||||
# Copyright 2014 Observational Health Data Sciences and Informatics
|
||||
#
|
||||
#
|
||||
# Licensed under the Apache License, Version 2.0 (the "License");
|
||||
# you may not use this file except in compliance with the License.
|
||||
# You may obtain a copy of the License at
|
||||
#
|
||||
# http://www.apache.org/licenses/LICENSE-2.0
|
||||
#
|
||||
# Unless required by applicable law or agreed to in writing, software
|
||||
# distributed under the License is distributed on an "AS IS" BASIS,
|
||||
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
|
||||
# See the License for the specific language governing permissions and
|
||||
# limitations under the License.
|
||||
********************************************************************************/
|
||||
|
||||
/************************
|
||||
|
||||
####### # # ####### ###### ##### ###### # # ####### ###
|
||||
# # ## ## # # # # # # # # ## ## # # # # # # ##### ###### # # ###### ####
|
||||
# # # # # # # # # # # # # # # # # # # # # ## # # # # # # # #
|
||||
# # # # # # # ###### # # # # # # # # ###### # # # # # # ##### ## ##### ####
|
||||
# # # # # # # # # # # # # # # # # # # # # # ## # #
|
||||
# # # # # # # # # # # # # # # # # # # ## # # # # # # # #
|
||||
####### # # ####### # ##### ###### # # ## ##### ### # # ##### ###### # # ###### ####
|
||||
|
||||
|
||||
script to create the required indexes within OMOP common data model, version 5.0 for PostgreSQL database
|
||||
|
||||
last revised: 12 Oct 2014
|
||||
|
||||
author: Patrick Ryan
|
||||
|
||||
description: These indices are considered a minimal requirement to ensure adequate performance of analyses.
|
||||
|
||||
*************************/
|
||||
|
||||
|
||||
/************************
|
||||
|
||||
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_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_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);
|
||||
|
||||
|
|
@ -7,12 +7,7 @@ In order to create your instantiation of the Common Data Model, we recommend fol
|
|||
|
||||
1. Create an empty schema.
|
||||
|
||||
2. Execute the script `OMOP CDM ddl - PostgreSQL.sql` to create the tables and fields.
|
||||
2. Execute the script `CDM V4 ddl.sql` to create the tables and fields.
|
||||
|
||||
3. Load your data into the schema.
|
||||
|
||||
4. Execute the script `OMOP CDM constraints - PostgreSQL.sql` to add the constraints (primary and foreign keys).
|
||||
|
||||
5. Execute the script `OMOP CDM indexes required - PostgreSQL.sql` to add the minimum set of indexes we recommend.
|
||||
|
||||
Note: you could also apply the constraints and/or the indexes before loading the data, but this will slow down the insertion of the data considerably.
|
||||
|
|
|
|||
|
|
@ -1,5 +1,5 @@
|
|||
/*********************************************************************************
|
||||
# Copyright 2014 Observational Health Data Sciences and Informatics
|
||||
# Copyright 2015 Observational Health Data Sciences and Informatics
|
||||
#
|
||||
#
|
||||
# Licensed under the Apache License, Version 2.0 (the "License");
|
||||
|
|
@ -26,38 +26,29 @@
|
|||
####### # # ####### # ##### ###### # # ## #####
|
||||
|
||||
|
||||
Script to load the common data model, version 5.0 vocabulary tables for PostgreSQL database on Windows (MS-DOS style file paths)
|
||||
The database account running this script must have the "superuser" permission in the database.
|
||||
Script to load the common data model, version 4.5 vocabulary tables for PostgreSQL database
|
||||
|
||||
Notes
|
||||
|
||||
1) There is no data file load for the SOURCE_TO_CONCEPT_MAP table because that table is deprecated in CDM version 5.0
|
||||
2) This script assumes the CDM version 5 vocabulary zip file has been unzipped into the "C:\CDMV5VOCAB" directory.
|
||||
3) If you unzipped your CDM version 5 vocabulary files into a different directory then replace all file paths below, with your directory path.
|
||||
4) Truncate each table that will be lodaed below, before running this script.
|
||||
1) This script assumes the CDM version 4.5 vocabulary zip file has been unzipped into the "C:\CDM" directory.
|
||||
2) If you unzipped your CDM version 4.5 vocabulary files into a different directory then replace all file paths below, with your directory path.
|
||||
3) Run this SQL query script in the database where you created your CDM Version 4.5 tables
|
||||
|
||||
last revised: 5 Dec 2014
|
||||
last revised: 20th March 2015
|
||||
|
||||
author: Lee Evans
|
||||
|
||||
|
||||
*************************/
|
||||
|
||||
COPY DRUG_STRENGTH FROM 'C:\CDMV5VOCAB\DRUG_STRENGTH.csv' WITH DELIMITER E'\t' CSV HEADER QUOTE E'\b' ;
|
||||
COPY CONCEPT FROM 'C:\CDM\CONCEPT.csv' WITH DELIMITER E'\t' CSV HEADER QUOTE E'\b' ;
|
||||
COPY CONCEPT_ANCESTOR FROM 'C:\CDM\CONCEPT_ANCESTOR.csv' WITH DELIMITER E'\t' CSV HEADER QUOTE E'\b' ;
|
||||
COPY CONCEPT_RELATIONSHIP FROM 'C:\CDM\CONCEPT_RELATIONSHIP.csv' WITH DELIMITER E'\t' CSV HEADER QUOTE E'\b' ;
|
||||
COPY CONCEPT_SYNONYM FROM 'C:\CDM\CONCEPT_SYNONYM.csv' WITH DELIMITER E'\t' CSV HEADER QUOTE E'\b' ;
|
||||
COPY DRUG_STRENGTH FROM 'C:\CDM\DRUG_STRENGTH.csv' WITH DELIMITER E'\t' CSV HEADER QUOTE E'\b' ;
|
||||
COPY RELATIONSHIP FROM 'C:\CDM\RELATIONSHIP.csv' WITH DELIMITER E'\t' CSV HEADER QUOTE E'\b' ;
|
||||
COPY SOURCE_TO_CONCEPT_MAP FROM 'C:\CDM\SOURCE_TO_CONCEPT_MAP.csv' WITH DELIMITER E'\t' CSV HEADER QUOTE E'\b' ;
|
||||
COPY VOCABULARY FROM 'C:\CDM\VOCABULARY.csv' WITH DELIMITER E'\t' CSV HEADER QUOTE E'\b' ;
|
||||
|
||||
COPY CONCEPT FROM 'C:\CDMV5VOCAB\CONCEPT.csv' WITH DELIMITER E'\t' CSV HEADER QUOTE E'\b' ;
|
||||
|
||||
COPY CONCEPT_RELATIONSHIP FROM 'C:\CDMV5VOCAB\CONCEPT_RELATIONSHIP.csv' WITH DELIMITER E'\t' CSV HEADER QUOTE E'\b' ;
|
||||
|
||||
COPY CONCEPT_ANCESTOR FROM 'C:\CDMV5VOCAB\CONCEPT_ANCESTOR.csv' WITH DELIMITER E'\t' CSV HEADER QUOTE E'\b' ;
|
||||
|
||||
COPY CONCEPT_SYNONYM FROM 'C:\CDMV5VOCAB\CONCEPT_SYNONYM.csv' WITH DELIMITER E'\t' CSV HEADER QUOTE E'\b' ;
|
||||
|
||||
COPY VOCABULARY FROM 'C:\CDMV5VOCAB\VOCABULARY.csv' WITH DELIMITER E'\t' CSV HEADER QUOTE E'\b' ;
|
||||
|
||||
COPY RELATIONSHIP FROM 'C:\CDMV5VOCAB\RELATIONSHIP.csv' WITH DELIMITER E'\t' CSV HEADER QUOTE E'\b' ;
|
||||
|
||||
COPY CONCEPT_CLASS FROM 'C:\CDMV5VOCAB\CONCEPT_CLASS.csv' WITH DELIMITER E'\t' CSV HEADER QUOTE E'\b' ;
|
||||
|
||||
COPY DOMAIN FROM 'C:\CDMV5VOCAB\DOMAIN.csv' WITH DELIMITER E'\t' CSV HEADER QUOTE E'\b' ;
|
||||
|
||||
|
|
|
|||
|
|
@ -1,545 +0,0 @@
|
|||
/*********************************************************************************
