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OMOP
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Impala, Oracle, and Netezza edits from testers

This commit is contained in:
clairblacketer 2018-09-24 12:00:16 -04:00
parent 8c6ebe5f95
commit eee81f61ad
9 changed files with 1069 additions and 1315 deletions
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2
Impala/DataImport/OMOP_CDM_synpuf_load_Impala.sql
View File

@ -1,6 +1,6 @@
LOAD DATA INPATH '${VAR:OMOP_SYNPUF_PATH}/CDM_CARE_SITE.csv' OVERWRITE INTO TABLE care_site;
LOAD DATA INPATH '${VAR:OMOP_SYNPUF_PATH}/CDM_CONDITION_OCCURRENCE.csv' OVERWRITE INTO TABLE condition_occurrence;
LOAD DATA INPATH '${VAR:OMOP_SYNPUF_PATH}/CDM_DEATH.csv' OVERWRITE INTO TABLE death;
--LOAD DATA INPATH '${VAR:OMOP_SYNPUF_PATH}/CDM_DEATH.csv' OVERWRITE INTO TABLE death;
LOAD DATA INPATH '${VAR:OMOP_SYNPUF_PATH}/CDM_DRUG_EXPOSURE.csv' OVERWRITE INTO TABLE drug_exposure;
LOAD DATA INPATH '${VAR:OMOP_SYNPUF_PATH}/CDM_DEVICE_EXPOSURE.csv' OVERWRITE INTO TABLE device_exposure;
LOAD DATA INPATH '${VAR:OMOP_SYNPUF_PATH}/CDM_LOCATION.csv' OVERWRITE INTO TABLE `location`;

