Data Warehouse of Diabetic Data

Dataset URL - https://archive.ics.uci.edu/ml/datasets/Diabetes+130-US+hospitals+for+years+1999-2008 Attribute Info - https://www.hindawi.com/journals/bmri/2014/781670/tab1/

Dimensional Model

Build Data Warehouse

Step 01 - Create Schema for Staging Area

Use following query to create the database named 'diabetes_dwh_staging' and tables.

Database: diabetes_dwh_staging
Tables:
1. dataset
2. admission_source
3. admission_type
4. discharge_disposition

Query to execute

DROP SCHEMA IF EXISTS `diabetes_DWH_staging` ;
CREATE SCHEMA `diabetes_DWH_staging` DEFAULT CHARACTER SET utf8 COLLATE utf8_general_ci ;
USE `diabetes_DWH_staging` ;

CREATE TABLE IF NOT EXISTS `diabetes_DWH_staging`.`dataset` (
  `encounter_id` INT NULL COMMENT '',
  `patient_nbr` INT NULL COMMENT '',
  `race` VARCHAR(45) NULL COMMENT '',
  `gender` VARCHAR(45) NULL COMMENT '',
  `age` VARCHAR(45) NULL COMMENT '',
  `weight` VARCHAR(45) NULL COMMENT '',
  `admission_type_id` INT NULL COMMENT '',
  `discharge_disposition_id` INT NULL COMMENT '',
  `admission_source_id` INT NULL COMMENT '',
  `time_in_hospital` INT NULL COMMENT '',
  `payer_code` VARCHAR(45) NULL COMMENT '',
  `medical_specialty` VARCHAR(45) NULL COMMENT '',
  `num_lab_procedures` INT NULL COMMENT '',
  `num_procedures` INT NULL COMMENT '',
  `num_medications` INT NULL COMMENT '',
  `number_outpatient` INT NULL COMMENT '',
  `number_emergency` INT NULL COMMENT '',
  `number_inpatient` INT NULL COMMENT '',
  `diag_1` VARCHAR(200) NULL COMMENT '',
  `diag_2` VARCHAR(200) NULL COMMENT '',
  `diag_3` VARCHAR(200) NULL COMMENT '',
  `number_diagnoses` INT NULL COMMENT '',
  `max_glu_serum` VARCHAR(45) NULL COMMENT '',
  `A1Cresult` VARCHAR(45) NULL COMMENT '',
  `metformin` VARCHAR(45) NULL COMMENT '',
  `repaglinide` VARCHAR(45) NULL COMMENT '',
  `nateglinide` VARCHAR(45) NULL COMMENT '',
  `chlorpropamide` VARCHAR(45) NULL COMMENT '',
  `glimepiride` VARCHAR(45) NULL COMMENT '',
  `acetohexamide` VARCHAR(45) NULL COMMENT '',
  `glipizide` VARCHAR(45) NULL COMMENT '',
  `glyburide` VARCHAR(45) NULL COMMENT '',
  `tolbutamide` VARCHAR(45) NULL COMMENT '',
  `pioglitazone` VARCHAR(45) NULL COMMENT '',
  `rosiglitazone` VARCHAR(45) NULL COMMENT '',
  `acarbose` VARCHAR(45) NULL COMMENT '',
  `miglitol` VARCHAR(45) NULL COMMENT '',
  `troglitazone` VARCHAR(45) NULL COMMENT '',
  `tolazamide` VARCHAR(45) NULL COMMENT '',
  `examide` VARCHAR(45) NULL COMMENT '',
  `citoglipton` VARCHAR(45) NULL COMMENT '',
  `insulin` VARCHAR(45) NULL COMMENT '',
  `glyburide-metformin` VARCHAR(45) NULL COMMENT '',
  `glipizide-metformin` VARCHAR(45) NULL COMMENT '',
  `glimepiride-pioglitazone` VARCHAR(45) NULL COMMENT '',
  `metformin-rosiglitazone` VARCHAR(45) NULL COMMENT '',
  `metformin-pioglitazone` VARCHAR(45) NULL COMMENT '',
  `change` VARCHAR(45) NULL COMMENT '',
  `diabetesMed` VARCHAR(45) NULL COMMENT '',
  `readmitted` VARCHAR(45) NULL COMMENT '')
ENGINE = InnoDB;

CREATE TABLE IF NOT EXISTS `diabetes_DWH_staging`.`admission_source` (
  `id` INT NULL COMMENT '',
  `description` VARCHAR(255) NULL COMMENT '')
ENGINE = InnoDB;

