mz-health/OMOP
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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
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@ -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_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_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_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_DEVICE_EXPOSURE.csv' OVERWRITE INTO TABLE device_exposure;
LOAD DATA INPATH '${VAR:OMOP_SYNPUF_PATH}/CDM_LOCATION.csv' OVERWRITE INTO TABLE `location`; LOAD DATA INPATH '${VAR:OMOP_SYNPUF_PATH}/CDM_LOCATION.csv' OVERWRITE INTO TABLE `location`;

135
Impala/OMOP CDM impala ddl.txt
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@ -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 Standardized meta-data
@ -210,8 +188,8 @@ CREATE TABLE `metadata`
) )
; ;
INSERT INTO metadata (name, value_as_string) --Added cdm version record 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 ('CDM Version', '6.0') VALUES (0,0,'CDM Version', '6.0',0,NULL,NULL)
; ;
@ -233,9 +211,9 @@ CREATE TABLE person
birth_datetime TIMESTAMP , birth_datetime TIMESTAMP ,
race_concept_id INTEGER , race_concept_id INTEGER ,
ethnicity_concept_id INTEGER , ethnicity_concept_id INTEGER ,
location_id INTEGER , location_id BIGINT ,
provider_id INTEGER , provider_id BIGINT ,
care_site_id INTEGER , care_site_id BIGINT ,
person_source_value VARCHAR(50), person_source_value VARCHAR(50),
gender_source_value VARCHAR(50), gender_source_value VARCHAR(50),
gender_source_concept_id INTEGER , 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) --HINT DISTRIBUTE_ON_KEY(person_id)
CREATE TABLE visit_occurrence CREATE TABLE visit_occurrence
( (
@ -306,8 +270,8 @@ CREATE TABLE visit_occurrence
visit_end_date TIMESTAMP , visit_end_date TIMESTAMP ,
visit_end_datetime TIMESTAMP , visit_end_datetime TIMESTAMP ,
visit_type_concept_id INTEGER , visit_type_concept_id INTEGER ,
provider_id INTEGER , provider_id BIGINT ,
care_site_id INTEGER , care_site_id BIGINT ,
visit_source_value VARCHAR(50), visit_source_value VARCHAR(50),
visit_source_concept_id INTEGER , visit_source_concept_id INTEGER ,
admitted_from_concept_id INTEGER , /*Changed from admitting_source_* */ 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) --HINT DISTRIBUTE_ON_KEY(person_id)
CREATE TABLE visit_detail CREATE TABLE visit_detail
( (
@ -330,8 +294,8 @@ CREATE TABLE visit_detail
visit_detail_end_date TIMESTAMP , visit_detail_end_date TIMESTAMP ,
visit_detail_end_datetime TIMESTAMP , visit_detail_end_datetime TIMESTAMP ,
visit_detail_type_concept_id INTEGER , visit_detail_type_concept_id INTEGER ,
provider_id INTEGER , provider_id BIGINT ,
care_site_id INTEGER , care_site_id BIGINT ,
discharge_to_concept_id INTEGER , discharge_to_concept_id INTEGER ,
admitted_from_concept_id INTEGER , /*Changed from admitting_source_* */ admitted_from_concept_id INTEGER , /*Changed from admitting_source_* */
admitted_from_source_value VARCHAR(50) , admitted_from_source_value VARCHAR(50) ,
@ -356,12 +320,12 @@ CREATE TABLE procedure_occurrence
procedure_type_concept_id INTEGER , procedure_type_concept_id INTEGER ,
modifier_concept_id INTEGER , modifier_concept_id INTEGER ,
quantity INTEGER , quantity INTEGER ,
provider_id INTEGER , provider_id BIGINT ,
visit_occurrence_id INTEGER , visit_occurrence_id BIGINT ,
visit_detail_id INTEGER , visit_detail_id BIGINT ,
procedure_source_value VARCHAR(50) , procedure_source_value VARCHAR(50) ,
procedure_source_concept_id INTEGER , 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 , sig STRING ,
route_concept_id INTEGER , route_concept_id INTEGER ,
lot_number VARCHAR(50) , lot_number VARCHAR(50) ,
provider_id INTEGER , provider_id BIGINT ,
visit_occurrence_id INTEGER , visit_occurrence_id BIGINT ,
visit_detail_id INTEGER , visit_detail_id BIGINT ,
drug_source_value VARCHAR(50) , drug_source_value VARCHAR(50) ,
drug_source_concept_id INTEGER , drug_source_concept_id INTEGER ,
route_source_value VARCHAR(50) , route_source_value VARCHAR(50) ,
@ -409,9 +373,9 @@ CREATE TABLE device_exposure
device_type_concept_id INTEGER , device_type_concept_id INTEGER ,
unique_device_id VARCHAR(50) , unique_device_id VARCHAR(50) ,
quantity INTEGER , quantity INTEGER ,
provider_id INTEGER , provider_id BIGINT ,
visit_occurrence_id INTEGER , visit_occurrence_id BIGINT ,