135
Impala/OMOP CDM impala ddl.txt
View File

@ -153,28 +153,6 @@ CREATE TABLE drug_strength (
;
CREATE TABLE cohort_definition (
cohort_definition_id INTEGER ,
cohort_definition_name VARCHAR(255),
cohort_definition_description STRING,
definition_type_concept_id INTEGER ,
cohort_definition_syntax STRING,
subject_concept_id INTEGER ,
cohort_initiation_date TIMESTAMP
)
;
CREATE TABLE attribute_definition (
attribute_definition_id INTEGER ,
attribute_name VARCHAR(255),
attribute_description STRING,
attribute_type_concept_id INTEGER ,
attribute_syntax STRING
)
;
/**************************
Standardized meta-data
@ -210,8 +188,8 @@ CREATE TABLE `metadata`
)
;
INSERT INTO metadata (name, value_as_string) --Added cdm version record
VALUES ('CDM Version', '6.0')
INSERT INTO `metadata` (metadata_concept_id, metadata_type_concept_id, name, value_as_string, value_as_concept_id, metadata_date, metadata_datetime) --Added cdm version record
VALUES (0,0,'CDM Version', '6.0',0,NULL,NULL)
;
@ -233,9 +211,9 @@ CREATE TABLE person
birth_datetime TIMESTAMP ,
race_concept_id INTEGER ,
ethnicity_concept_id INTEGER ,
location_id INTEGER ,
provider_id INTEGER ,
care_site_id INTEGER ,
location_id BIGINT ,
provider_id BIGINT ,
care_site_id BIGINT ,
person_source_value VARCHAR(50),
gender_source_value VARCHAR(50),
gender_source_concept_id INTEGER ,
@ -281,20 +259,6 @@ CREATE TABLE specimen
;
--HINT DISTRIBUTE_ON_KEY(person_id)
CREATE TABLE death
(
person_id BIGINT ,
death_date TIMESTAMP ,
death_datetime TIMESTAMP ,
death_type_concept_id INTEGER ,
cause_concept_id INTEGER ,
cause_source_value VARCHAR(50),
cause_source_concept_id INTEGER
)
;
--HINT DISTRIBUTE_ON_KEY(person_id)
CREATE TABLE visit_occurrence
(
@ -306,8 +270,8 @@ CREATE TABLE visit_occurrence
visit_end_date TIMESTAMP ,
visit_end_datetime TIMESTAMP ,
visit_type_concept_id INTEGER ,
provider_id INTEGER ,
care_site_id INTEGER ,
provider_id BIGINT ,
care_site_id BIGINT ,
visit_source_value VARCHAR(50),
visit_source_concept_id INTEGER ,
admitted_from_concept_id INTEGER , /*Changed from admitting_source_* */
@ -318,7 +282,7 @@ CREATE TABLE visit_occurrence
)
;
--todo admitting 'source'
--HINT DISTRIBUTE_ON_KEY(person_id)
CREATE TABLE visit_detail
(
@ -330,8 +294,8 @@ CREATE TABLE visit_detail
visit_detail_end_date TIMESTAMP ,
visit_detail_end_datetime TIMESTAMP ,
visit_detail_type_concept_id INTEGER ,
provider_id INTEGER ,
care_site_id INTEGER ,
provider_id BIGINT ,
care_site_id BIGINT ,
discharge_to_concept_id INTEGER ,
admitted_from_concept_id INTEGER , /*Changed from admitting_source_* */
admitted_from_source_value VARCHAR(50) ,
@ -356,12 +320,12 @@ CREATE TABLE procedure_occurrence
procedure_type_concept_id INTEGER ,
modifier_concept_id INTEGER ,
quantity INTEGER ,
provider_id INTEGER ,
visit_occurrence_id INTEGER ,
visit_detail_id INTEGER ,
provider_id BIGINT ,
visit_occurrence_id BIGINT ,
visit_detail_id BIGINT ,
procedure_source_value VARCHAR(50) ,
procedure_source_concept_id INTEGER ,
modifier_source_value VARCHAR(50) ,
modifier_source_value VARCHAR(50)
)
;
@ -385,9 +349,9 @@ CREATE TABLE drug_exposure
sig STRING ,
route_concept_id INTEGER ,
lot_number VARCHAR(50) ,
provider_id INTEGER ,
visit_occurrence_id INTEGER ,
visit_detail_id INTEGER ,
provider_id BIGINT ,
visit_occurrence_id BIGINT ,
visit_detail_id BIGINT ,
drug_source_value VARCHAR(50) ,
drug_source_concept_id INTEGER ,
route_source_value VARCHAR(50) ,
@ -409,9 +373,9 @@ CREATE TABLE device_exposure
device_type_concept_id INTEGER ,
unique_device_id VARCHAR(50) ,
quantity INTEGER ,
provider_id INTEGER ,
visit_occurrence_id INTEGER ,
visit_detail_id INTEGER ,
provider_id BIGINT ,
visit_occurrence_id BIGINT ,
visit_detail_id BIGINT ,
device_source_value VARCHAR(100) ,
device_source_concept_id INTEGER
)
@ -431,9 +395,9 @@ CREATE TABLE condition_occurrence
condition_type_concept_id INTEGER ,
condition_status_concept_id INTEGER ,
stop_reason VARCHAR(20) ,
provider_id INTEGER ,
visit_occurrence_id INTEGER ,
visit_detail_id INTEGER ,
provider_id BIGINT ,
visit_occurrence_id BIGINT ,
visit_detail_id BIGINT ,
condition_source_value VARCHAR(50) ,
condition_source_concept_id INTEGER ,
condition_status_source_value VARCHAR(50)
@ -457,9 +421,9 @@ CREATE TABLE measurement
unit_concept_id INTEGER ,
range_low FLOAT ,
range_high FLOAT ,
provider_id INTEGER ,
visit_occurrence_id INTEGER ,
visit_detail_id INTEGER ,
provider_id BIGINT ,
visit_occurrence_id BIGINT ,
visit_detail_id BIGINT ,
measurement_source_value VARCHAR(50) ,
measurement_source_concept_id INTEGER ,
unit_source_value VARCHAR(50) ,
@ -473,9 +437,8 @@ CREATE TABLE note
(
note_id BIGINT ,
person_id BIGINT ,
note_event_id BIGINT , --This and the field below added
note_domain_id VARCHAR(20) , --This field may be removed in favor of the one below
--note_event_table_concept_id INTEGER , --This may be added based on 9/4 meeting
note_event_id BIGINT ,
note_event_field_concept_id INTEGER ,
note_date TIMESTAMP ,
note_datetime TIMESTAMP ,
note_type_concept_id INTEGER ,
@ -484,15 +447,14 @@ CREATE TABLE note
note_text STRING ,
encoding_concept_id INTEGER ,
language_concept_id INTEGER ,
provider_id INTEGER ,
visit_occurrence_id INTEGER ,
visit_detail_id INTEGER ,
provider_id BIGINT ,
visit_occurrence_id BIGINT ,
visit_detail_id BIGINT ,
note_source_value VARCHAR(50)
)
;
CREATE TABLE note_nlp
(
note_nlp_id BIGINT ,
@ -527,7 +489,7 @@ CREATE TABLE observation
value_as_concept_id INTEGER ,
qualifier_concept_id INTEGER ,
unit_concept_id INTEGER ,
provider_id INTEGER ,
provider_id BIGINT ,
visit_occurrence_id BIGINT ,
visit_detail_id BIGINT ,
observation_source_value VARCHAR(50) ,
@ -535,8 +497,7 @@ CREATE TABLE observation
unit_source_value VARCHAR(50) ,
qualifier_source_value VARCHAR(50) ,
observation_event_id BIGINT , /* This will link back to the event table (SURVEY) on SURVEY_OCCURRENCE_ID, changed name to comply with COST and NOTE*/
observation_event_domain_id VARCHAR(20) ,
--obs_event_table_concept_id INTEGER , /* Changed name to comply with COST and NOTE. This should be 'Survey'. Had to use 'obs' for oracle restriction, may be added on 9/4*/
obs_event_field_concept_id INTEGER , /* Changed name to comply with COST and NOTE. This should be 'Survey'. Had to use 'obs' for oracle restriction, may be added on 9/4*/
value_as_datetime TIMESTAMP
)
;
@ -593,7 +554,7 @@ Standardized health system data
************************/
CREATE TABLE location
CREATE TABLE `location`
(
location_id BIGINT ,
address_1 VARCHAR(50) ,
@ -693,8 +654,7 @@ CREATE TABLE cost
cost_id BIGINT ,
person_id BIGINT,
cost_event_id BIGINT ,
cost_domain_id VARCHAR(20) ,
--cost_event_table_concept_id INTEGER , /*This is still in discussion and most likely will replace cost_domain_id at 9/4 meeting*/
cost_event_field_concept_id INTEGER , /*This is still in discussion and most likely will replace cost_domain_id at 9/4 meeting*/
cost_concept_id INTEGER ,
cost_type_concept_id INTEGER ,
currency_concept_id INTEGER ,
@ -720,31 +680,6 @@ Standardized derived elements
************************/
--HINT DISTRIBUTE_ON_KEY(subject_id)
CREATE TABLE cohort
(
cohort_definition_id BIGINT ,
subject_id BIGINT ,
cohort_start_date TIMESTAMP ,
cohort_end_date TIMESTAMP
)
;
--HINT DISTRIBUTE_ON_KEY(subject_id)
CREATE TABLE cohort_attribute
(
cohort_definition_id BIGINT ,
subject_id BIGINT ,
cohort_start_date TIMESTAMP ,
cohort_end_date TIMESTAMP ,
attribute_definition_id BIGINT ,
value_as_number FLOAT ,
value_as_concept_id INTEGER
)
;
--HINT DISTRIBUTE_ON_KEY(person_id)
CREATE TABLE drug_era
(

4
Impala/README.md
View File

@ -11,10 +11,11 @@ In order to create your instantiation of the Common Data Model, we recommend fol
impala-shell -q 'CREATE DATABASE omop_cdm'
```
2. Execute the script `OMOP CDM impala ddl.txt` (you will need to convert it to a sql file first) to create the tables and fields.
2. Execute the scripts `OMOP CDM impala ddl.txt` and `OMOP CDM Results impala ddl.txt` (you will need to convert them to sql files first) to create the tables and fields.
```bash
impala-shell -d omop_cdm -f OMOP_CDM_impala_ddl.sql
impala-shell -d omop_cdm -f OMOP_CDM_Results_impala_ddl.sql
```
3. Load your data into the schema.
@ -42,6 +43,7 @@ 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
```
* Note that these tables are in CDM v5.2.2 format
4. Convert to Parquet format.