CREATE TABLE IF NOT EXISTS `diabetes_DWH_staging`.`admission_type` (
  `id` INT NULL COMMENT '',
  `description` VARCHAR(255) NULL COMMENT '')
ENGINE = InnoDB;

CREATE TABLE IF NOT EXISTS `diabetes_DWH_staging`.`discharge_disposition` (
  `id` INT NULL COMMENT '',
  `description` VARCHAR(255) NULL COMMENT '')
ENGINE = InnoDB;

Step 02 - Extract (Import CSV Dataset) to Staging Area

Use the following query to import data to 'datase' table. Use absolute path to the 'diabetic_data.csv' file as <dataset_directory>/diabetic_data.csv in the query. In windows use '/' characters instead of '\' as path name separator character (eg: instead of 'D:\dwh\diabetic_data.csv' use 'D:/dwh/diabetic_data.csv')

USE `diabetes_DWH_staging` ;

LOAD DATA INFILE '<dataset_directory>/diabetic_data.csv'
INTO TABLE `dataset`
FIELDS TERMINATED BY ',' ENCLOSED BY '"'
LINES TERMINATED BY '\r\n'
IGNORE 1 LINES;

If secure_file_priv is enabled copy 'diabetic_data.csv' file to the directory given by following query and use that path.
SHOW VARIABLES LIKE "secure_file_priv";

Check whether all 101766 recoreds are imported with executing the query below.

SELECT COUNT(*) FROM `dataset`;

Import IDs_mapping_admission_source.csv, IDs_mapping_admission_type.csv and IDs_mapping_discharge_disposition.csv files as the same way as below.

LOAD DATA INFILE '<dataset_directory>/IDs_mapping_admission_source.csv'
INTO TABLE `admission_source`
FIELDS TERMINATED BY ',' ENCLOSED BY '"'
LINES TERMINATED BY '\r\n'
IGNORE 1 LINES;

LOAD DATA INFILE '<dataset_directory>/IDs_mapping_admission_type.csv'
INTO TABLE `admission_type`
FIELDS TERMINATED BY ',' ENCLOSED BY '"'
LINES TERMINATED BY '\r\n'
IGNORE 1 LINES;

LOAD DATA INFILE '<dataset_directory>/IDs_mapping_discharge_disposition.csv'
INTO TABLE `discharge_disposition`
FIELDS TERMINATED BY ',' ENCLOSED BY '"'
LINES TERMINATED BY '\r\n'
IGNORE 1 LINES;

Step 03 - Data Cleansing

3.1 Create a duplicate data set to make changes

CREATE TABLE IF NOT EXISTS `diabetes_DWH_staging`.`dataset_modified` (
  `encounter_id` INT NULL COMMENT '',
  `patient_nbr` INT NULL COMMENT '',
  `race` VARCHAR(45) NULL COMMENT '',
  `gender` VARCHAR(45) NULL COMMENT '',
  `age` VARCHAR(45) NULL COMMENT '',
  `weight` VARCHAR(45) NULL COMMENT '',
  `admission_type_id` INT NULL COMMENT '',
  `discharge_disposition_id` INT NULL COMMENT '',
  `admission_source_id` INT NULL COMMENT '',
  `time_in_hospital` INT NULL COMMENT '',
  `payer_code` VARCHAR(45) NULL COMMENT '',
  `medical_specialty` VARCHAR(45) NULL COMMENT '',
  `num_lab_procedures` INT NULL COMMENT '',
  `num_procedures` INT NULL COMMENT '',
  `num_medications` INT NULL COMMENT '',
  `number_outpatient` INT NULL COMMENT '',
  `number_emergency` INT NULL COMMENT '',
  `number_inpatient` INT NULL COMMENT '',
  `diag_1` VARCHAR(200) NULL COMMENT '',
  `diag_2` VARCHAR(200) NULL COMMENT '',
  `diag_3` VARCHAR(200) NULL COMMENT '',
  `number_diagnoses` INT NULL COMMENT '',
  `max_glu_serum` VARCHAR(45) NULL COMMENT '',
  `A1Cresult` VARCHAR(45) NULL COMMENT '',
  `metformin` VARCHAR(45) NULL COMMENT '',
  `repaglinide` VARCHAR(45) NULL COMMENT '',
  `nateglinide` VARCHAR(45) NULL COMMENT '',
  `chlorpropamide` VARCHAR(45) NULL COMMENT '',
  `glimepiride` VARCHAR(45) NULL COMMENT '',
  `acetohexamide` VARCHAR(45) NULL COMMENT '',
  `glipizide` VARCHAR(45) NULL COMMENT '',
  `glyburide` VARCHAR(45) NULL COMMENT '',
  `tolbutamide` VARCHAR(45) NULL COMMENT '',
  `pioglitazone` VARCHAR(45) NULL COMMENT '',
  `rosiglitazone` VARCHAR(45) NULL COMMENT '',
  `acarbose` VARCHAR(45) NULL COMMENT '',
  `miglitol` VARCHAR(45) NULL COMMENT '',
  `troglitazone` VARCHAR(45) NULL COMMENT '',
  `tolazamide` VARCHAR(45) NULL COMMENT '',
  `examide` VARCHAR(45) NULL COMMENT '',
  `citoglipton` VARCHAR(45) NULL COMMENT '',
  `insulin` VARCHAR(45) NULL COMMENT '',
  `glyburide-metformin` VARCHAR(45) NULL COMMENT '',
  `glipizide-metformin` VARCHAR(45) NULL COMMENT '',
  `glimepiride-pioglitazone` VARCHAR(45) NULL COMMENT '',
  `metformin-rosiglitazone` VARCHAR(45) NULL COMMENT '',
  `metformin-pioglitazone` VARCHAR(45) NULL COMMENT '',
  `change` VARCHAR(45) NULL COMMENT '',
  `diabetesMed` VARCHAR(45) NULL COMMENT '',
  `readmitted` VARCHAR(45) NULL COMMENT '')
ENGINE = InnoDB;