visit_detail_id INTEGER , visit_detail_id BIGINT ,
device_source_value VARCHAR(100) , device_source_value VARCHAR(100) ,
device_source_concept_id INTEGER device_source_concept_id INTEGER
) )
@ -431,9 +395,9 @@ CREATE TABLE condition_occurrence
condition_type_concept_id INTEGER , condition_type_concept_id INTEGER ,
condition_status_concept_id INTEGER , condition_status_concept_id INTEGER ,
stop_reason VARCHAR(20) , stop_reason VARCHAR(20) ,
provider_id INTEGER , provider_id BIGINT ,
visit_occurrence_id INTEGER , visit_occurrence_id BIGINT ,
visit_detail_id INTEGER , visit_detail_id BIGINT ,
condition_source_value VARCHAR(50) , condition_source_value VARCHAR(50) ,
condition_source_concept_id INTEGER , condition_source_concept_id INTEGER ,
condition_status_source_value VARCHAR(50) condition_status_source_value VARCHAR(50)
@ -457,9 +421,9 @@ CREATE TABLE measurement
unit_concept_id INTEGER , unit_concept_id INTEGER ,
range_low FLOAT , range_low FLOAT ,
range_high FLOAT , range_high FLOAT ,
provider_id INTEGER , provider_id BIGINT ,
visit_occurrence_id INTEGER , visit_occurrence_id BIGINT ,
visit_detail_id INTEGER , visit_detail_id BIGINT ,
measurement_source_value VARCHAR(50) , measurement_source_value VARCHAR(50) ,
measurement_source_concept_id INTEGER , measurement_source_concept_id INTEGER ,
unit_source_value VARCHAR(50) , unit_source_value VARCHAR(50) ,
@ -473,9 +437,8 @@ CREATE TABLE note
( (
note_id BIGINT , note_id BIGINT ,
person_id BIGINT , person_id BIGINT ,
note_event_id BIGINT , --This and the field below added note_event_id BIGINT ,
note_domain_id VARCHAR(20) , --This field may be removed in favor of the one below note_event_field_concept_id INTEGER ,
--note_event_table_concept_id INTEGER , --This may be added based on 9/4 meeting
note_date TIMESTAMP , note_date TIMESTAMP ,
note_datetime TIMESTAMP , note_datetime TIMESTAMP ,
note_type_concept_id INTEGER , note_type_concept_id INTEGER ,
@ -484,15 +447,14 @@ CREATE TABLE note
note_text STRING , note_text STRING ,
encoding_concept_id INTEGER , encoding_concept_id INTEGER ,
language_concept_id INTEGER , language_concept_id INTEGER ,
provider_id INTEGER , provider_id BIGINT ,
visit_occurrence_id INTEGER , visit_occurrence_id BIGINT ,
visit_detail_id INTEGER , visit_detail_id BIGINT ,
note_source_value VARCHAR(50) note_source_value VARCHAR(50)
) )
; ;
CREATE TABLE note_nlp CREATE TABLE note_nlp
( (
note_nlp_id BIGINT , note_nlp_id BIGINT ,
@ -527,7 +489,7 @@ CREATE TABLE observation
value_as_concept_id INTEGER , value_as_concept_id INTEGER ,
qualifier_concept_id INTEGER , qualifier_concept_id INTEGER ,
unit_concept_id INTEGER , unit_concept_id INTEGER ,
provider_id INTEGER , provider_id BIGINT ,
visit_occurrence_id BIGINT , visit_occurrence_id BIGINT ,
visit_detail_id BIGINT , visit_detail_id BIGINT ,
observation_source_value VARCHAR(50) , observation_source_value VARCHAR(50) ,
@ -535,8 +497,7 @@ CREATE TABLE observation
unit_source_value VARCHAR(50) , unit_source_value VARCHAR(50) ,
qualifier_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_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_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*/
--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*/
value_as_datetime TIMESTAMP value_as_datetime TIMESTAMP
) )
; ;
@ -593,7 +554,7 @@ Standardized health system data
************************/ ************************/
CREATE TABLE location CREATE TABLE `location`
( (
location_id BIGINT , location_id BIGINT ,
address_1 VARCHAR(50) , address_1 VARCHAR(50) ,
@ -693,8 +654,7 @@ CREATE TABLE cost
cost_id BIGINT , cost_id BIGINT ,
person_id BIGINT, person_id BIGINT,
cost_event_id BIGINT , cost_event_id BIGINT ,
cost_domain_id VARCHAR(20) , cost_event_field_concept_id INTEGER , /*This is still in discussion and most likely will replace cost_domain_id at 9/4 meeting*/
--cost_event_table_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_concept_id INTEGER ,
cost_type_concept_id INTEGER , cost_type_concept_id INTEGER ,
currency_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) --HINT DISTRIBUTE_ON_KEY(person_id)
CREATE TABLE drug_era 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' 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 ```bash
impala-shell -d omop_cdm -f OMOP_CDM_impala_ddl.sql 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. 3. Load your data into the schema.