|
||||
# Copyright 2014 Observational Health Data Sciences and Informatics
|
||||
#
|
||||
#
|
||||
# Licensed under the Apache License, Version 2.0 (the "License");
|
||||
# you may not use this file except in compliance with the License.
|
||||
# You may obtain a copy of the License at
|
||||
#
|
||||
# http://www.apache.org/licenses/LICENSE-2.0
|
||||
#
|
||||
# Unless required by applicable law or agreed to in writing, software
|
||||
# distributed under the License is distributed on an "AS IS" BASIS,
|
||||
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
|
||||
# See the License for the specific language governing permissions and
|
||||
# limitations under the License.
|
||||
********************************************************************************/
|
||||
|
||||
/************************
|
||||
|
||||
####### # # ####### ###### ##### ###### # # ####### #####
|
||||
# # ## ## # # # # # # # # ## ## # # # # # #### # # #### ##### ##### ## # # # ##### ####
|
||||
# # # # # # # # # # # # # # # # # # # # # # # ## # # # # # # # # ## # # #
|
||||
# # # # # # # ###### # # # # # # # # ###### # # # # # # #### # # # # # # # # # # ####
|
||||
# # # # # # # # # # # # # # # # # # # # # # # ##### ###### # # # # # #
|
||||
# # # # # # # # # # # # # # # # # # # # # # ## # # # # # # # # # ## # # #
|
||||
####### # # ####### # ##### ###### # # ## ##### ##### #### # # #### # # # # # # # # # ####
|
||||
|
||||
|
||||
script to create constraints within OMOP common data model, version 5.0 for SQL Server database
|
||||
|
||||
last revised: 12 Oct 2014
|
||||
|
||||
author: Patrick Ryan
|
||||
|
||||
|
||||
*************************/
|
||||
|
||||
|
||||
/************************
|
||||
*************************
|
||||
*************************
|
||||
*************************
|
||||
|
||||
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 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 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 visit_cost ADD CONSTRAINT xpk_visit_cost PRIMARY KEY NONCLUSTERED ( visit_cost_id ) ;
|
||||
|
||||
ALTER TABLE procedure_cost ADD CONSTRAINT xpk_procedure_cost PRIMARY KEY NONCLUSTERED ( procedure_cost_id ) ;
|
||||
|
||||
ALTER TABLE drug_cost ADD CONSTRAINT xpk_drug_cost PRIMARY KEY NONCLUSTERED ( drug_cost_id ) ;
|
||||
|
||||
ALTER TABLE device_cost ADD CONSTRAINT xpk_device_cost PRIMARY KEY NONCLUSTERED ( device_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 ) ;
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
/************************
|
||||
*************************
|
||||
*************************
|
||||
*************************
|
||||
|
||||
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 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_dose_unit_concept FOREIGN KEY (dose_unit_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 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_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 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 visit_cost ADD CONSTRAINT fpk_visit_cost_id FOREIGN KEY (visit_occurrence_id) REFERENCES visit_occurrence (visit_occurrence_id);
|
||||
|
||||
ALTER TABLE visit_cost ADD CONSTRAINT fpk_visit_cost_currency FOREIGN KEY (currency_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE visit_cost ADD CONSTRAINT fpk_visit_cost_period FOREIGN KEY (payer_plan_period_id) REFERENCES payer_plan_period (payer_plan_period_id);
|
||||
|
||||
|
||||
ALTER TABLE procedure_cost ADD CONSTRAINT fpk_procedure_cost_id FOREIGN KEY (procedure_occurrence_id) REFERENCES procedure_occurrence (procedure_occurrence_id);
|
||||
|
||||
ALTER TABLE procedure_cost ADD CONSTRAINT fpk_procedure_cost_currency FOREIGN KEY (currency_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE procedure_cost ADD CONSTRAINT fpk_procedure_cost_period FOREIGN KEY (payer_plan_period_id) REFERENCES payer_plan_period (payer_plan_period_id);
|
||||
|
||||
ALTER TABLE procedure_cost ADD CONSTRAINT fpk_procedure_cost_revenue FOREIGN KEY (revenue_code_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
|
||||
ALTER TABLE drug_cost ADD CONSTRAINT fpk_drug_cost_id FOREIGN KEY (drug_exposure_id) REFERENCES drug_exposure (drug_exposure_id);
|
||||
|
||||
ALTER TABLE drug_cost ADD CONSTRAINT fpk_drug_cost_currency FOREIGN KEY (currency_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE drug_cost ADD CONSTRAINT fpk_drug_cost_period FOREIGN KEY (payer_plan_period_id) REFERENCES payer_plan_period (payer_plan_period_id);
|
||||
|
||||
|
||||
ALTER TABLE device_cost ADD CONSTRAINT fpk_device_cost_id FOREIGN KEY (device_exposure_id) REFERENCES device_exposure (device_exposure_id);
|
||||
|
||||
ALTER TABLE device_cost ADD CONSTRAINT fpk_device_cost_currency FOREIGN KEY (currency_concept_id) REFERENCES concept (concept_id);
|
||||
|
||||
ALTER TABLE device_cost ADD CONSTRAINT fpk_device_cost_period FOREIGN KEY (payer_plan_period_id) REFERENCES payer_plan_period (payer_plan_period_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);
|
||||
|
||||
|
|
@ -1,738 +0,0 @@
|
|||
/*********************************************************************************