INSERT INTO `diabetes_DWH_staging`.`dataset_modified`
SELECT * FROM `diabetes_DWH_staging`.`dataset`;

Horizontal Filtering

Some importants attributes that should be considered are missing in the dataset. Lets discard them.

DELETE FROM `diabetes_dwh_staging`.`dataset_modified`
WHERE `payer_code` = '?';

DELETE FROM `diabetes_dwh_staging`.`dataset_modified`
WHERE `medical_specialty` = '?';

DELETE FROM `diabetes_dwh_staging`.`dataset_modified`
WHERE `race` = '?';

DELETE FROM `diabetes_dwh_staging`.`dataset_modified`
WHERE `diag_1` = '?';

DELETE FROM `diabetes_dwh_staging`.`dataset_modified`
WHERE `diag_2` = '?';

DELETE FROM `diabetes_dwh_staging`.`dataset_modified`
WHERE `diag_3` = '?';

SELECT COUNT(*) FROM `diabetes_dwh_staging`.`dataset_modified`;

We have 26755 data records.

Cleansing Patient Data

Select diry data wrt gender of the patient

CREATE OR REPLACE VIEW `diabetes_dwh_staging`.`dirty_patient_gender` AS
SELECT *
FROM `diabetes_dwh_staging`.`dataset_modified`
WHERE `patient_nbr` in (
	SELECT `patient_nbr`
	FROM `diabetes_dwh_staging`.`dataset_modified`
	WHERE `gender` = 'Female'
) AND `patient_nbr` in (
	SELECT `patient_nbr`
	FROM `diabetes_dwh_staging`.`dataset_modified`
	WHERE `gender` = 'Male'
);

SELECT `encounter_id`, `patient_nbr`, `race`, `gender`
FROM `diabetes_dwh_staging`.`dirty_patient_gender`;

There are 2 dirty records with 1 patient and cleaned with selecting most frequent and latest data.

UPDATE `diabetes_dwh_staging`.`dataset_modified`
SET `gender` = 'Male'
WHERE `patient_nbr` = 109210482;

Select diry data wrt race of the patient

SELECT distinct `race`
FROM `diabetes_dwh_staging`.`dataset_modified`;
-- 6 distinct races are found. (Caucasian, AfricanAmerican, ?, Other, Asian, Hispanic)

-- Views to identify dirty data
CREATE OR REPLACE VIEW `diabetes_dwh_staging`.`dirty_patient_race` AS
SELECT `patient_nbr`, count(distinct `race`) as `race_count`
FROM `diabetes_dwh_staging`.`dataset_modified`
group by `patient_nbr` having `race_count` > 1;

SELECT count(`patient_nbr`)
FROM `diabetes_dwh_staging`.`dirty_patient_race`;

SELECT `encounter_id`, `patient_nbr`, `race`
FROM `diabetes_dwh_staging`.`dataset_modified`
WHERE `patient_nbr` in (
	SELECT `patient_nbr`
    FROM `diabetes_dwh_staging`.`dirty_patient_race`
)
ORDER BY `patient_nbr`, `encounter_id`;

There are 165 dirty records with 50 patients and cleaned with selecting most frequent and latest data.