@ -42,6 +43,7 @@ hadoop fs -put synpuf synpuf
hadoop fs -chmod +w synpuf hadoop fs -chmod +w synpuf
impala-shell -d omop_cdm -f DataImport/OMOP_CDM_synpuf_load_Impala.sql --var=OMOP_SYNPUF_PATH=/user/$USER/synpuf impala-shell -d omop_cdm -f DataImport/OMOP_CDM_synpuf_load_Impala.sql --var=OMOP_SYNPUF_PATH=/user/$USER/synpuf
``` ```
* Note that these tables are in CDM v5.2.2 format
4. Convert to Parquet format. 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 Standardized meta-data
@ -238,8 +212,8 @@ CREATE TABLE metadata
DISTRIBUTE ON RANDOM DISTRIBUTE ON RANDOM
; ;
INSERT INTO metadata (name, value_as_string) --Added cdm version record 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 ('CDM Version', '6.0') VALUES (0,0,'CDM Version', '6.0',0,NULL,NULL)
; ;
@ -261,9 +235,9 @@ CREATE TABLE person
birth_datetime DATETIME NULL, birth_datetime DATETIME NULL,
race_concept_id INTEGER NOT NULL, race_concept_id INTEGER NOT NULL,
ethnicity_concept_id INTEGER NOT NULL, ethnicity_concept_id INTEGER NOT NULL,
location_id INTEGER NULL, location_id BIGINT NULL,
provider_id INTEGER NULL, provider_id BIGINT NULL,
care_site_id INTEGER NULL, care_site_id BIGINT NULL,
person_source_value VARCHAR(50) NULL, person_source_value VARCHAR(50) NULL,
gender_source_value VARCHAR(50) NULL, gender_source_value VARCHAR(50) NULL,
gender_source_concept_id INTEGER NULL, gender_source_concept_id INTEGER NULL,
@ -273,7 +247,7 @@ CREATE TABLE person
ethnicity_source_concept_id INTEGER NULL ethnicity_source_concept_id INTEGER NULL
) )
DISTRUBTE ON (person_id); DISTRIBUTE ON (person_id);
--HINT DISTRIBUTE_ON_KEY(person_id) --HINT DISTRIBUTE_ON_KEY(person_id)
@ -286,7 +260,7 @@ CREATE TABLE observation_period
period_type_concept_id INTEGER NOT NULL period_type_concept_id INTEGER NOT NULL
) )
DISTRUBTE ON (person_id); DISTRIBUTE ON (person_id);
--HINT DISTRIBUTE_ON_KEY(person_id) --HINT DISTRIBUTE_ON_KEY(person_id)
@ -309,22 +283,7 @@ CREATE TABLE specimen
disease_status_source_value VARCHAR(50) NULL disease_status_source_value VARCHAR(50) NULL
) )
DISTRUBTE ON (person_id); DISTRIBUTE 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);
--HINT DISTRIBUTE_ON_KEY(person_id) --HINT DISTRIBUTE_ON_KEY(person_id)
@ -338,8 +297,8 @@ CREATE TABLE visit_occurrence
visit_end_date DATE NULL , visit_end_date DATE NULL ,
visit_end_datetime DATETIME NOT NULL , visit_end_datetime DATETIME NOT NULL ,
visit_type_concept_id INTEGER NOT NULL , visit_type_concept_id INTEGER NOT NULL ,
provider_id INTEGER NULL, provider_id BIGINT NULL,
care_site_id INTEGER NULL, care_site_id BIGINT NULL,
visit_source_value VARCHAR(50) NULL, visit_source_value VARCHAR(50) NULL,
visit_source_concept_id INTEGER NULL , visit_source_concept_id INTEGER NULL ,
admitted_from_concept_id INTEGER NULL , admitted_from_concept_id INTEGER NULL ,
@ -349,7 +308,7 @@ CREATE TABLE visit_occurrence
preceding_visit_occurrence_id INTEGER NULL preceding_visit_occurrence_id INTEGER NULL
) )
DISTRUBTE ON (person_id); DISTRIBUTE ON (person_id);
--HINT DISTRIBUTE_ON_KEY(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_date DATE NULL ,
visit_detail_end_datetime DATETIME NOT NULL , visit_detail_end_datetime DATETIME NOT NULL ,
visit_detail_type_concept_id INTEGER NOT NULL , visit_detail_type_concept_id INTEGER NOT NULL ,
provider_id INTEGER NULL , provider_id BIGINT NULL ,
care_site_id INTEGER NULL , care_site_id BIGINT NULL ,
discharge_to_concept_id INTEGER NULL , discharge_to_concept_id INTEGER NULL ,
admitted_from_concept_id INTEGER NULL , admitted_from_concept_id INTEGER NULL ,
admitted_from_source_value VARCHAR(50) NULL , admitted_from_source_value VARCHAR(50) NULL ,
@ -376,7 +335,7 @@ CREATE TABLE visit_detail
visit_occurrence_id BIGINT NOT NULL visit_occurrence_id BIGINT NOT NULL
) )
DISTRUBTE ON (person_id); DISTRIBUTE ON (person_id);
--HINT DISTRIBUTE_ON_KEY(person_id) --HINT DISTRIBUTE_ON_KEY(person_id)
@ -390,15 +349,15 @@ CREATE TABLE procedure_occurrence
procedure_type_concept_id INTEGER NOT NULL , procedure_type_concept_id INTEGER NOT NULL ,
modifier_concept_id INTEGER NULL , modifier_concept_id INTEGER NULL ,
quantity INTEGER NULL , quantity INTEGER NULL ,
provider_id INTEGER NULL , provider_id BIGINT NULL ,
visit_occurrence_id INTEGER NULL , visit_occurrence_id BIGINT NULL ,
visit_detail_id INTEGER NULL , visit_detail_id BIGINT NULL ,