|
||||
# Copyright 2014-6 Observational Health Data Sciences and Informatics
|
||||
#
|
||||
#
|
||||
# Licensed under the Apache License, Version 2.0 (the "License");
|
||||
# you may not use this file except in compliance with the License.
|
||||
# You may obtain a copy of the License at
|
||||
#
|
||||
# http://www.apache.org/licenses/LICENSE-2.0
|
||||
#
|
||||
# Unless required by applicable law or agreed to in writing, software
|
||||
# distributed under the License is distributed on an "AS IS" BASIS,
|
||||
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
|
||||
# See the License for the specific language governing permissions and
|
||||
# limitations under the License.
|
||||
********************************************************************************/
|
||||
|
||||
/************************
|
||||
|
||||
####### # # ####### ###### ##### ###### # # #######
|
||||
# # ## ## # # # # # # # # ## ## # # #
|
||||
# # # # # # # # # # # # # # # # # # # #
|
||||
# # # # # # # ###### # # # # # # # # ######
|
||||
# # # # # # # # # # # # # # #
|
||||
# # # # # # # # # # # # # # # # #
|
||||
####### # # ####### # ##### ###### # # ## #####
|
||||
|
||||
|
||||
script to create OMOP common data model, version 5.0 for SQL Server database
|
||||
|
||||
last revised: 1-May-2016
|
||||
|
||||
Authors: Patrick Ryan, Christian Reich
|
||||
|
||||
|
||||
*************************/
|
||||
|
||||
|
||||
/************************
|
||||
|
||||
Standardized vocabulary
|
||||
|
||||
************************/
|
||||
|
||||
|
||||
CREATE TABLE concept (
|
||||
concept_id INTEGER NOT NULL,
|
||||
concept_name VARCHAR(255) NOT NULL,
|
||||
domain_id VARCHAR(20) NOT NULL,
|
||||
vocabulary_id VARCHAR(20) NOT NULL,
|
||||
concept_class_id VARCHAR(20) NOT NULL,
|
||||
standard_concept VARCHAR(1) NULL,
|
||||
concept_code VARCHAR(50) NOT NULL,
|
||||
valid_start_date DATE NOT NULL,
|
||||
valid_end_date DATE NOT NULL,
|
||||
invalid_reason VARCHAR(1) NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
|
||||
CREATE TABLE vocabulary (
|
||||
vocabulary_id VARCHAR(20) NOT NULL,
|
||||
vocabulary_name VARCHAR(255) NOT NULL,
|
||||
vocabulary_reference VARCHAR(255) NULL,
|
||||
vocabulary_version VARCHAR(255) NULL,
|
||||
vocabulary_concept_id INTEGER NOT NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
|
||||
CREATE TABLE domain (
|
||||
domain_id VARCHAR(20) NOT NULL,
|
||||
domain_name VARCHAR(255) NOT NULL,
|
||||
domain_concept_id INTEGER NOT NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
CREATE TABLE concept_class (
|
||||
concept_class_id VARCHAR(20) NOT NULL,
|
||||
concept_class_name VARCHAR(255) NOT NULL,
|
||||
concept_class_concept_id INTEGER NOT NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
|
||||
CREATE TABLE concept_relationship (
|
||||
concept_id_1 INTEGER NOT NULL,
|
||||
concept_id_2 INTEGER NOT NULL,
|
||||
relationship_id VARCHAR(20) NOT NULL,
|
||||
valid_start_date DATE NOT NULL,
|
||||
valid_end_date DATE NOT NULL,
|
||||
invalid_reason VARCHAR(1) NULL)
|
||||
;
|
||||
|
||||
|
||||
|
||||
CREATE TABLE relationship (
|
||||
relationship_id VARCHAR(20) NOT NULL,
|
||||
relationship_name VARCHAR(255) NOT NULL,
|
||||
is_hierarchical VARCHAR(1) NOT NULL,
|
||||
defines_ancestry VARCHAR(1) NOT NULL,
|
||||
reverse_relationship_id VARCHAR(20) NOT NULL,
|
||||
relationship_concept_id INTEGER NOT NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
CREATE TABLE concept_synonym (
|
||||
concept_id INTEGER NOT NULL,
|
||||
concept_synonym_name VARCHAR(1000) NOT NULL,
|
||||
language_concept_id INTEGER NOT NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
CREATE TABLE concept_ancestor (
|
||||
ancestor_concept_id INTEGER NOT NULL,
|
||||
descendant_concept_id INTEGER NOT NULL,
|
||||
min_levels_of_separation INTEGER NOT NULL,
|
||||
max_levels_of_separation INTEGER NOT NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
CREATE TABLE source_to_concept_map (
|
||||
source_code VARCHAR(50) NOT NULL,
|
||||
source_concept_id INTEGER NOT NULL,
|
||||
source_vocabulary_id VARCHAR(20) NOT NULL,
|
||||
source_code_description VARCHAR(255) NULL,
|
||||
target_concept_id INTEGER NOT NULL,
|
||||
target_vocabulary_id VARCHAR(20) NOT NULL,
|
||||
valid_start_date DATE NOT NULL,
|
||||
valid_end_date DATE NOT NULL,
|
||||
invalid_reason VARCHAR(1) NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
|
||||
CREATE TABLE drug_strength (
|
||||
drug_concept_id INTEGER NOT NULL,
|
||||
ingredient_concept_id INTEGER NOT NULL,
|
||||
amount_value FLOAT NULL,
|
||||
amount_unit_concept_id INTEGER NULL,
|
||||
numerator_value FLOAT NULL,
|
||||
numerator_unit_concept_id INTEGER NULL,
|
||||
denominator_value FLOAT NULL,
|
||||
denominator_unit_concept_id INTEGER NULL,
|
||||
box_size INTEGER NULL,
|
||||
valid_start_date DATE NOT NULL,
|
||||
valid_end_date DATE NOT NULL,
|
||||
invalid_reason VARCHAR(1) NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
CREATE TABLE cohort_definition (
|
||||
cohort_definition_id INTEGER NOT NULL,
|
||||
cohort_definition_name VARCHAR(255) NOT NULL,
|
||||
cohort_definition_description VARCHAR(MAX) NULL,
|
||||
definition_type_concept_id INTEGER NOT NULL,
|
||||
cohort_definition_syntax VARCHAR(MAX) NULL,
|
||||
subject_concept_id INTEGER NOT NULL,
|
||||
cohort_initiation_date DATE NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
CREATE TABLE attribute_definition (
|
||||
attribute_definition_id INTEGER NOT NULL,
|
||||
attribute_name VARCHAR(255) NOT NULL,
|
||||
attribute_description VARCHAR(MAX) NULL,
|
||||
attribute_type_concept_id INTEGER NOT NULL,
|
||||
attribute_syntax VARCHAR(MAX) NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
/**************************
|
||||
|
||||
Standardized meta-data
|
||||
|
||||
***************************/
|
||||
|
||||
|
||||
CREATE TABLE cdm_source
|
||||
(
|
||||
cdm_source_name VARCHAR(255) NOT NULL,
|
||||
cdm_source_abbreviation VARCHAR(25) NULL,
|
||||
cdm_holder VARCHAR(255) NULL,
|
||||
source_description VARCHAR(MAX) NULL,
|
||||
source_documentation_reference VARCHAR(255) NULL,
|
||||
cdm_etl_reference VARCHAR(255) NULL,
|
||||
source_release_date DATE NULL,
|
||||
cdm_release_date DATE NULL,
|
||||
cdm_version VARCHAR(10) NULL,
|
||||
vocabulary_version VARCHAR(20) NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
/************************
|
||||
|
||||
Standardized clinical data
|
||||
|
||||
************************/
|
||||
|
||||
|
||||
CREATE TABLE person
|
||||
(
|
||||
person_id INTEGER NOT NULL ,
|
||||
gender_concept_id INTEGER NOT NULL ,
|
||||
year_of_birth INTEGER NOT NULL ,
|
||||
month_of_birth INTEGER NULL,
|
||||
day_of_birth INTEGER NULL,
|
||||
time_of_birth VARCHAR(10) NULL,
|
||||
race_concept_id INTEGER NOT NULL,
|
||||
ethnicity_concept_id INTEGER NOT NULL,
|
||||
location_id INTEGER NULL,
|
||||
provider_id INTEGER NULL,
|
||||
care_site_id INTEGER NULL,
|
||||
person_source_value VARCHAR(50) NULL,
|
||||
gender_source_value VARCHAR(50) NULL,
|
||||
gender_source_concept_id INTEGER NULL,
|
||||
race_source_value VARCHAR(50) NULL,
|
||||
race_source_concept_id INTEGER NULL,
|
||||
ethnicity_source_value VARCHAR(50) NULL,