172
Netezza/OMOP CDM netezza ddl.txt
View File

@ -173,32 +173,6 @@ DISTRIBUTE ON RANDOM
;
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE cohort_definition (
cohort_definition_id INTEGER NOT NULL,
cohort_definition_name VARCHAR(255) NOT NULL,
cohort_definition_description VARCHAR(1000) NULL,
definition_type_concept_id INTEGER NOT NULL,
cohort_definition_syntax VARCHAR(1000) NULL,
subject_concept_id INTEGER NOT NULL,
cohort_initiation_date DATE NULL
)
DISTRIBUTE ON RANDOM
;
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE attribute_definition (
attribute_definition_id INTEGER NOT NULL,
attribute_name VARCHAR(255) NOT NULL,
attribute_description VARCHAR(1000) NULL,
attribute_type_concept_id INTEGER NOT NULL,
attribute_syntax VARCHAR(1000) NULL
)
DISTRIBUTE ON RANDOM
;
/**************************
Standardized meta-data
@ -238,8 +212,8 @@ CREATE TABLE metadata
DISTRIBUTE ON RANDOM
;
INSERT INTO metadata (name, value_as_string) --Added cdm version record
VALUES ('CDM Version', '6.0')
INSERT INTO metadata (metadata_concept_id, metadata_type_concept_id, name, value_as_string, value_as_concept_id, metadata_date, metadata_datetime) --Added cdm version record
VALUES (0,0,'CDM Version', '6.0',0,NULL,NULL)
;
@ -261,9 +235,9 @@ CREATE TABLE person
birth_datetime DATETIME 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,
location_id BIGINT NULL,
provider_id BIGINT NULL,
care_site_id BIGINT NULL,
person_source_value VARCHAR(50) NULL,
gender_source_value VARCHAR(50) NULL,
gender_source_concept_id INTEGER NULL,
@ -273,7 +247,7 @@ CREATE TABLE person
ethnicity_source_concept_id INTEGER NULL
)
DISTRUBTE ON (person_id);
DISTRIBUTE ON (person_id);
--HINT DISTRIBUTE_ON_KEY(person_id)
@ -286,7 +260,7 @@ CREATE TABLE observation_period
period_type_concept_id INTEGER NOT NULL
)
DISTRUBTE ON (person_id);
DISTRIBUTE ON (person_id);
--HINT DISTRIBUTE_ON_KEY(person_id)
@ -309,22 +283,7 @@ CREATE TABLE specimen
disease_status_source_value VARCHAR(50) NULL
)
DISTRUBTE ON (person_id);
--HINT DISTRIBUTE_ON_KEY(person_id)
CREATE TABLE death
(
person_id BIGINT NOT NULL ,
death_date DATE NULL ,
death_datetime DATETIME 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
)
DISTRUBTE ON (person_id);
DISTRIBUTE ON (person_id);
--HINT DISTRIBUTE_ON_KEY(person_id)
@ -338,8 +297,8 @@ CREATE TABLE visit_occurrence
visit_end_date DATE NULL ,
visit_end_datetime DATETIME NOT NULL ,
visit_type_concept_id INTEGER NOT NULL ,
provider_id INTEGER NULL,
care_site_id INTEGER NULL,
provider_id BIGINT NULL,
care_site_id BIGINT NULL,
visit_source_value VARCHAR(50) NULL,
visit_source_concept_id INTEGER NULL ,
admitted_from_concept_id INTEGER NULL ,
@ -349,7 +308,7 @@ CREATE TABLE visit_occurrence
preceding_visit_occurrence_id INTEGER NULL
)
DISTRUBTE ON (person_id);
DISTRIBUTE ON (person_id);
--HINT DISTRIBUTE_ON_KEY(person_id)
@ -363,8 +322,8 @@ CREATE TABLE visit_detail
visit_detail_end_date DATE NULL ,
visit_detail_end_datetime DATETIME NOT NULL ,
visit_detail_type_concept_id INTEGER NOT NULL ,
provider_id INTEGER NULL ,
care_site_id INTEGER NULL ,
provider_id BIGINT NULL ,
care_site_id BIGINT NULL ,
discharge_to_concept_id INTEGER NULL ,
admitted_from_concept_id INTEGER NULL ,
admitted_from_source_value VARCHAR(50) NULL ,
@ -376,7 +335,7 @@ CREATE TABLE visit_detail
visit_occurrence_id BIGINT NOT NULL
)
DISTRUBTE ON (person_id);
DISTRIBUTE ON (person_id);
--HINT DISTRIBUTE_ON_KEY(person_id)
@ -390,15 +349,15 @@ CREATE TABLE procedure_occurrence
procedure_type_concept_id INTEGER NOT NULL ,
modifier_concept_id INTEGER NULL ,
quantity INTEGER NULL ,
provider_id INTEGER NULL ,
visit_occurrence_id INTEGER NULL ,
visit_detail_id INTEGER NULL ,
provider_id BIGINT NULL ,
visit_occurrence_id BIGINT NULL ,
visit_detail_id BIGINT NULL ,
procedure_source_value VARCHAR(50) NULL ,
procedure_source_concept_id INTEGER NULL ,
modifier_source_value VARCHAR(50) NULL ,
modifier_source_value VARCHAR(50) NULL
)
DISTRUBTE ON (person_id);
DISTRIBUTE ON (person_id);
--HINT DISTRIBUTE_ON_KEY(person_id)
@ -420,16 +379,16 @@ CREATE TABLE drug_exposure
sig VARCHAR(1000) NULL ,
route_concept_id INTEGER NULL ,
lot_number VARCHAR(50) NULL ,
provider_id INTEGER NULL ,
visit_occurrence_id INTEGER NULL ,
visit_detail_id INTEGER NULL ,
provider_id BIGINT NULL ,
visit_occurrence_id BIGINT NULL ,
visit_detail_id BIGINT 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
)
DISTRUBTE ON (person_id);
DISTRIBUTE ON (person_id);
--HINT DISTRIBUTE_ON_KEY(person_id)
@ -445,14 +404,14 @@ CREATE TABLE device_exposure
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 ,
visit_detail_id INTEGER NULL ,
provider_id BIGINT NULL ,
visit_occurrence_id BIGINT NULL ,
visit_detail_id BIGINT NULL ,
device_source_value VARCHAR(100) NULL ,
device_source_concept_id INTEGER NULL
)