procedure_source_value VARCHAR(50) NULL , procedure_source_value VARCHAR(50) NULL ,
procedure_source_concept_id INTEGER 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) --HINT DISTRIBUTE_ON_KEY(person_id)
@ -420,16 +379,16 @@ CREATE TABLE drug_exposure
sig VARCHAR(1000) NULL , sig VARCHAR(1000) NULL ,
route_concept_id INTEGER NULL , route_concept_id INTEGER NULL ,
lot_number VARCHAR(50) NULL , lot_number VARCHAR(50) NULL ,
provider_id INTEGER NULL , provider_id BIGINT NULL ,
visit_occurrence_id INTEGER NULL , visit_occurrence_id BIGINT NULL ,
visit_detail_id INTEGER NULL , visit_detail_id BIGINT NULL ,
drug_source_value VARCHAR(50) NULL , drug_source_value VARCHAR(50) NULL ,
drug_source_concept_id INTEGER NULL , drug_source_concept_id INTEGER NULL ,
route_source_value VARCHAR(50) NULL , route_source_value VARCHAR(50) NULL ,
dose_unit_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) --HINT DISTRIBUTE_ON_KEY(person_id)
@ -445,14 +404,14 @@ CREATE TABLE device_exposure
device_type_concept_id INTEGER NOT NULL , device_type_concept_id INTEGER NOT NULL ,
unique_device_id VARCHAR(50) NULL , unique_device_id VARCHAR(50) NULL ,
quantity INTEGER NULL , quantity INTEGER NULL ,
provider_id INTEGER NULL , provider_id BIGINT NULL ,
visit_occurrence_id INTEGER NULL , visit_occurrence_id BIGINT NULL ,
visit_detail_id INTEGER NULL , visit_detail_id BIGINT NULL ,
device_source_value VARCHAR(100) NULL , device_source_value VARCHAR(100) NULL ,
device_source_concept_id INTEGER NULL device_source_concept_id INTEGER NULL
) )
DISTRUBTE ON (person_id); DISTRIBUTE ON (person_id);
--HINT DISTRIBUTE_ON_KEY(person_id) --HINT DISTRIBUTE_ON_KEY(person_id)
@ -468,15 +427,15 @@ CREATE TABLE condition_occurrence
condition_type_concept_id INTEGER NOT NULL , condition_type_concept_id INTEGER NOT NULL ,
condition_status_concept_id INTEGER NULL , condition_status_concept_id INTEGER NULL ,
stop_reason VARCHAR(20) NULL , stop_reason VARCHAR(20) NULL ,
provider_id INTEGER NULL , provider_id BIGINT NULL ,
visit_occurrence_id INTEGER NULL , visit_occurrence_id BIGINT NULL ,
visit_detail_id INTEGER NULL , visit_detail_id BIGINT NULL ,
condition_source_value VARCHAR(50) NULL , condition_source_value VARCHAR(50) NULL ,
condition_source_concept_id INTEGER NULL , condition_source_concept_id INTEGER NULL ,
condition_status_source_value VARCHAR(50) NULL condition_status_source_value VARCHAR(50) NULL
) )
DISTRUBTE ON (person_id); DISTRIBUTE ON (person_id);
--HINT DISTRIBUTE_ON_KEY(person_id) --HINT DISTRIBUTE_ON_KEY(person_id)
@ -495,15 +454,15 @@ CREATE TABLE measurement
unit_concept_id INTEGER NULL , unit_concept_id INTEGER NULL ,
range_low REAL NULL , range_low REAL NULL ,
range_high REAL NULL , range_high REAL NULL ,
provider_id INTEGER NULL , provider_id BIGINT NULL ,
visit_occurrence_id INTEGER NULL , visit_occurrence_id BIGINT NULL ,
visit_detail_id INTEGER NULL , visit_detail_id BIGINT NULL ,
measurement_source_value VARCHAR(50) NULL , measurement_source_value VARCHAR(50) NULL ,
measurement_source_concept_id INTEGER NULL , measurement_source_concept_id INTEGER NULL ,
unit_source_value VARCHAR(50) NULL , unit_source_value VARCHAR(50) NULL ,
value_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 , note_id BIGINT NOT NULL ,
person_id BIGINT NOT NULL , person_id BIGINT NOT NULL ,
note_event_id BIGINT NULL , --This and the field below added note_event_id BIGINT NULL ,
note_domain_id VARCHAR(20) NULL , --This field may be removed in favor of the one below note_event_field_concept_id INTEGER NULL ,
--note_event_table_concept_id INTEGER NULL , --This may be added based on 9/4 meeting
note_date DATE NULL , note_date DATE NULL ,
note_datetime DATETIME NOT NULL , note_datetime DATETIME NOT NULL ,
note_type_concept_id INTEGER NOT NULL , note_type_concept_id INTEGER NOT NULL ,
@ -523,12 +481,12 @@ CREATE TABLE note
note_text VARCHAR(1000) NULL , note_text VARCHAR(1000) NULL ,
encoding_concept_id INTEGER NOT NULL , encoding_concept_id INTEGER NOT NULL ,
language_concept_id INTEGER NOT NULL , language_concept_id INTEGER NOT NULL ,
provider_id INTEGER NULL , provider_id BIGINT NULL ,
visit_occurrence_id INTEGER NULL , visit_occurrence_id BIGINT NULL ,
visit_detail_id INTEGER NULL , visit_detail_id BIGINT NULL ,
note_source_value VARCHAR(50) 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 , value_as_concept_id INTEGER NULL ,