|
||||
ethnicity_source_concept_id INTEGER NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
CREATE TABLE observation_period
|
||||
(
|
||||
observation_period_id INTEGER NOT NULL ,
|
||||
person_id INTEGER NOT NULL ,
|
||||
observation_period_start_date DATE NOT NULL ,
|
||||
observation_period_end_date DATE NOT NULL ,
|
||||
period_type_concept_id INTEGER NOT NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
CREATE TABLE specimen
|
||||
(
|
||||
specimen_id INTEGER NOT NULL ,
|
||||
person_id INTEGER NOT NULL ,
|
||||
specimen_concept_id INTEGER NOT NULL ,
|
||||
specimen_type_concept_id INTEGER NOT NULL ,
|
||||
specimen_date DATE NOT NULL ,
|
||||
specimen_time VARCHAR(10) NULL ,
|
||||
quantity FLOAT NULL ,
|
||||
unit_concept_id INTEGER NULL ,
|
||||
anatomic_site_concept_id INTEGER NULL ,
|
||||
disease_status_concept_id INTEGER NULL ,
|
||||
specimen_source_id VARCHAR(50) NULL ,
|
||||
specimen_source_value VARCHAR(50) NULL ,
|
||||
unit_source_value VARCHAR(50) NULL ,
|
||||
anatomic_site_source_value VARCHAR(50) NULL ,
|
||||
disease_status_source_value VARCHAR(50) NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
CREATE TABLE death
|
||||
(
|
||||
person_id INTEGER NOT NULL ,
|
||||
death_date DATE NOT NULL ,
|
||||
death_type_concept_id INTEGER NOT NULL ,
|
||||
cause_concept_id INTEGER NULL ,
|
||||
cause_source_value VARCHAR(50) NULL,
|
||||
cause_source_concept_id INTEGER NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
CREATE TABLE visit_occurrence
|
||||
(
|
||||
visit_occurrence_id INTEGER NOT NULL ,
|
||||
person_id INTEGER NOT NULL ,
|
||||
visit_concept_id INTEGER NOT NULL ,
|
||||
visit_start_date DATE NOT NULL ,
|
||||
visit_start_time VARCHAR(10) NULL ,
|
||||
visit_end_date DATE NOT NULL ,
|
||||
visit_end_time VARCHAR(10) NULL ,
|
||||
visit_type_concept_id INTEGER NOT NULL ,
|
||||
provider_id INTEGER NULL,
|
||||
care_site_id INTEGER NULL,
|
||||
visit_source_value VARCHAR(50) NULL,
|
||||
visit_source_concept_id INTEGER NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
CREATE TABLE procedure_occurrence
|
||||
(
|
||||
procedure_occurrence_id INTEGER NOT NULL ,
|
||||
person_id INTEGER NOT NULL ,
|
||||
procedure_concept_id INTEGER NOT NULL ,
|
||||
procedure_date DATE NOT NULL ,
|
||||
procedure_type_concept_id INTEGER NOT NULL ,
|
||||
modifier_concept_id INTEGER NULL ,
|
||||
quantity INTEGER NULL ,
|
||||
provider_id INTEGER NULL ,
|
||||
visit_occurrence_id INTEGER NULL ,
|
||||
procedure_source_value VARCHAR(50) NULL ,
|
||||
procedure_source_concept_id INTEGER NULL ,
|
||||
qualifier_source_value VARCHAR(50) NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
CREATE TABLE drug_exposure
|
||||
(
|
||||
drug_exposure_id INTEGER NOT NULL ,
|
||||
person_id INTEGER NOT NULL ,
|
||||
drug_concept_id INTEGER NOT NULL ,
|
||||
drug_exposure_start_date DATE NOT NULL ,
|
||||
drug_exposure_end_date DATE NULL ,
|
||||
drug_type_concept_id INTEGER NOT NULL ,
|
||||
stop_reason VARCHAR(20) NULL ,
|
||||
refills INTEGER NULL ,
|
||||
quantity FLOAT NULL ,
|
||||
days_supply INTEGER NULL ,
|
||||
sig VARCHAR(MAX) NULL ,
|
||||
route_concept_id INTEGER NULL ,
|
||||
effective_drug_dose FLOAT NULL ,
|
||||
dose_unit_concept_id INTEGER NULL ,
|
||||
lot_number VARCHAR(50) NULL ,
|
||||
provider_id INTEGER NULL ,
|
||||
visit_occurrence_id INTEGER NULL ,
|
||||
drug_source_value VARCHAR(50) NULL ,
|
||||
drug_source_concept_id INTEGER NULL ,
|
||||
route_source_value VARCHAR(50) NULL ,
|
||||
dose_unit_source_value VARCHAR(50) NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
CREATE TABLE device_exposure
|
||||
(
|
||||
device_exposure_id INTEGER NOT NULL ,
|
||||
person_id INTEGER NOT NULL ,
|
||||
device_concept_id INTEGER NOT NULL ,
|
||||
device_exposure_start_date DATE NOT NULL ,
|
||||
device_exposure_end_date DATE NULL ,
|
||||
device_type_concept_id INTEGER NOT NULL ,
|
||||
unique_device_id VARCHAR(50) NULL ,
|
||||
quantity INTEGER NULL ,
|
||||
provider_id INTEGER NULL ,
|
||||
visit_occurrence_id INTEGER NULL ,
|
||||
device_source_value VARCHAR(100) NULL ,
|
||||
device_source_concept_id INTEGER NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
CREATE TABLE condition_occurrence
|
||||
(
|
||||
condition_occurrence_id INTEGER NOT NULL ,
|
||||
person_id INTEGER NOT NULL ,
|
||||
condition_concept_id INTEGER NOT NULL ,
|
||||
condition_start_date DATE NOT NULL ,
|
||||
condition_end_date DATE NULL ,
|
||||
condition_type_concept_id INTEGER NOT NULL ,
|
||||
stop_reason VARCHAR(20) NULL ,
|
||||
provider_id INTEGER NULL ,
|
||||
visit_occurrence_id INTEGER NULL ,
|
||||
condition_source_value VARCHAR(50) NULL ,
|
||||
condition_source_concept_id INTEGER NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
CREATE TABLE measurement
|
||||
(
|
||||
measurement_id INTEGER NOT NULL ,
|
||||
person_id INTEGER NOT NULL ,
|
||||
measurement_concept_id INTEGER NOT NULL ,
|
||||
measurement_date DATE NOT NULL ,
|
||||
measurement_time VARCHAR(10) NULL ,
|
||||
measurement_type_concept_id INTEGER NOT NULL ,
|
||||
operator_concept_id INTEGER NULL ,
|
||||
value_as_number FLOAT NULL ,
|
||||
value_as_concept_id INTEGER NULL ,
|
||||
unit_concept_id INTEGER NULL ,
|
||||
range_low FLOAT NULL ,
|
||||
range_high FLOAT NULL ,
|
||||
provider_id INTEGER NULL ,
|
||||
visit_occurrence_id INTEGER NULL ,
|
||||
measurement_source_value VARCHAR(50) NULL ,
|
||||
measurement_source_concept_id INTEGER NULL ,
|
||||
unit_source_value VARCHAR(50) NULL ,
|
||||
value_source_value VARCHAR(50) NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
CREATE TABLE note
|
||||
(
|
||||
note_id INTEGER NOT NULL ,
|
||||
person_id INTEGER NOT NULL ,
|
||||
note_date DATE NOT NULL ,
|
||||
note_time VARCHAR(10) NULL ,
|
||||
note_type_concept_id INTEGER NOT NULL ,
|
||||
note_text VARCHAR(MAX) NOT NULL ,
|
||||
provider_id INTEGER NULL ,
|
||||
visit_occurrence_id INTEGER NULL ,
|
||||
note_source_value VARCHAR(50) NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
CREATE TABLE observation
|
||||
(
|
||||
observation_id INTEGER NOT NULL ,
|
||||
person_id INTEGER NOT NULL ,
|
||||
observation_concept_id INTEGER NOT NULL ,
|
||||
observation_date DATE NOT NULL ,
|
||||
observation_time VARCHAR(10) NULL ,
|
||||
observation_type_concept_id INTEGER NOT NULL ,
|
||||
value_as_number FLOAT NULL ,
|
||||
value_as_string VARCHAR(60) NULL ,
|
||||
value_as_concept_id INTEGER NULL ,
|
||||
qualifier_concept_id INTEGER NULL ,
|
||||
unit_concept_id INTEGER NULL ,
|
||||
provider_id INTEGER NULL ,
|
||||
visit_occurrence_id INTEGER NULL ,
|
||||
observation_source_value VARCHAR(50) NULL ,
|
||||
observation_source_concept_id INTEGER NULL ,
|
||||
unit_source_value VARCHAR(50) NULL ,
|
||||
qualifier_source_value VARCHAR(50) NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
CREATE TABLE fact_relationship
|
||||
(
|
||||
domain_concept_id_1 INTEGER NOT NULL ,
|
||||
fact_id_1 INTEGER NOT NULL ,
|
||||
domain_concept_id_2 INTEGER NOT NULL ,
|
||||
fact_id_2 INTEGER NOT NULL ,
|
||||
relationship_concept_id INTEGER NOT NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
|
||||
/************************