DISTRUBTE ON (person_id);
DISTRIBUTE ON (person_id);
--HINT DISTRIBUTE_ON_KEY(person_id)
@ -468,15 +427,15 @@ CREATE TABLE condition_occurrence
condition_type_concept_id INTEGER NOT NULL ,
condition_status_concept_id INTEGER NULL ,
stop_reason VARCHAR(20) NULL ,
provider_id INTEGER NULL ,
visit_occurrence_id INTEGER NULL ,
visit_detail_id INTEGER NULL ,
provider_id BIGINT NULL ,
visit_occurrence_id BIGINT NULL ,
visit_detail_id BIGINT NULL ,
condition_source_value VARCHAR(50) NULL ,
condition_source_concept_id INTEGER NULL ,
condition_status_source_value VARCHAR(50) NULL
)
DISTRUBTE ON (person_id);
DISTRIBUTE ON (person_id);
--HINT DISTRIBUTE_ON_KEY(person_id)
@ -495,15 +454,15 @@ CREATE TABLE measurement
unit_concept_id INTEGER NULL ,
range_low REAL NULL ,
range_high REAL NULL ,
provider_id INTEGER NULL ,
visit_occurrence_id INTEGER NULL ,
visit_detail_id INTEGER NULL ,
provider_id BIGINT NULL ,
visit_occurrence_id BIGINT NULL ,
visit_detail_id BIGINT 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
)
DISTRUBTE ON (person_id)
DISTRIBUTE ON (person_id)
;
@ -512,9 +471,8 @@ CREATE TABLE note
(
note_id BIGINT NOT NULL ,
person_id BIGINT NOT NULL ,
note_event_id BIGINT NULL , --This and the field below added
note_domain_id VARCHAR(20) NULL , --This field may be removed in favor of the one below
--note_event_table_concept_id INTEGER NULL , --This may be added based on 9/4 meeting
note_event_id BIGINT NULL ,
note_event_field_concept_id INTEGER NULL ,
note_date DATE NULL ,
note_datetime DATETIME NOT NULL ,
note_type_concept_id INTEGER NOT NULL ,
@ -523,12 +481,12 @@ CREATE TABLE note
note_text VARCHAR(1000) NULL ,
encoding_concept_id INTEGER NOT NULL ,
language_concept_id INTEGER NOT NULL ,
provider_id INTEGER NULL ,
visit_occurrence_id INTEGER NULL ,
visit_detail_id INTEGER NULL ,
provider_id BIGINT NULL ,
visit_occurrence_id BIGINT NULL ,
visit_detail_id BIGINT NULL ,
note_source_value VARCHAR(50) NULL
)
DISTRUBTE ON (person_id)
DISTRIBUTE ON (person_id)
;
@ -568,19 +526,18 @@ CREATE TABLE observation
value_as_concept_id INTEGER NULL ,
qualifier_concept_id INTEGER NULL ,
unit_concept_id INTEGER NULL ,
provider_id INTEGER NULL ,
provider_id BIGINT NULL ,
visit_occurrence_id BIGINT NULL ,
visit_detail_id BIGINT 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 ,
observation_event_id BIGINT NULL , /* This will link back to the event table (SURVEY) on SURVEY_OCCURRENCE_ID, changed name to comply with COST and NOTE*/
observation_event_domain_id VARCHAR(20) NULL ,
--obs_event_table_concept_id INTEGER NULL , /* Changed name to comply with COST and NOTE. This should be 'Survey'. Had to use 'obs' for oracle restriction, may be added on 9/4*/
observation_event_id BIGINT NULL ,
obs_event_field_concept_id INTEGER NULL ,
value_as_datetime DATETIME NULL
)
DISTRUBTE ON (person_id)
DISTRIBUTE ON (person_id)
;
@ -630,7 +587,6 @@ DISTRIBUTE ON RANDOM
;
/************************
Standardized health system data
@ -739,7 +695,7 @@ CREATE TABLE payer_plan_period
stop_reason_source_value VARCHAR(50) NULL ,
stop_reason_source_concept_id INTEGER NULL
)
DISTRUBTE ON (person_id)
DISTRIBUTE ON (person_id)
;
@ -749,8 +705,7 @@ CREATE TABLE cost
cost_id BIGINT NOT NULL ,
person_id BIGINT NOT NULL,
cost_event_id BIGINT NOT NULL ,
cost_domain_id VARCHAR(20) NOT NULL ,
--cost_event_table_concept_id INTEGER NOT NULL , /*This is still in discussion and most likely will replace cost_domain_id at 9/4 meeting*/
cost_event_field_concept_id INTEGER NOT NULL ,
cost_concept_id INTEGER NOT NULL ,
cost_type_concept_id INTEGER NOT NULL ,
currency_concept_id INTEGER NULL ,
@ -777,33 +732,6 @@ Standardized derived elements
************************/
--HINT DISTRIBUTE_ON_KEY(subject_id)
CREATE TABLE cohort
(
cohort_definition_id BIGINT NOT NULL ,
subject_id BIGINT NOT NULL ,
cohort_start_date DATE NOT NULL ,
cohort_end_date DATE NOT NULL
)
DISTRUBTE ON (subject_id)
;
--HINT DISTRIBUTE_ON_KEY(subject_id)
CREATE TABLE cohort_attribute
(
cohort_definition_id BIGINT NOT NULL ,
subject_id BIGINT NOT NULL ,
cohort_start_date DATE NOT NULL ,
cohort_end_date DATE NOT NULL ,
attribute_definition_id BIGINT NOT NULL ,
value_as_number REAL NULL ,
value_as_concept_id INTEGER NULL
)
DISTRUBTE ON (subject_id)
;
--HINT DISTRIBUTE_ON_KEY(person_id)
CREATE TABLE drug_era
(
@ -815,7 +743,7 @@ CREATE TABLE drug_era
drug_exposure_count INTEGER NULL ,
gap_days INTEGER NULL
)
DISTRUBTE ON (person_id)
DISTRIBUTE ON (person_id)
;
@ -830,7 +758,7 @@ CREATE TABLE dose_era
dose_era_start_date DATE NOT NULL ,
dose_era_end_date DATE NOT NULL
)
DISTRUBTE ON (person_id)
DISTRIBUTE ON (person_id)
;
@ -844,5 +772,5 @@ CREATE TABLE condition_era
condition_era_end_date DATE NOT NULL ,
condition_occurrence_count INTEGER NULL
)
DISTRUBTE ON (person_id)
DISTRIBUTE ON (person_id)
;