qualifier_concept_id INTEGER NULL , qualifier_concept_id INTEGER NULL ,
unit_concept_id INTEGER NULL , unit_concept_id INTEGER NULL ,
provider_id INTEGER NULL , provider_id BIGINT NULL ,
visit_occurrence_id BIGINT NULL , visit_occurrence_id BIGINT NULL ,
visit_detail_id BIGINT NULL , visit_detail_id BIGINT NULL ,
observation_source_value VARCHAR(50) NULL , observation_source_value VARCHAR(50) NULL ,
observation_source_concept_id INTEGER NULL , observation_source_concept_id INTEGER NULL ,
unit_source_value VARCHAR(50) NULL , unit_source_value VARCHAR(50) NULL ,
qualifier_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_id BIGINT NULL ,
observation_event_domain_id VARCHAR(20) NULL , obs_event_field_concept_id INTEGER 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*/
value_as_datetime DATETIME 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 Standardized health system data
@ -739,7 +695,7 @@ CREATE TABLE payer_plan_period
stop_reason_source_value VARCHAR(50) NULL , stop_reason_source_value VARCHAR(50) NULL ,
stop_reason_source_concept_id INTEGER 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 , cost_id BIGINT NOT NULL ,
person_id BIGINT NOT NULL, person_id BIGINT NOT NULL,
cost_event_id BIGINT NOT NULL , cost_event_id BIGINT NOT NULL ,
cost_domain_id VARCHAR(20) NOT NULL , cost_event_field_concept_id INTEGER 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_concept_id INTEGER NOT NULL , cost_concept_id INTEGER NOT NULL ,
cost_type_concept_id INTEGER NOT NULL , cost_type_concept_id INTEGER NOT NULL ,
currency_concept_id INTEGER 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) --HINT DISTRIBUTE_ON_KEY(person_id)
CREATE TABLE drug_era CREATE TABLE drug_era
( (
@ -815,7 +743,7 @@ CREATE TABLE drug_era
drug_exposure_count INTEGER NULL , drug_exposure_count INTEGER NULL ,
gap_days 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_start_date DATE NOT NULL ,
dose_era_end_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_era_end_date DATE NOT NULL ,
condition_occurrence_count INTEGER 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 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 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 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 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 ) ; 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 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 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 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 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 (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); 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 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 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_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); 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_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); 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_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 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 Standardized meta-data
@ -220,12 +196,12 @@ CREATE TABLE metadata
value_as_string CLOB NULL , value_as_string CLOB NULL ,
value_as_concept_id INTEGER NULL , value_as_concept_id INTEGER NULL ,
metadata_date DATE NULL , metadata_date DATE NULL ,
metadata_datetime DATETIME2 NULL metadata_datetime TIMESTAMP NULL
) )
; ;
INSERT INTO metadata (name, value_as_string) --Added cdm version record 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 ('CDM Version', '6.0') VALUES (0,0,'CDM Version', '6.0',0,NULL,NULL)
; ;
@ -244,12 +220,12 @@ CREATE TABLE person
year_of_birth INTEGER NOT NULL , year_of_birth INTEGER NOT NULL ,
month_of_birth INTEGER NULL, month_of_birth INTEGER NULL,
day_of_birth INTEGER NULL, day_of_birth INTEGER NULL,
birth_datetime DATETIME2 NULL, birth_datetime TIMESTAMP NULL,
race_concept_id INTEGER NOT NULL, race_concept_id INTEGER NOT NULL,
ethnicity_concept_id INTEGER NOT NULL, ethnicity_concept_id INTEGER NOT NULL,
location_id INTEGER NULL, location_id NUMBER(19) NULL,
provider_id INTEGER NULL, provider_id NUMBER(19) NULL,
care_site_id INTEGER NULL, care_site_id NUMBER(19) NULL,
person_source_value VARCHAR(50) NULL, person_source_value VARCHAR(50) NULL,