|
||||
|
||||
Standardized health system data
|
||||
|
||||
************************/
|
||||
|
||||
|
||||
|
||||
CREATE TABLE location
|
||||
(
|
||||
location_id INTEGER NOT NULL ,
|
||||
address_1 VARCHAR(50) NULL ,
|
||||
address_2 VARCHAR(50) NULL ,
|
||||
city VARCHAR(50) NULL ,
|
||||
state VARCHAR(2) NULL ,
|
||||
zip VARCHAR(9) NULL ,
|
||||
county VARCHAR(20) NULL ,
|
||||
location_source_value VARCHAR(50) NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
CREATE TABLE care_site
|
||||
(
|
||||
care_site_id INTEGER NOT NULL ,
|
||||
care_site_name VARCHAR(255) NULL ,
|
||||
place_of_service_concept_id INTEGER NULL ,
|
||||
location_id INTEGER NULL ,
|
||||
care_site_source_value VARCHAR(50) NULL ,
|
||||
place_of_service_source_value VARCHAR(50) NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
CREATE TABLE provider
|
||||
(
|
||||
provider_id INTEGER NOT NULL ,
|
||||
provider_name VARCHAR(255) NULL ,
|
||||
NPI VARCHAR(20) NULL ,
|
||||
DEA VARCHAR(20) NULL ,
|
||||
specialty_concept_id INTEGER NULL ,
|
||||
care_site_id INTEGER NULL ,
|
||||
year_of_birth INTEGER NULL ,
|
||||
gender_concept_id INTEGER NULL ,
|
||||
provider_source_value VARCHAR(50) NULL ,
|
||||
specialty_source_value VARCHAR(50) NULL ,
|
||||
specialty_source_concept_id INTEGER NULL ,
|
||||
gender_source_value VARCHAR(50) NULL ,
|
||||
gender_source_concept_id INTEGER NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
|
||||
/************************
|
||||
|
||||
Standardized health economics
|
||||
|
||||
************************/
|
||||
|
||||
|
||||
CREATE TABLE payer_plan_period
|
||||
(
|
||||
payer_plan_period_id INTEGER NOT NULL ,
|
||||
person_id INTEGER NOT NULL ,
|
||||
payer_plan_period_start_date DATE NOT NULL ,
|
||||
payer_plan_period_end_date DATE NOT NULL ,
|
||||
payer_source_value VARCHAR (50) NULL ,
|
||||
plan_source_value VARCHAR (50) NULL ,
|
||||
family_source_value VARCHAR (50) NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
/* The individual cost tables are being phased out and will disappear
|
||||
|
||||
CREATE TABLE visit_cost
|
||||
(
|
||||
visit_cost_id INTEGER NOT NULL ,
|
||||
visit_occurrence_id INTEGER NOT NULL ,
|
||||
currency_concept_id INTEGER NULL ,
|
||||
paid_copay FLOAT NULL ,
|
||||
paid_coinsurance FLOAT NULL ,
|
||||
paid_toward_deductible FLOAT NULL ,
|
||||
paid_by_payer FLOAT NULL ,
|
||||
paid_by_coordination_benefits FLOAT NULL ,
|
||||
total_out_of_pocket FLOAT NULL ,
|
||||
total_paid FLOAT NULL ,
|
||||
payer_plan_period_id INTEGER NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
CREATE TABLE procedure_cost
|
||||
(
|
||||
procedure_cost_id INTEGER NOT NULL ,
|
||||
procedure_occurrence_id INTEGER NOT NULL ,
|
||||
currency_concept_id INTEGER NULL ,
|
||||
paid_copay FLOAT NULL ,
|
||||
paid_coinsurance FLOAT NULL ,
|
||||
paid_toward_deductible FLOAT NULL ,
|
||||
paid_by_payer FLOAT NULL ,
|
||||
paid_by_coordination_benefits FLOAT NULL ,
|
||||
total_out_of_pocket FLOAT NULL ,
|
||||
total_paid FLOAT NULL ,
|
||||
revenue_code_concept_id INTEGER NULL ,
|
||||
payer_plan_period_id INTEGER NULL ,
|
||||
revenue_code_source_value VARCHAR(50) NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
CREATE TABLE drug_cost
|
||||
(
|
||||
drug_cost_id INTEGER NOT NULL ,
|
||||
drug_exposure_id INTEGER NOT NULL ,
|
||||
currency_concept_id INTEGER NULL ,
|
||||
paid_copay FLOAT NULL ,
|
||||
paid_coinsurance FLOAT NULL ,
|
||||
paid_toward_deductible FLOAT NULL ,
|
||||
paid_by_payer FLOAT NULL ,
|
||||
paid_by_coordination_benefits FLOAT NULL ,
|
||||
total_out_of_pocket FLOAT NULL ,
|
||||
total_paid FLOAT NULL ,
|
||||
ingredient_cost FLOAT NULL ,
|
||||
dispensing_fee FLOAT NULL ,
|
||||
average_wholesale_price FLOAT NULL ,
|
||||
payer_plan_period_id INTEGER NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
CREATE TABLE device_cost
|
||||
(
|
||||
device_cost_id INTEGER NOT NULL ,
|
||||
device_exposure_id INTEGER NOT NULL ,
|
||||
currency_concept_id INTEGER NULL ,
|
||||
paid_copay FLOAT NULL ,
|
||||
paid_coinsurance FLOAT NULL ,
|
||||
paid_toward_deductible FLOAT NULL ,
|
||||
paid_by_payer FLOAT NULL ,
|
||||
paid_by_coordination_benefits FLOAT NULL ,
|
||||
total_out_of_pocket FLOAT NULL ,
|
||||
total_paid FLOAT NULL ,
|
||||
payer_plan_period_id INTEGER NULL
|
||||
)
|
||||
;
|
||||
*/
|
||||
|
||||
|
||||
CREATE TABLE cost
|
||||
(
|
||||
cost_id INTEGER NOT NULL ,
|
||||
cost_event_id INTEGER NOT NULL ,
|
||||
cost_domain_id VARCHAR(20) NOT NULL ,
|
||||
cost_type_concept_id INTEGER NOT NULL ,
|
||||
currency_concept_id INTEGER NULL ,
|
||||
total_charge FLOAT NULL ,
|
||||
total_cost FLOAT NULL ,
|
||||
total_paid FLOAT NULL ,
|
||||
paid_by_payer FLOAT NULL ,
|
||||
paid_by_patient FLOAT NULL ,
|
||||
paid_patient_copay FLOAT NULL ,
|
||||
paid_patient_coinsurance FLOAT NULL ,
|
||||
paid_patient_deductible FLOAT NULL ,
|
||||
paid_by_primary FLOAT NULL ,
|
||||
paid_ingredient_cost FLOAT NULL ,
|
||||
paid_dispensing_fee FLOAT NULL ,
|
||||
payer_plan_period_id INTEGER NULL ,
|
||||
amount_allowed FLOAT NULL ,
|
||||
revenue_code_concept_id INTEGER NULL ,
|
||||
reveue_code_source_value VARCHAR(50) NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
/************************
|
||||
|
||||
Standardized derived elements
|
||||
|
||||
************************/
|
||||
|
||||
CREATE TABLE cohort
|
||||
(
|
||||
cohort_definition_id INTEGER NOT NULL ,
|
||||
subject_id INTEGER NOT NULL ,
|
||||
cohort_start_date DATE NOT NULL ,
|
||||
cohort_end_date DATE NOT NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
CREATE TABLE cohort_attribute
|
||||
(
|
||||
cohort_definition_id INTEGER NOT NULL ,
|
||||
cohort_start_date DATE NOT NULL ,
|
||||
cohort_end_date DATE NOT NULL ,
|
||||
subject_id INTEGER NOT NULL ,
|
||||
attribute_definition_id INTEGER NOT NULL ,
|
||||
value_as_number FLOAT NULL ,
|
||||
value_as_concept_id INTEGER NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
|
||||
CREATE TABLE drug_era
|
||||
(
|
||||
drug_era_id INTEGER NOT NULL ,
|
||||
person_id INTEGER NOT NULL ,
|
||||
drug_concept_id INTEGER NOT NULL ,
|
||||
drug_era_start_date DATE NOT NULL ,
|
||||
drug_era_end_date DATE NOT NULL ,
|
||||
drug_exposure_count INTEGER NULL ,
|
||||
gap_days INTEGER NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
CREATE TABLE dose_era
|
||||
(
|
||||
dose_era_id INTEGER NOT NULL ,
|
||||
person_id INTEGER NOT NULL ,
|
||||
drug_concept_id INTEGER NOT NULL ,
|
||||
unit_concept_id INTEGER NOT NULL ,
|
||||
dose_value FLOAT NOT NULL ,
|
||||
dose_era_start_date DATE NOT NULL ,
|
||||
dose_era_end_date DATE NOT NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
|
||||
CREATE TABLE condition_era
|
||||
(
|
||||
condition_era_id INTEGER NOT NULL ,
|
||||
person_id INTEGER NOT NULL ,
|
||||
condition_concept_id INTEGER NOT NULL ,
|
||||
condition_era_start_date DATE NOT NULL ,
|
||||
condition_era_end_date DATE NOT NULL ,
|
||||
condition_occurrence_count INTEGER NULL
|
||||
)
|
||||
;
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
|
@ -1,187 +0,0 @@
|
|||
/*********************************************************************************