-- Set race as Caucasian
UPDATE `diabetes_dwh_staging`.`dataset_modified`
SET `race` = 'Caucasian'
WHERE `patient_nbr` IN (1553220, 23724792, 38893887, 42246738, 52316388, 112367349);

-- Set race as AfricanAmerican
UPDATE `diabetes_dwh_staging`.`dataset_modified`
SET `race` = 'AfricanAmerican'
WHERE `patient_nbr` IN (6919587, 10980891, 40090752, 54643194, 101753730, 107849052);

-- Set race as Other
UPDATE `diabetes_dwh_staging`.`dataset_modified`
SET `race` = 'Other'
WHERE `patient_nbr` IN (28532295, 30689766, 32314608, 33247647, 36967347, 37547937, 37638306, 38774187, 39160719, 42096384, 90817893, 93105117, 93662784, 94027644, 98584524, 100322946, 103228398, 103690161, 105125598, 106425234);

-- Set race as Asian
UPDATE `diabetes_dwh_staging`.`dataset_modified`
SET `race` = 'Asian'
WHERE `patient_nbr` IN (24332220, 31812075, 34248078, 94539465, 97024806, 103305528, 104622570, 110657970, 111534210);

-- Set race as Hispanic
UPDATE `diabetes_dwh_staging`.`dataset_modified`
SET `race` = 'Hispanic'
WHERE `patient_nbr` IN (37572957, 44744166, 45113778, 90035874, 91107549, 93809358, 94088088, 98934615, 106895331, 109448541);

Step 04 - Transforming

4.1 Transform primary, secondary and additional diagnosis based on "International Statistical Classification of Diseases and Related Health Problems"

Visit http://icd9.chrisendres.com/index.php?action=contents for Diseases and Injuries Tabular Index

Values are stored to the file data_transforming/diseases_and_injuries_tabular_index.csv.

id	disease	code_letter	code_from	code_to
1	INFECTIOUS AND PARASITIC DISEASES		1	139
2	NEOPLASMS		140	239
3	ENDOCRINE, NUTRITIONAL AND METABOLIC DISEASES, AND IMMUNITY DISORDERS		240	279
4	DISEASES OF THE BLOOD AND BLOOD-FORMING ORGANS		280	289
5	MENTAL DISORDERS		290	319
6	DISEASES OF THE NERVOUS SYSTEM AND SENSE ORGANS		320	389
7	DISEASES OF THE CIRCULATORY SYSTEM		390	459
8	DISEASES OF THE RESPIRATORY SYSTEM		460	519
9	DISEASES OF THE DIGESTIVE SYSTEM		520	579
10	DISEASES OF THE GENITOURINARY SYSTEM		580	629
11	COMPLICATIONS OF PREGNANCY, CHILDBIRTH, AND THE PUERPERIUM		630	679
12	DISEASES OF THE SKIN AND SUBCUTANEOUS TISSUE		680	709
13	DISEASES OF THE MUSCULOSKELETAL SYSTEM AND CONNECTIVE TISSUE		710	739
14	CONGENITAL ANOMALIES		740	759
15	CERTAIN CONDITIONS ORIGINATING IN THE PERINATAL PERIOD		760	779
16	SYMPTOMS, SIGNS, AND ILL-DEFINED CONDITIONS		780	799
17	INJURY AND POISONING		800	999
18	SUPPLEMENTARY CLASSIFICATION OF FACTORS INFLUENCING HEALTH STATUS AND CONTACT WITH HEALTH SERVICES	V	1	89
19	SUPPLEMENTARY CLASSIFICATION OF EXTERNAL CAUSES OF INJURY AND POISONING	E	800	999

Lets load this csv file into a table.