gender_source_value VARCHAR(50) NULL, gender_source_value VARCHAR(50) NULL,
gender_source_concept_id INTEGER NULL, gender_source_concept_id INTEGER NULL,
@ -281,7 +257,7 @@ CREATE TABLE specimen
specimen_concept_id INTEGER NOT NULL , specimen_concept_id INTEGER NOT NULL ,
specimen_type_concept_id INTEGER NOT NULL , specimen_type_concept_id INTEGER NOT NULL ,
specimen_date DATE NULL , specimen_date DATE NULL ,
specimen_datetime DATETIME2 NOT NULL , specimen_datetime TIMESTAMP NOT NULL ,
quantity FLOAT NULL , quantity FLOAT NULL ,
unit_concept_id INTEGER NULL , unit_concept_id INTEGER NULL ,
anatomic_site_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) --HINT DISTRIBUTE_ON_KEY(person_id)
CREATE TABLE visit_occurrence CREATE TABLE visit_occurrence
( (
@ -316,15 +278,15 @@ CREATE TABLE visit_occurrence
person_id NUMBER(19) NOT NULL , person_id NUMBER(19) NOT NULL ,
visit_concept_id INTEGER NOT NULL , visit_concept_id INTEGER NOT NULL ,
visit_start_date DATE 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_date DATE NULL ,
visit_end_datetime DATETIME2 NOT NULL , visit_end_datetime TIMESTAMP NOT NULL ,
visit_type_concept_id INTEGER NOT NULL , visit_type_concept_id INTEGER NOT NULL ,
provider_id INTEGER NULL, provider_id NUMBER(19) NULL,
care_site_id INTEGER NULL, care_site_id NUMBER(19) NULL,
visit_source_value VARCHAR(50) NULL, visit_source_value VARCHAR(50) NULL,
visit_source_concept_id INTEGER 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 , admitted_from_source_value VARCHAR(50) NULL ,
discharge_to_source_value VARCHAR(50) NULL , discharge_to_source_value VARCHAR(50) NULL ,
discharge_to_concept_id INTEGER NULL , discharge_to_concept_id INTEGER NULL ,
@ -340,12 +302,12 @@ CREATE TABLE visit_detail
person_id NUMBER(19) NOT NULL , person_id NUMBER(19) NOT NULL ,
visit_detail_concept_id INTEGER NOT NULL , visit_detail_concept_id INTEGER NOT NULL ,
visit_detail_start_date DATE 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_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 , visit_detail_type_concept_id INTEGER NOT NULL ,
provider_id INTEGER NULL , provider_id NUMBER(19) NULL ,
care_site_id INTEGER NULL , care_site_id NUMBER(19) NULL ,
discharge_to_concept_id INTEGER NULL , discharge_to_concept_id INTEGER NULL ,
admitted_from_concept_id INTEGER NULL , /*Changed from admitting_source_* */ admitted_from_concept_id INTEGER NULL , /*Changed from admitting_source_* */
admitted_from_source_value VARCHAR(50) NULL , admitted_from_source_value VARCHAR(50) NULL ,
@ -366,16 +328,16 @@ CREATE TABLE procedure_occurrence
person_id NUMBER(19) NOT NULL , person_id NUMBER(19) NOT NULL ,
procedure_concept_id INTEGER NOT NULL , procedure_concept_id INTEGER NOT NULL ,
procedure_date DATE NULL , procedure_date DATE NULL ,
procedure_datetime DATETIME2 NOT NULL , procedure_datetime TIMESTAMP NOT NULL ,
procedure_type_concept_id INTEGER NOT NULL , procedure_type_concept_id INTEGER NOT NULL ,
modifier_concept_id INTEGER NULL , modifier_concept_id INTEGER NULL ,
quantity INTEGER NULL , quantity INTEGER NULL ,
provider_id INTEGER NULL , provider_id NUMBER(19) NULL ,
visit_occurrence_id INTEGER NULL , visit_occurrence_id NUMBER(19) NULL ,
visit_detail_id INTEGER NULL , visit_detail_id NUMBER(19) NULL ,
procedure_source_value VARCHAR(50) NULL , procedure_source_value VARCHAR(50) NULL ,
procedure_source_concept_id INTEGER 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 , person_id NUMBER(19) NOT NULL ,
drug_concept_id INTEGER NOT NULL , drug_concept_id INTEGER NOT NULL ,
drug_exposure_start_date DATE 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_date DATE NULL ,
drug_exposure_end_datetime DATETIME2 NOT NULL , drug_exposure_end_datetime TIMESTAMP NOT NULL ,
verbatim_end_date DATE NULL , verbatim_end_date DATE NULL ,
drug_type_concept_id INTEGER NOT NULL , drug_type_concept_id INTEGER NOT NULL ,
stop_reason VARCHAR(20) NULL , stop_reason VARCHAR(20) NULL ,
@ -399,9 +361,9 @@ CREATE TABLE drug_exposure
sig CLOB NULL , sig CLOB NULL ,
route_concept_id INTEGER NULL , route_concept_id INTEGER NULL ,
lot_number VARCHAR(50) NULL , lot_number VARCHAR(50) NULL ,
provider_id INTEGER NULL , provider_id NUMBER(19) NULL ,
visit_occurrence_id INTEGER NULL , visit_occurrence_id NUMBER(19) NULL ,
visit_detail_id INTEGER NULL , visit_detail_id NUMBER(19) NULL ,