|
||||
# Copyright 2014 Observational Health Data Sciences and Informatics
|
||||
#
|
||||
#
|
||||
# Licensed under the Apache License, Version 2.0 (the "License");
|
||||
# you may not use this file except in compliance with the License.
|
||||
# You may obtain a copy of the License at
|
||||
#
|
||||
# http://www.apache.org/licenses/LICENSE-2.0
|
||||
#
|
||||
# Unless required by applicable law or agreed to in writing, software
|
||||
# distributed under the License is distributed on an "AS IS" BASIS,
|
||||
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
|
||||
# See the License for the specific language governing permissions and
|
||||
# limitations under the License.
|
||||
********************************************************************************/
|
||||
|
||||
/************************
|
||||
|
||||
####### # # ####### ###### ##### ###### # # ####### ###
|
||||
# # ## ## # # # # # # # # ## ## # # # # # # ##### ###### # # ###### ####
|
||||
# # # # # # # # # # # # # # # # # # # # # ## # # # # # # # #
|
||||
# # # # # # # ###### # # # # # # # # ###### # # # # # # ##### ## ##### ####
|
||||
# # # # # # # # # # # # # # # # # # # # # # ## # #
|
||||
# # # # # # # # # # # # # # # # # # # ## # # # # # # # #
|
||||
####### # # ####### # ##### ###### # # ## ##### ### # # ##### ###### # # ###### ####
|
||||
|
||||
|
||||
script to create the required indexes within OMOP common data model, version 5.0 for SQL Server database
|
||||
|
||||
last revised: 12 Oct 2014
|
||||
|
||||
author: Patrick Ryan
|
||||
|
||||
description: These indices are considered a minimal requirement to ensure adequate performance of analyses.
|
||||
|
||||
*************************/
|
||||
|
||||
|
||||
/************************
|
||||
|
||||
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_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_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);
|
||||
|
||||
|
|
@ -1,18 +0,0 @@
|
|||
Common-Data-Model / SQL Server
|
||||
=================
|
||||
|
||||
This folder contains the SQL scripts for SQL Server.
|
||||
|
||||
In order to create your instantiation of the Common Data Model, we recommend following these steps:
|
||||
|
||||
1. Create an empty schema.
|
||||
|
||||
2. Execute the script `OMOP CDM ddl - SQL Server.sql` to create the tables and fields.
|
||||
|
||||
3. Load your data into the schema.
|
||||
|
||||
4. Execute the script `OMOP CDM constraints - SQL Server.sql` to add the constraints (primary and foreign keys).
|
||||
|
||||
5. Execute the script `OMOP CDM indexes required - SQL Server.sql` to add the minimum set of indexes we recommend.
|
||||
|
||||
Note: you could also apply the constraints and/or the indexes before loading the data, but this will slow down the insertion of the data considerably.
|
||||
|
|
@ -1,142 +0,0 @@
|
|||
/*********************************************************************************
|
||||
# Copyright 2014 Observational Health Data Sciences and Informatics
|
||||
#
|
||||
#
|
||||
# Licensed under the Apache License, Version 2.0 (the "License");
|
||||
# you may not use this file except in compliance with the License.
|
||||
# You may obtain a copy of the License at
|
||||
#
|
||||
# http://www.apache.org/licenses/LICENSE-2.0
|
||||
#
|
||||
# Unless required by applicable law or agreed to in writing, software
|
||||
# distributed under the License is distributed on an "AS IS" BASIS,
|
||||
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
|
||||
# See the License for the specific language governing permissions and
|
||||
# limitations under the License.
|
||||
********************************************************************************/
|
||||
|
||||
/************************
|
||||
|
||||
####### # # ####### ###### ##### ###### # # #######
|
||||
# # ## ## # # # # # # # # ## ## # # #
|
||||
# # # # # # # # # # # # # # # # # # # #
|
||||
# # # # # # # ###### # # # # # # # # ######
|
||||
# # # # # # # # # # # # # # #
|
||||
# # # # # # # # # # # # # # # # #
|
||||
####### # # ####### # ##### ###### # # ## #####
|
||||
|
||||
|
||||
Script to load the common data model, version 5.0 vocabulary tables for SQL Server database
|
||||
|
||||
Notes
|
||||
|
||||
1) There is no data file load for the SOURCE_TO_CONCEPT_MAP table because that table is deprecated in CDM version 5.0
|
||||
2) This script assumes the CDM version 5 vocabulary zip file has been unzipped into the "C:\CDMV5Vocabulary" directory.
|
||||
3) If you unzipped your CDM version 5 vocabulary files into a different directory then replace all file paths below, with your directory path.
|
||||
4) Run this SQL query script in the database where you created your CDM Version 5 tables
|
||||
|
||||
last revised: 26 Nov 2014
|
||||
|
||||
author: Lee Evans
|
||||
|
||||
|
||||
*************************/
|
||||
|
||||
TRUNCATE TABLE DRUG_STRENGTH;
|
||||
BULK INSERT DRUG_STRENGTH
|
||||
FROM 'C:\CDMV5VOCAB\DRUG_STRENGTH.csv'
|
||||
WITH (
|
||||
FIRSTROW = 2,
|
||||
FIELDTERMINATOR = '\t',
|
||||
ROWTERMINATOR = '0x0a',
|
||||
ERRORFILE = 'C:\CDMV5VOCAB\DRUG_STRENGTH.bad',
|
||||
TABLOCK
|
||||
);
|
||||
|
||||
TRUNCATE TABLE CONCEPT;
|
||||
BULK INSERT CONCEPT
|
||||