13
Netezza/OMOP CDM netezza primary keys.txt
View File

@ -77,11 +77,6 @@ ALTER TABLE source_to_concept_map ADD CONSTRAINT xpk_source_to_concept_map PRIMA
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
@ -127,7 +122,7 @@ ALTER TABLE note_nlp ADD CONSTRAINT xpk_note_nlp PRIMARY KEY ( note_nlp_id ) ;
ALTER TABLE observation ADD CONSTRAINT xpk_observation PRIMARY KEY ( observation_id ) ;
ALTER TABLE survey ADD CONSTRAINT xpk_survey PRIMARY KEY ( survey_occurrence_id ) ;
ALTER TABLE survey_conduct ADD CONSTRAINT xpk_survey_conduct PRIMARY KEY ( survey_conduct_id ) ;
/************************
@ -139,7 +134,7 @@ Standardized health system data
ALTER TABLE location ADD CONSTRAINT xpk_location PRIMARY KEY ( location_id ) ;
ALTER TABLE location_history ADD CONSTRAINT xpk_location_history PRIMARY KEY ( location_history_id ) ; -- May need to remove this one
ALTER TABLE location_history ADD CONSTRAINT xpk_location_history PRIMARY KEY ( location_history_id ) ;
ALTER TABLE care_site ADD CONSTRAINT xpk_care_site PRIMARY KEY ( care_site_id ) ;
@ -165,10 +160,6 @@ 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 ) ;

26
Oracle/OMOP CDM oracle constraints.txt
View File

@ -28,7 +28,7 @@
oracle script to create foreign key, unique, and check constraints within the OMOP common data model, version 6.0
last revised: 30-Aug┌-2018
last revised: 30-Aug-2018
author: Patrick Ryan, Clair Blacketer
@ -86,7 +86,7 @@ ALTER TABLE relationship ADD CONSTRAINT fpk_relationship_reverse FOREIGN KEY (re
ALTER TABLE concept_synonym ADD CONSTRAINT fpk_concept_synonym_concept FOREIGN KEY (concept_id) REFERENCES concept (concept_id);
ALTER TABLE concept_synonym ADD CONSTRAINT fpk_concept_synonym_concept FOREIGN KEY (language_concept_id) REFERENCES concept (concept_id);
ALTER TABLE concept_synonym ADD CONSTRAINT fpk_synonym_language FOREIGN KEY (language_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);
@ -112,14 +112,6 @@ ALTER TABLE drug_strength ADD CONSTRAINT fpk_drug_strength_unit_2 FOREIGN KEY (n
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);
ALTER TABLE cohort_definition ADD CONSTRAINT fpk_subject_concept FOREIGN KEY (subject_concept_id) REFERENCES concept (concept_id);
ALTER TABLE attribute_definition ADD CONSTRAINT fpk_attribute_type_concept FOREIGN KEY (attribute_type_concept_id) REFERENCES concept (concept_id);
/**************************
Standardized meta-data
@ -196,7 +188,7 @@ ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_care_site FOREIGN KEY (car
ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_concept_s FOREIGN KEY (visit_source_concept_id) REFERENCES concept (concept_id);
ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_admitting_s FOREIGN KEY (admitting_source_concept_id) REFERENCES concept (concept_id);
ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_admitting_s FOREIGN KEY (admitted_from_concept_id) REFERENCES concept (concept_id);
ALTER TABLE visit_occurrence ADD CONSTRAINT fpk_visit_discharge FOREIGN KEY (discharge_to_concept_id) REFERENCES concept (concept_id);
@ -215,7 +207,7 @@ ALTER TABLE visit_detail ADD CONSTRAINT fpk_v_detail_care_site FOREIGN KEY (care
ALTER TABLE visit_detail ADD CONSTRAINT fpk_v_detail_discharge FOREIGN KEY (discharge_to_concept_id) REFERENCES concept (concept_id);
ALTER TABLE visit_detail ADD CONSTRAINT fpk_v_detail_admitting_s FOREIGN KEY (admitting_source_concept_id) REFERENCES concept (concept_id);
ALTER TABLE visit_detail ADD CONSTRAINT fpk_v_detail_admitting_s FOREIGN KEY (admitted_from_concept_id) REFERENCES concept (concept_id);
ALTER TABLE visit_detail ADD CONSTRAINT fpk_v_detail_concept_s FOREIGN KEY (visit_detail_source_concept_id) REFERENCES concept (concept_id);
@ -476,16 +468,6 @@ 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);