drug_source_value VARCHAR(50) NULL , drug_source_value VARCHAR(50) NULL ,
drug_source_concept_id INTEGER NULL , drug_source_concept_id INTEGER NULL ,
route_source_value VARCHAR(50) NULL , route_source_value VARCHAR(50) NULL ,
@ -417,15 +379,15 @@ CREATE TABLE device_exposure
person_id NUMBER(19) NOT NULL , person_id NUMBER(19) NOT NULL ,
device_concept_id INTEGER NOT NULL , device_concept_id INTEGER NOT NULL ,
device_exposure_start_date DATE 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_date DATE NULL ,
device_exposure_end_datetime DATETIME2 NULL , device_exposure_end_datetime TIMESTAMP NULL ,
device_type_concept_id INTEGER NOT NULL , device_type_concept_id INTEGER NOT NULL ,
unique_device_id VARCHAR(50) NULL , unique_device_id VARCHAR(50) NULL ,
quantity INTEGER NULL , quantity INTEGER NULL ,
provider_id INTEGER NULL , provider_id NUMBER(19) NULL ,
visit_occurrence_id INTEGER NULL , visit_occurrence_id NUMBER(19) NULL ,
visit_detail_id INTEGER NULL , visit_detail_id NUMBER(19) NULL ,
device_source_value VARCHAR(100) NULL , device_source_value VARCHAR(100) NULL ,
device_source_concept_id INTEGER NULL device_source_concept_id INTEGER NULL
) )
@ -439,15 +401,15 @@ CREATE TABLE condition_occurrence
person_id NUMBER(19) NOT NULL , person_id NUMBER(19) NOT NULL ,
condition_concept_id INTEGER NOT NULL , condition_concept_id INTEGER NOT NULL ,
condition_start_date DATE 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_date DATE NULL ,
condition_end_datetime DATETIME2 NULL , condition_end_datetime TIMESTAMP NULL ,
condition_type_concept_id INTEGER NOT NULL , condition_type_concept_id INTEGER NOT NULL ,
condition_status_concept_id INTEGER NULL , condition_status_concept_id INTEGER NULL ,
stop_reason VARCHAR(20) NULL , stop_reason VARCHAR(20) NULL ,
provider_id INTEGER NULL , provider_id NUMBER(19) NULL ,
visit_occurrence_id INTEGER NULL , visit_occurrence_id NUMBER(19) NULL ,
visit_detail_id INTEGER NULL , visit_detail_id NUMBER(19) NULL ,
condition_source_value VARCHAR(50) NULL , condition_source_value VARCHAR(50) NULL ,
condition_source_concept_id INTEGER NULL , condition_source_concept_id INTEGER NULL ,
condition_status_source_value VARCHAR(50) NULL condition_status_source_value VARCHAR(50) NULL
@ -462,7 +424,7 @@ CREATE TABLE measurement
person_id NUMBER(19) NOT NULL , person_id NUMBER(19) NOT NULL ,
measurement_concept_id INTEGER NOT NULL , measurement_concept_id INTEGER NOT NULL ,
measurement_date DATE NULL , measurement_date DATE NULL ,
measurement_datetime DATETIME2 NOT NULL , measurement_datetime TIMESTAMP NOT NULL ,
measurement_time VARCHAR(10) NULL, measurement_time VARCHAR(10) NULL,
measurement_type_concept_id INTEGER NOT NULL , measurement_type_concept_id INTEGER NOT NULL ,
operator_concept_id INTEGER NULL , operator_concept_id INTEGER NULL ,
@ -471,9 +433,9 @@ CREATE TABLE measurement
unit_concept_id INTEGER NULL , unit_concept_id INTEGER NULL ,
range_low FLOAT NULL , range_low FLOAT NULL ,
range_high FLOAT NULL , range_high FLOAT NULL ,
provider_id INTEGER NULL , provider_id NUMBER(19) NULL ,
visit_occurrence_id INTEGER NULL , visit_occurrence_id NUMBER(19) NULL ,
visit_detail_id INTEGER NULL , visit_detail_id NUMBER(19) NULL ,
measurement_source_value VARCHAR(50) NULL , measurement_source_value VARCHAR(50) NULL ,
measurement_source_concept_id INTEGER NULL , measurement_source_concept_id INTEGER NULL ,
unit_source_value VARCHAR(50) NULL , unit_source_value VARCHAR(50) NULL ,
@ -487,20 +449,19 @@ CREATE TABLE note
( (
note_id NUMBER(19) NOT NULL , note_id NUMBER(19) NOT NULL ,
person_id NUMBER(19) NOT NULL , person_id NUMBER(19) NOT NULL ,
note_event_id NUMBER(19) NULL , --This and the field below added note_event_id NUMBER(19) NULL ,
note_domain_id VARCHAR(20) NULL , --This field may be removed in favor of the one below note_event_field_concept_id INTEGER NULL ,
--note_event_table_concept_id INTEGER NULL , --This may be added based on 9/4 meeting
note_date DATE NULL , note_date DATE NULL ,
note_datetime DATETIME2 NOT NULL , note_datetime TIMESTAMP NOT NULL ,
note_type_concept_id INTEGER NOT NULL , note_type_concept_id INTEGER NOT NULL ,
note_class_concept_id INTEGER NOT NULL , note_class_concept_id INTEGER NOT NULL ,
note_title VARCHAR(250) NULL , note_title VARCHAR(250) NULL ,
note_text CLOB NULL , note_text CLOB NULL ,
encoding_concept_id INTEGER NOT NULL , encoding_concept_id INTEGER NOT NULL ,