FROM 'C:\CDMV5VOCAB\CONCEPT.csv'
|
||||
WITH (
|
||||
FIRSTROW = 2,
|
||||
FIELDTERMINATOR = '\t',
|
||||
ROWTERMINATOR = '0x0a',
|
||||
ERRORFILE = 'C:\CDMV5VOCAB\CONCEPT.bad',
|
||||
TABLOCK
|
||||
);
|
||||
|
||||
TRUNCATE TABLE CONCEPT_RELATIONSHIP;
|
||||
BULK INSERT CONCEPT_RELATIONSHIP
|
||||
FROM 'C:\CDMV5VOCAB\CONCEPT_RELATIONSHIP.csv'
|
||||
WITH (
|
||||
FIRSTROW = 2,
|
||||
FIELDTERMINATOR = '\t',
|
||||
ROWTERMINATOR = '0x0a',
|
||||
ERRORFILE = 'C:\CDMV5VOCAB\CONCEPT_RELATIONSHIP.bad',
|
||||
TABLOCK
|
||||
);
|
||||
|
||||
TRUNCATE TABLE CONCEPT_ANCESTOR;
|
||||
BULK INSERT CONCEPT_ANCESTOR
|
||||
FROM 'C:\CDMV5VOCAB\CONCEPT_ANCESTOR.csv'
|
||||
WITH (
|
||||
FIRSTROW = 2,
|
||||
FIELDTERMINATOR = '\t',
|
||||
ROWTERMINATOR = '0x0a',
|
||||
ERRORFILE = 'C:\CDMV5VOCAB\CONCEPT_ANCESTOR.bad',
|
||||
TABLOCK
|
||||
);
|
||||
|
||||
TRUNCATE TABLE CONCEPT_SYNONYM;
|
||||
BULK INSERT CONCEPT_SYNONYM
|
||||
FROM 'C:\CDMV5VOCAB\CONCEPT_SYNONYM.csv'
|
||||
WITH (
|
||||
FIRSTROW = 2,
|
||||
FIELDTERMINATOR = '\t',
|
||||
ROWTERMINATOR = '0x0a',
|
||||
ERRORFILE = 'C:\CDMV5VOCAB\CONCEPT_SYNONYM.bad',
|
||||
TABLOCK
|
||||
);
|
||||
|
||||
TRUNCATE TABLE VOCABULARY;
|
||||
BULK INSERT VOCABULARY
|
||||
FROM 'C:\CDMV5VOCAB\VOCABULARY.csv'
|
||||
WITH (
|
||||
FIRSTROW = 2,
|
||||
FIELDTERMINATOR = '\t',
|
||||
ROWTERMINATOR = '0x0a',
|
||||
ERRORFILE = 'C:\CDMV5VOCAB\VOCABULARY.bad',
|
||||
TABLOCK
|
||||
);
|
||||
|
||||
TRUNCATE TABLE RELATIONSHIP;
|
||||
BULK INSERT RELATIONSHIP
|
||||
FROM 'C:\CDMV5VOCAB\RELATIONSHIP.csv'
|
||||
WITH (
|
||||
FIRSTROW = 2,
|
||||
FIELDTERMINATOR = '\t',
|
||||
ROWTERMINATOR = '0x0a',
|
||||
ERRORFILE = 'C:\CDMV5VOCAB\RELATIONSHIP.bad',
|
||||
TABLOCK
|
||||
);
|
||||
|
||||
TRUNCATE TABLE CONCEPT_CLASS;
|
||||
BULK INSERT CONCEPT_CLASS
|
||||
FROM 'C:\CDMV5VOCAB\CONCEPT_CLASS.csv'
|
||||
WITH (
|
||||
FIRSTROW = 2,
|
||||
FIELDTERMINATOR = '\t',
|
||||
ROWTERMINATOR = '0x0a',
|
||||
ERRORFILE = 'C:\CDMV5VOCAB\CONCEPT_CLASS.bad',
|
||||
TABLOCK
|
||||
);
|
||||
|
||||
TRUNCATE TABLE DOMAIN;
|
||||
BULK INSERT DOMAIN
|
||||
FROM 'C:\CDMV5VOCAB\DOMAIN.csv'
|
||||
WITH (
|
||||
FIRSTROW = 2,
|
||||
FIELDTERMINATOR = '\t',
|
||||
ROWTERMINATOR = '0x0a',
|
||||
ERRORFILE = 'C:\CDMV5VOCAB\DOMAIN.bad',
|
||||
TABLOCK
|
||||
);
|
||||
0
Version4 To Version5 Conversion/Oracle/OMOP CDMv4 to CDMv5 - Oracle.sql
Normal file → Executable file
0
Version4 To Version5 Conversion/Oracle/OMOP CDMv4 to CDMv5 - Oracle.sql
Normal file → Executable file
0
Version4 To Version5 Conversion/PostgreSQL/OMOP CDMv4 to CDMv5 - PostgreSQL.sql
Normal file → Executable file
0
Version4 To Version5 Conversion/PostgreSQL/OMOP CDMv4 to CDMv5 - PostgreSQL.sql
Normal file → Executable file
0
Version4 To Version5 Conversion/Redshift/OMOP CDMv4 to CDMv5 - Redshift.sql
Normal file → Executable file
0
Version4 To Version5 Conversion/Redshift/OMOP CDMv4 to CDMv5 - Redshift.sql
Normal file → Executable file
0
Version4 To Version5 Conversion/Sql Server PDW/OMOP CDMv4 to CDMv5 - Sql Server PDW.dsql
Normal file → Executable file
0
Version4 To Version5 Conversion/Sql Server PDW/OMOP CDMv4 to CDMv5 - Sql Server PDW.dsql
Normal file → Executable file
0
Version4 To Version5 Conversion/Sql Server/OMOP CDMv4 to CDMv5 - SQL Server.sql
Normal file → Executable file
0
Version4 To Version5 Conversion/Sql Server/OMOP CDMv4 to CDMv5 - SQL Server.sql
Normal file → Executable file
|
|
@ -1,14 +0,0 @@
|
|||
Common-Data-Model / Oracle
|
||||
=================
|
||||
|
||||
This folder contains the SQL scripts for Oracle.
|
||||
|
||||
In order to create your instantiation of the Common Data Model, we recommend following these steps:
|
||||
|
||||
1. Create an empty schema.
|
||||
|
||||
2. Execute the script `CDM V4 ddl.sql` to create the tables and fields.
|
||||
|
||||
3. Load your data into the schema using the loading scripts in VocabImport
|
||||
|
||||
Note: you could also apply the constraints and the indexes after loading the data, this will speed up the insertion of the data considerably.
|
||||
|
|
@ -1,51 +0,0 @@
|
|||
/*********************************************************************************
|
||||
# Copyright 2015 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.4
|
||||
********************************************************************************/
|
||||
|
||||
/************************
|
||||
|
||||
####### # # ####### ###### ##### ###### # # ## #######
|
||||
# # ## ## # # # # # # # # ## ## # # # # #
|
||||
# # # # # # # # # # # # # # # # # # # # # #
|
||||
# # # # # # # ###### # # # # # # # # ####### #######
|
||||
# # # # # # # # # # # # # # # #
|
||||
# # # # # # # # # # # # # # # # # #
|
||||
####### # # ####### # ##### ###### # # ## # # #####
|
||||
|
||||
|
||||
script to load the Vocabulary related tables in the OMOP common data model, version 4.5 for Oracle database
|
||||
|
||||
last revised: 19 Mar 2015
|
||||
|
||||
author: Lee Evans
|
||||
|
||||
Notes
|
||||
|
||||
1) This script assumes the CDM version 4.5 vocabulary zip file has been unzipped into the "C:\CDM" directory.
|
||||
2) If you unzipped your CDM version 4.5 vocabulary files into a different directory then replace all file paths below, with your directory path.