178
Oracle/OMOP CDM oracle ddl.txt
View File

@ -163,30 +163,6 @@ CREATE TABLE drug_strength (
;
--HINT DISTRIBUTE ON RANDOM
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
)
;
--HINT DISTRIBUTE ON RANDOM
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
@ -220,12 +196,12 @@ CREATE TABLE metadata
value_as_string CLOB NULL ,
value_as_concept_id INTEGER NULL ,
metadata_date DATE NULL ,
metadata_datetime DATETIME2 NULL
metadata_datetime TIMESTAMP NULL
)
;
INSERT INTO metadata (name, value_as_string) --Added cdm version record
VALUES ('CDM Version', '6.0')
INSERT INTO metadata (metadata_concept_id, metadata_type_concept_id, name, value_as_string, value_as_concept_id, metadata_date, metadata_datetime) --Added cdm version record
VALUES (0,0,'CDM Version', '6.0',0,NULL,NULL)
;
@ -244,12 +220,12 @@ CREATE TABLE person
year_of_birth INTEGER NOT NULL ,
month_of_birth INTEGER NULL,
day_of_birth INTEGER NULL,
birth_datetime DATETIME2 NULL,
birth_datetime TIMESTAMP 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,
location_id NUMBER(19) NULL,
provider_id NUMBER(19) NULL,
care_site_id NUMBER(19) NULL,
person_source_value VARCHAR(50) NULL,
gender_source_value VARCHAR(50) NULL,
gender_source_concept_id INTEGER NULL,
@ -281,7 +257,7 @@ CREATE TABLE specimen
specimen_concept_id INTEGER NOT NULL ,
specimen_type_concept_id INTEGER NOT NULL ,
specimen_date DATE NULL ,
specimen_datetime DATETIME2 NOT NULL ,
specimen_datetime TIMESTAMP NOT NULL ,
quantity FLOAT NULL ,
unit_concept_id INTEGER NULL ,
anatomic_site_concept_id INTEGER NULL ,
@ -295,20 +271,6 @@ CREATE TABLE specimen
;
--HINT DISTRIBUTE_ON_KEY(person_id)
CREATE TABLE death
(
person_id NUMBER(19) NOT NULL ,
death_date DATE NULL ,
death_datetime DATETIME2 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
)
;
--HINT DISTRIBUTE_ON_KEY(person_id)
CREATE TABLE visit_occurrence
(
@ -316,15 +278,15 @@ CREATE TABLE visit_occurrence
person_id NUMBER(19) NOT NULL ,
visit_concept_id INTEGER NOT NULL ,
visit_start_date DATE NULL ,
visit_start_datetime DATETIME2 NOT NULL ,
visit_start_datetime TIMESTAMP NOT NULL ,
visit_end_date DATE NULL ,
visit_end_datetime DATETIME2 NOT NULL ,
visit_end_datetime TIMESTAMP NOT NULL ,
visit_type_concept_id INTEGER NOT NULL ,
provider_id INTEGER NULL,
care_site_id INTEGER NULL,
provider_id NUMBER(19) NULL,
care_site_id NUMBER(19) NULL,
visit_source_value VARCHAR(50) NULL,
visit_source_concept_id INTEGER NULL ,
admitted_from_concept_id INTEGER NULL , /*Changed from admitting_source_* */
admitted_from_concept_id INTEGER NULL ,
admitted_from_source_value VARCHAR(50) NULL ,
discharge_to_source_value VARCHAR(50) NULL ,
discharge_to_concept_id INTEGER NULL ,
@ -340,12 +302,12 @@ CREATE TABLE visit_detail
person_id NUMBER(19) NOT NULL ,
visit_detail_concept_id INTEGER NOT NULL ,
visit_detail_start_date DATE NULL ,
visit_detail_start_datetime DATETIME2 NOT NULL ,
visit_detail_start_datetime TIMESTAMP NOT NULL ,
visit_detail_end_date DATE NULL ,
visit_detail_end_datetime DATETIME2 NOT NULL ,
visit_detail_end_datetime TIMESTAMP NOT NULL ,
visit_detail_type_concept_id INTEGER NOT NULL ,
provider_id INTEGER NULL ,
care_site_id INTEGER NULL ,
provider_id NUMBER(19) NULL ,
care_site_id NUMBER(19) NULL ,
discharge_to_concept_id INTEGER NULL ,
admitted_from_concept_id INTEGER NULL , /*Changed from admitting_source_* */
admitted_from_source_value VARCHAR(50) NULL ,
@ -366,16 +328,16 @@ CREATE TABLE procedure_occurrence
person_id NUMBER(19) NOT NULL ,
procedure_concept_id INTEGER NOT NULL ,
procedure_date DATE NULL ,
procedure_datetime DATETIME2 NOT NULL ,
procedure_datetime TIMESTAMP 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 ,
visit_detail_id INTEGER NULL ,
provider_id NUMBER(19) NULL ,
visit_occurrence_id NUMBER(19) NULL ,
visit_detail_id NUMBER(19) NULL ,
procedure_source_value VARCHAR(50) NULL ,
procedure_source_concept_id INTEGER NULL ,
modifier_source_value VARCHAR(50) NULL ,
modifier_source_value VARCHAR(50) NULL
)
;
@ -387,9 +349,9 @@ CREATE TABLE drug_exposure
person_id NUMBER(19) NOT NULL ,
drug_concept_id INTEGER NOT NULL ,
drug_exposure_start_date DATE NULL ,
drug_exposure_start_datetime DATETIME2 NOT NULL ,
drug_exposure_start_datetime TIMESTAMP NOT NULL ,
drug_exposure_end_date DATE NULL ,
drug_exposure_end_datetime DATETIME2 NOT NULL ,
drug_exposure_end_datetime TIMESTAMP NOT NULL ,
verbatim_end_date DATE NULL ,
drug_type_concept_id INTEGER NOT NULL ,
stop_reason VARCHAR(20) NULL ,
@ -399,9 +361,9 @@ CREATE TABLE drug_exposure
sig CLOB NULL ,
route_concept_id INTEGER NULL ,
lot_number VARCHAR(50) NULL ,
provider_id INTEGER NULL ,
visit_occurrence_id INTEGER NULL ,
visit_detail_id INTEGER NULL ,
provider_id NUMBER(19) NULL ,
visit_occurrence_id NUMBER(19) NULL ,
visit_detail_id NUMBER(19) NULL ,
drug_source_value VARCHAR(50) NULL ,
drug_source_concept_id INTEGER NULL ,
route_source_value VARCHAR(50) NULL ,
@ -417,15 +379,15 @@ CREATE TABLE device_exposure
person_id NUMBER(19) NOT NULL ,
device_concept_id INTEGER NOT NULL ,
device_exposure_start_date DATE NULL ,
device_exposure_start_datetime DATETIME2 NOT NULL ,
device_exposure_start_datetime TIMESTAMP NOT NULL ,
device_exposure_end_date DATE NULL ,
device_exposure_end_datetime DATETIME2 NULL ,
device_exposure_end_datetime TIMESTAMP 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 ,
visit_detail_id INTEGER NULL ,
provider_id NUMBER(19) NULL ,
visit_occurrence_id NUMBER(19) NULL ,
visit_detail_id NUMBER(19) NULL ,
device_source_value VARCHAR(100) NULL ,
device_source_concept_id INTEGER NULL
)
@ -439,15 +401,15 @@ CREATE TABLE condition_occurrence
person_id NUMBER(19) NOT NULL ,
condition_concept_id INTEGER NOT NULL ,
condition_start_date DATE NULL ,