language_concept_id INTEGER NOT NULL , language_concept_id INTEGER NOT NULL ,
provider_id INTEGER NULL , provider_id NUMBER(19) NULL ,
visit_occurrence_id INTEGER NULL , visit_occurrence_id NUMBER(19) NULL ,
visit_detail_id INTEGER NULL , visit_detail_id NUMBER(19) NULL ,
note_source_value VARCHAR(50) NULL note_source_value VARCHAR(50) NULL
) )
; ;
@ -518,7 +479,7 @@ CREATE TABLE note_nlp
note_nlp_concept_id INTEGER NULL , note_nlp_concept_id INTEGER NULL ,
nlp_system VARCHAR(250) NULL , nlp_system VARCHAR(250) NULL ,
nlp_date DATE NOT NULL , nlp_date DATE NOT NULL ,
nlp_datetime DATETIME2 NULL , nlp_datetime TIMESTAMP NULL ,
term_exists VARCHAR(1) NULL , term_exists VARCHAR(1) NULL ,
term_temporal VARCHAR(50) NULL , term_temporal VARCHAR(50) NULL ,
term_modifiers VARCHAR(2000) NULL , term_modifiers VARCHAR(2000) NULL ,
@ -534,14 +495,14 @@ CREATE TABLE observation
person_id NUMBER(19) NOT NULL , person_id NUMBER(19) NOT NULL ,
observation_concept_id INTEGER NOT NULL , observation_concept_id INTEGER NOT NULL ,
observation_date DATE NULL , observation_date DATE NULL ,
observation_datetime DATETIME2 NOT NULL , observation_datetime TIMESTAMP NOT NULL ,
observation_type_concept_id INTEGER NOT NULL , observation_type_concept_id INTEGER NOT NULL ,
value_as_number FLOAT NULL , value_as_number FLOAT NULL ,
value_as_string VARCHAR(60) NULL , value_as_string VARCHAR(60) NULL ,
value_as_concept_id INTEGER NULL , value_as_concept_id INTEGER NULL ,
qualifier_concept_id INTEGER NULL , qualifier_concept_id INTEGER NULL ,
unit_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_occurrence_id NUMBER(19) NULL ,
visit_detail_id NUMBER(19) NULL , visit_detail_id NUMBER(19) NULL ,
observation_source_value VARCHAR(50) NULL , observation_source_value VARCHAR(50) NULL ,
@ -549,9 +510,8 @@ CREATE TABLE observation
unit_source_value VARCHAR(50) NULL , unit_source_value VARCHAR(50) NULL ,
qualifier_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_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_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*/
--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 TIMESTAMP NULL
value_as_datetime DATETIME2 NULL
) )
; ;
@ -563,9 +523,9 @@ CREATE TABLE survey_conduct --Table added
person_id NUMBER(19) NOT NULL , person_id NUMBER(19) NOT NULL ,
survey_concept_id INTEGER NOT NULL , survey_concept_id INTEGER NOT NULL ,
survey_start_date DATE NULL , survey_start_date DATE NULL ,
survey_start_datetime DATETIME2 NULL , survey_start_datetime TIMESTAMP NULL ,
survey_end_date DATE NULL , survey_end_date DATE NULL ,
survey_end_datetime DATETIME2 NOT NULL , survey_end_datetime TIMESTAMP NOT NULL ,
provider_id NUMBER(19) NULL , provider_id NUMBER(19) NULL ,
assisted_concept_id INTEGER NULL , assisted_concept_id INTEGER NULL ,
respondent_type_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 , survey_version_number VARCHAR(20) NULL ,
visit_occurrence_id NUMBER(19) NULL , visit_occurrence_id NUMBER(19) NULL ,
visit_detail_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 , cost_id NUMBER(19) NOT NULL ,
person_id NUMBER(19) NOT NULL, person_id NUMBER(19) NOT NULL,
cost_event_id NUMBER(19) NOT NULL , cost_event_id NUMBER(19) NOT NULL ,
cost_domain_id VARCHAR(20) NOT NULL , cost_event_field_concept_id INTEGER 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_concept_id INTEGER NOT NULL , cost_concept_id INTEGER NOT NULL ,
cost_type_concept_id INTEGER NOT NULL , cost_type_concept_id INTEGER NOT NULL ,
currency_concept_id INTEGER 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) --HINT DISTRIBUTE_ON_KEY(person_id)
CREATE TABLE drug_era 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 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 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 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 ) ; 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 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 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_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_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_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_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. 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. 3. Load your data into the schema.