|
||||
3) If you have existing data in your CDM vocabulary tables then backup that data (if needed) and truncate those tables before loading
|
||||
|
||||
|
||||
*************************/
|
||||
|
||||
sqlldr CDM/<password> CONTROL=CONCEPT.ctl LOG=C:\CDM\CONCEPT.log BAD=C:\CDM\CONCEPT.bad
|
||||
sqlldr CDM/<password> CONTROL=CONCEPT_ANCESTOR.ctl LOG=C:\CDM\CONCEPT_ANCESTOR.log BAD=C:\CDM\CONCEPT_ANCESTOR.bad
|
||||
sqlldr CDM/<password> CONTROL=CONCEPT_RELATIONSHIP.ctl LOG=C:\CDM\CONCEPT_RELATIONSHIP.log BAD=C:\CDM\CONCEPT_RELATIONSHIP.bad
|
||||
sqlldr CDM/<password> CONTROL=CONCEPT_SYNONYM.ctl LOG=C:\CDM\CONCEPT_SYNONYM.log BAD=C:\CDM\CONCEPT_SYNONYM.bad
|
||||
sqlldr CDM/<password> CONTROL=DRUG_STRENGTH.ctl LOG=C:\CDM\DRUG_STRENGTH.log BAD=C:\CDM\DRUG_STRENGTH.bad
|
||||
sqlldr CDM/<password> CONTROL=RELATIONSHIP.ctl LOG=C:\CDM\RELATIONSHIP.log BAD=C:\CDM\RELATIONSHIP.bad
|
||||
sqlldr CDM/<password> CONTROL=VOCABULARY.ctl LOG=C:\CDM\VOCABULARY.log BAD=C:\CDM\VOCABULARY.bad
|
||||
sqlldr CDM/<password> CONTROL=SOURCE_TO_CONCEPT_MAP.ctl LOG=C:\CDM\SOURCE_TO_CONCEPT_MAP.log BAD=C:\CDM\SOURCE_TO_CONCEPT_MAP.bad
|
||||
|
|
@ -1,18 +0,0 @@
|
|||
options (skip=1)
|
||||
load data
|
||||
infile concept.csv
|
||||
into table concept
|
||||
replace
|
||||
fields terminated by '\t'
|
||||
trailing nullcols
|
||||
(
|
||||
concept_id,
|
||||
concept_name CHAR(256),
|
||||
concept_level,
|
||||
concept_class,
|
||||
vocabulary_id,
|
||||
concept_code,
|
||||
valid_start_date DATE 'YYYYMMDD',
|
||||
valid_end_date DATE 'YYYYMMDD',
|
||||
invalid_reason
|
||||
)
|
||||
|
|
@ -1,13 +0,0 @@
|
|||
options (skip=1)
|
||||
load data
|
||||
infile concept_ancestor.csv
|
||||
into table concept_ancestor
|
||||
replace
|
||||
fields terminated by '\t'
|
||||
trailing nullcols
|
||||
(
|
||||
ancestor_concept_id,
|
||||
descendant_concept_id,
|
||||
min_levels_of_separation,
|
||||
max_levels_of_separation
|
||||
)
|
||||
|
|
@ -1,15 +0,0 @@
|
|||
options (skip=1)
|
||||
load data
|
||||
infile concept_relationship.csv
|
||||
into table concept_relationship
|
||||
replace
|
||||
fields terminated by '\t'
|
||||
trailing nullcols
|
||||
(
|
||||
concept_id_1,
|
||||
concept_id_2,
|
||||
relationship_id,
|
||||
valid_start_date DATE 'YYYYMMDD',
|
||||
valid_end_date DATE 'YYYYMMDD',
|
||||
invalid_reason
|
||||
)
|
||||
|
|
@ -1,12 +0,0 @@
|
|||
options (skip=1)
|
||||
load data
|
||||
infile concept_synonym.csv
|
||||
into table concept_synonym
|
||||
replace
|
||||
fields terminated by '\t'
|
||||
trailing nullcols
|
||||
(
|
||||
concept_synonym_id,
|
||||
concept_id,
|
||||
concept_synonym_name CHAR(1000)
|
||||
)
|
||||
|
|
@ -1,19 +0,0 @@
|
|||
options (skip=1)
|
||||
load data
|
||||
infile drug_strength.csv
|
||||
into table drug_strength
|
||||
replace
|
||||
fields terminated by '\t'
|
||||
trailing nullcols
|
||||
(
|
||||
drug_concept_id,
|
||||
ingredient_concept_id,
|
||||
amount_value,
|
||||
amount_unit,
|
||||
concentration_value,
|
||||
concentration_enum_unit,
|
||||
concentration_denom_unit,
|
||||
valid_start_date DATE 'YYYYMMDD',
|
||||
valid_end_date DATE 'YYYYMMDD',
|
||||
invalid_reason
|
||||
)
|
||||
|
|
@ -1,14 +0,0 @@
|
|||
options (skip=1)
|
||||
load data
|
||||
infile relationship.csv
|
||||
into table relationship
|
||||
replace
|
||||
fields terminated by '\t'
|
||||
trailing nullcols
|
||||
(
|
||||
relationship_id,
|
||||
relationship_name,
|
||||
is_hierarchical,
|
||||
defines_ancestry,
|
||||
reverse_relationship
|
||||
)
|
||||
|
|
@ -1,11 +0,0 @@
|
|||
options (skip=1)
|
||||
load data
|
||||
infile vocabulary.csv
|
||||
into table vocabulary
|
||||
replace
|
||||
fields terminated by '\t'
|
||||
trailing nullcols
|
||||
(
|
||||
vocabulary_id,
|
||||
vocabulary_name
|
||||
)
|
||||
|
|
@ -1,13 +0,0 @@
|
|||
Common-Data-Model / PostgreSQL
|
||||
=================
|
||||
|
||||
This folder contains the SQL scripts for PostgreSQL.
|
||||
|
||||
In order to create your instantiation of the Common Data Model, we recommend following these steps:
|
||||
|
||||
1. Create an empty schema.
|
||||
|
||||
2. Execute the script `CDM V4 ddl.sql` to create the tables and fields.
|
||||
|
||||
3. Load your data into the schema.
|
||||
|
||||
|
|
@ -1,54 +0,0 @@
|
|||
/*********************************************************************************
|
||||
# Copyright 2015 Observational Health Data Sciences and Informatics
|
||||
#
|
||||
#
|
||||
# Licensed under the Apache License, Version 2.0 (the "License");
|
||||
# you may not use this file except in compliance with the License.
|
||||
# You may obtain a copy of the License at
|
||||
#
|
||||
# http://www.apache.org/licenses/LICENSE-2.0
|
||||
#
|
||||
# Unless required by applicable law or agreed to in writing, software
|
||||
# distributed under the License is distributed on an "AS IS" BASIS,
|
||||
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
|
||||
# See the License for the specific language governing permissions and
|
||||
# limitations under the License.
|
||||
********************************************************************************/
|
||||
|
||||
/************************
|
||||
|
||||
####### # # ####### ###### ##### ###### # # #######
|
||||
# # ## ## # # # # # # # # ## ## # # #
|
||||
# # # # # # # # # # # # # # # # # # # #
|
||||
# # # # # # # ###### # # # # # # # # ######
|
||||
# # # # # # # # # # # # # # #
|
||||
# # # # # # # # # # # # # # # # #
|
||||
####### # # ####### # ##### ###### # # ## #####
|
||||
|
||||
|
||||
Script to load the common data model, version 4.5 vocabulary tables for PostgreSQL database
|
||||
|
||||
Notes
|
||||
|
||||
1) This script assumes the CDM version 4.5 vocabulary zip file has been unzipped into the "C:\CDM" directory.
|
||||
2) If you unzipped your CDM version 4.5 vocabulary files into a different directory then replace all file paths below, with your directory path.
|
||||
3) Run this SQL query script in the database where you created your CDM Version 4.5 tables
|
||||
|
||||
last revised: 20th March 2015
|
||||
|
||||
author: Lee Evans
|
||||
|
||||
|
||||
*************************/
|
||||
|
||||
COPY CONCEPT FROM 'C:\CDM\CONCEPT.csv' WITH DELIMITER E'\t' CSV HEADER QUOTE E'\b' ;
|
||||
COPY CONCEPT_ANCESTOR FROM 'C:\CDM\CONCEPT_ANCESTOR.csv' WITH DELIMITER E'\t' CSV HEADER QUOTE E'\b' ;
|
||||
COPY CONCEPT_RELATIONSHIP FROM 'C:\CDM\CONCEPT_RELATIONSHIP.csv' WITH DELIMITER E'\t' CSV HEADER QUOTE E'\b' ;
|
||||
COPY CONCEPT_SYNONYM FROM 'C:\CDM\CONCEPT_SYNONYM.csv' WITH DELIMITER E'\t' CSV HEADER QUOTE E'\b' ;
|
||||
COPY DRUG_STRENGTH FROM 'C:\CDM\DRUG_STRENGTH.csv' WITH DELIMITER E'\t' CSV HEADER QUOTE E'\b' ;
|
||||
COPY RELATIONSHIP FROM 'C:\CDM\RELATIONSHIP.csv' WITH DELIMITER E'\t' CSV HEADER QUOTE E'\b' ;
|
||||
COPY SOURCE_TO_CONCEPT_MAP FROM 'C:\CDM\SOURCE_TO_CONCEPT_MAP.csv' WITH DELIMITER E'\t' CSV HEADER QUOTE E'\b' ;
|
||||
COPY VOCABULARY FROM 'C:\CDM\VOCABULARY.csv' WITH DELIMITER E'\t' CSV HEADER QUOTE E'\b' ;
|
||||
|
||||
|
||||
|
||||
Loading…
Reference in New Issue