condition_start_datetime DATETIME2 NOT NULL ,
condition_start_datetime TIMESTAMP NOT NULL ,
condition_end_date DATE NULL ,
condition_end_datetime DATETIME2 NULL ,
condition_end_datetime TIMESTAMP NULL ,
condition_type_concept_id INTEGER NOT NULL ,
condition_status_concept_id INTEGER NULL ,
stop_reason VARCHAR(20) NULL ,
provider_id INTEGER NULL ,
visit_occurrence_id INTEGER NULL ,
visit_detail_id INTEGER NULL ,
provider_id NUMBER(19) NULL ,
visit_occurrence_id NUMBER(19) NULL ,
visit_detail_id NUMBER(19) NULL ,
condition_source_value VARCHAR(50) NULL ,
condition_source_concept_id INTEGER NULL ,
condition_status_source_value VARCHAR(50) NULL
@ -462,7 +424,7 @@ CREATE TABLE measurement
person_id NUMBER(19) NOT NULL ,
measurement_concept_id INTEGER NOT NULL ,
measurement_date DATE NULL ,
measurement_datetime DATETIME2 NOT NULL ,
measurement_datetime TIMESTAMP NOT NULL ,
measurement_time VARCHAR(10) NULL,
measurement_type_concept_id INTEGER NOT NULL ,
operator_concept_id INTEGER NULL ,
@ -471,9 +433,9 @@ CREATE TABLE measurement
unit_concept_id INTEGER NULL ,
range_low FLOAT NULL ,
range_high FLOAT NULL ,
provider_id INTEGER NULL ,
visit_occurrence_id INTEGER NULL ,
visit_detail_id INTEGER NULL ,
provider_id NUMBER(19) NULL ,
visit_occurrence_id NUMBER(19) NULL ,
visit_detail_id NUMBER(19) NULL ,
measurement_source_value VARCHAR(50) NULL ,
measurement_source_concept_id INTEGER NULL ,
unit_source_value VARCHAR(50) NULL ,
@ -487,20 +449,19 @@ CREATE TABLE note
(
note_id NUMBER(19) NOT NULL ,
person_id NUMBER(19) NOT NULL ,
note_event_id NUMBER(19) NULL , --This and the field below added
note_domain_id VARCHAR(20) NULL , --This field may be removed in favor of the one below
--note_event_table_concept_id INTEGER NULL , --This may be added based on 9/4 meeting
note_event_id NUMBER(19) NULL ,
note_event_field_concept_id INTEGER NULL ,
note_date DATE NULL ,
note_datetime DATETIME2 NOT NULL ,
note_datetime TIMESTAMP NOT NULL ,
note_type_concept_id INTEGER NOT NULL ,
note_class_concept_id INTEGER NOT NULL ,
note_title VARCHAR(250) NULL ,
note_text CLOB NULL ,
encoding_concept_id INTEGER NOT NULL ,
language_concept_id INTEGER NOT NULL ,
provider_id INTEGER NULL ,
visit_occurrence_id INTEGER NULL ,
visit_detail_id INTEGER NULL ,
provider_id NUMBER(19) NULL ,
visit_occurrence_id NUMBER(19) NULL ,
visit_detail_id NUMBER(19) NULL ,
note_source_value VARCHAR(50) NULL
)
;
@ -518,7 +479,7 @@ CREATE TABLE note_nlp
note_nlp_concept_id INTEGER NULL ,
nlp_system VARCHAR(250) NULL ,
nlp_date DATE NOT NULL ,
nlp_datetime DATETIME2 NULL ,
nlp_datetime TIMESTAMP NULL ,
term_exists VARCHAR(1) NULL ,
term_temporal VARCHAR(50) NULL ,
term_modifiers VARCHAR(2000) NULL ,
@ -534,14 +495,14 @@ CREATE TABLE observation
person_id NUMBER(19) NOT NULL ,
observation_concept_id INTEGER NOT NULL ,
observation_date DATE NULL ,
observation_datetime DATETIME2 NOT NULL ,
observation_datetime TIMESTAMP NOT 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 ,
provider_id NUMBER(19) NULL ,
visit_occurrence_id NUMBER(19) NULL ,
visit_detail_id NUMBER(19) NULL ,
observation_source_value VARCHAR(50) NULL ,
@ -549,9 +510,8 @@ CREATE TABLE observation
unit_source_value VARCHAR(50) NULL ,
qualifier_source_value VARCHAR(50) NULL ,
observation_event_id NUMBER(19) NULL , /* This will link back to the event table (SURVEY) on SURVEY_OCCURRENCE_ID, changed name to comply with COST and NOTE*/
observation_event_domain_id VARCHAR(20) NULL ,
--obs_event_table_concept_id INTEGER NULL , /* Changed name to comply with COST and NOTE. Had to use 'obs' for oracle restriction, may be added on 9/4*/
value_as_datetime DATETIME2 NULL
obs_event_field_concept_id INTEGER NULL , /* Changed name to comply with COST and NOTE. Had to use 'obs' for oracle restriction, may be added on 9/4*/
value_as_datetime TIMESTAMP NULL
)
;
@ -563,9 +523,9 @@ CREATE TABLE survey_conduct --Table added
person_id NUMBER(19) NOT NULL ,
survey_concept_id INTEGER NOT NULL ,
survey_start_date DATE NULL ,
survey_start_datetime DATETIME2 NULL ,
survey_start_datetime TIMESTAMP NULL ,
survey_end_date DATE NULL ,
survey_end_datetime DATETIME2 NOT NULL ,
survey_end_datetime TIMESTAMP NOT NULL ,
provider_id NUMBER(19) NULL ,
assisted_concept_id INTEGER NULL ,
respondent_type_concept_id INTEGER NULL ,
@ -583,7 +543,7 @@ CREATE TABLE survey_conduct --Table added
survey_version_number VARCHAR(20) NULL ,
visit_occurrence_id NUMBER(19) NULL ,
visit_detail_id NUMBER(19) NULL ,
response_to_visit_occurrence_id NUMBER(19) NULL
response_visit_occurrence_id NUMBER(19) NULL
)
;
@ -714,8 +674,7 @@ CREATE TABLE cost
cost_id NUMBER(19) NOT NULL ,
person_id NUMBER(19) NOT NULL,
cost_event_id NUMBER(19) NOT NULL ,
cost_domain_id VARCHAR(20) NOT NULL ,
--cost_event_table_concept_id INTEGER NOT NULL , /*This is still in discussion and most likely will replace cost_domain_id at 9/4 meeting*/
cost_event_field_concept_id INTEGER NOT NULL ,
cost_concept_id INTEGER NOT NULL ,
cost_type_concept_id INTEGER NOT NULL ,
currency_concept_id INTEGER NULL ,
@ -741,31 +700,6 @@ Standardized derived elements
************************/
--HINT DISTRIBUTE_ON_KEY(subject_id)
CREATE TABLE cohort
(
cohort_definition_id NUMBER(19) NOT NULL ,
subject_id NUMBER(19) NOT NULL ,
cohort_start_date DATE NOT NULL ,
cohort_end_date DATE NOT NULL
)
;
--HINT DISTRIBUTE_ON_KEY(subject_id)
CREATE TABLE cohort_attribute
(
cohort_definition_id NUMBER(19) NOT NULL ,
subject_id NUMBER(19) NOT NULL ,
cohort_start_date DATE NOT NULL ,
cohort_end_date DATE NOT NULL ,
attribute_definition_id NUMBER(19) NOT NULL ,
value_as_number FLOAT NULL ,
value_as_concept_id INTEGER NULL
)
;
--HINT DISTRIBUTE_ON_KEY(person_id)
CREATE TABLE drug_era
(

22
Oracle/OMOP CDM oracle pk indexes.txt
View File

@ -77,10 +77,6 @@ ALTER TABLE source_to_concept_map ADD CONSTRAINT xpk_source_to_concept_map PRIMA
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);
/**************************
@ -127,7 +123,7 @@ ALTER TABLE note_nlp ADD CONSTRAINT xpk_note_nlp PRIMARY KEY ( note_nlp_id ) ;
ALTER TABLE observation ADD CONSTRAINT xpk_observation PRIMARY KEY ( observation_id ) ;
ALTER TABLE survey ADD CONSTRAINT xpk_survey PRIMARY KEY ( survey_occurrence_id ) ;
ALTER TABLE survey_conduct ADD CONSTRAINT xpk_survey_conduct PRIMARY KEY ( survey_conduct_id ) ;
/************************
@ -139,7 +135,7 @@ Standardized health system data
ALTER TABLE location ADD CONSTRAINT xpk_location PRIMARY KEY ( location_id ) ;
ALTER TABLE location_history ADD CONSTRAINT xpk_location_history PRIMARY KEY ( location_history_id ) ; --Assuming this should be added
ALTER TABLE location_history ADD CONSTRAINT xpk_location_history PRIMARY KEY ( location_history_id ) ;
ALTER TABLE care_site ADD CONSTRAINT xpk_care_site PRIMARY KEY ( care_site_id ) ;
@ -165,10 +161,6 @@ 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 ) ;
@ -260,10 +252,6 @@ CREATE INDEX idx_source_to_concept_map_code ON source_to_concept_map (source_cod
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);
/**************************
@ -370,12 +358,6 @@ 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);

2
Oracle/README.md
View File

@ -7,7 +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 oracle ddl.txt` to create the tables and fields.
2. Execute the script `OMOP CDM oracle ddl.txt` and `OMOP CDM Results oracle ddl.txt` to create the tables and fields.
3. Load your data into the schema.