Replace <dataset_directory> directory in the query with the absolute path of the file. Use '/' as path seperator.

use diabetes_dwh_staging;

CREATE TABLE IF NOT EXISTS `diabetes_DWH_staging`.`icd9_index` (
  `id` INT NOT NULL COMMENT '',
  `disease` VARCHAR(200) NOT NULL COMMENT '',
  `code_letter` VARCHAR(10) NULL COMMENT '',
  `code_from` INT NOT NULL COMMENT '',
  `code_to` INT NOT NULL COMMENT '',
  PRIMARY KEY (`id`)  COMMENT '')
ENGINE = InnoDB;

LOAD DATA INFILE '<dataset_directory>/diseases_and_injuries_tabular_index.csv'
INTO TABLE `icd9_index`
FIELDS TERMINATED BY ',' ENCLOSED BY '"'
LINES TERMINATED BY '\r\n'
IGNORE 1 LINES;

Transforming ICD9 Details

This query may take several time (~30 seconds) to execute.

DROP PROCEDURE IF EXISTS `diabetes_dwh_staging`.`TRANSFORM_ICD9`;
DELIMITER ;;

CREATE PROCEDURE `diabetes_dwh_staging`.`TRANSFORM_ICD9`()
BEGIN

DECLARE n INT DEFAULT 0;
DECLARE i INT DEFAULT 0;

-- Transform values starts with V and E
-- Transform "diag_1" values
UPDATE `diabetes_dwh_staging`.`dataset_modified`
SET `diag_1` = (
	SELECT `disease`
    FROM `diabetes_dwh_staging`.`icd9_index`
    WHERE `code_letter` = 'V'
)
WHERE LEFT(`diag_1`, 1) = 'V';

UPDATE `diabetes_dwh_staging`.`dataset_modified`
SET `diag_1` = (
	SELECT `disease`
    FROM `diabetes_dwh_staging`.`icd9_index`
    WHERE `code_letter` = 'E'
)
WHERE LEFT(`diag_1`, 1) = 'E';

-- Transform "diag_2" values
UPDATE `diabetes_dwh_staging`.`dataset_modified`
SET `diag_2` = (
	SELECT `disease`
    FROM `diabetes_dwh_staging`.`icd9_index`
    WHERE `code_letter` = 'V'
)
WHERE LEFT(`diag_2`, 1) = 'V';

UPDATE `diabetes_dwh_staging`.`dataset_modified`
SET `diag_2` = (
	SELECT `disease`
    FROM `diabetes_dwh_staging`.`icd9_index`
    WHERE `code_letter` = 'E'
)
WHERE LEFT(`diag_2`, 1) = 'E';

-- Transform "diag_3" values
UPDATE `diabetes_dwh_staging`.`dataset_modified`
SET `diag_3` = (
	SELECT `disease`
    FROM `diabetes_dwh_staging`.`icd9_index`
    WHERE `code_letter` = 'V'
)
WHERE LEFT(`diag_3`, 1) = 'V';

UPDATE `diabetes_dwh_staging`.`dataset_modified`
SET `diag_3` = (
	SELECT `disease`
    FROM `diabetes_dwh_staging`.`icd9_index`
    WHERE `code_letter` = 'E'
)
WHERE LEFT(`diag_3`, 1) = 'E';


-- Transform values with digits only
SELECT COUNT(*) FROM `diabetes_dwh_staging`.`icd9_index`
WHERE `code_letter` = ''
INTO n;

SET i = 0;
WHILE i < n DO 
	-- Transform "diag_1" values
	UPDATE `diabetes_dwh_staging`.`dataset_modified`
    SET `diag_1` = (
		SELECT `disease`
        FROM `diabetes_dwh_staging`.`icd9_index`
        LIMIT i, 1
	)
    WHERE `diag_1` REGEXP '^[0-9]+\\.?[0-9]*$' AND (
		`diag_1` >= (
			SELECT `code_from`
            FROM `diabetes_dwh_staging`.`icd9_index`
            LIMIT i, 1
		) AND
		`diag_1` <= (
			SELECT `code_to`
            FROM `diabetes_dwh_staging`.`icd9_index`
            LIMIT i, 1
		)
	);
    
	-- Transform "diag_2" values
	UPDATE `diabetes_dwh_staging`.`dataset_modified` SET `diag_2` = (
		SELECT `disease`
        FROM `diabetes_dwh_staging`.`icd9_index`
        LIMIT i, 1
	)
    WHERE `diag_2` REGEXP '^[0-9]+\\.?[0-9]*$' AND (
		`diag_2` >= (
			SELECT `code_from`
            FROM `diabetes_dwh_staging`.`icd9_index`
            LIMIT i, 1
		) AND
		`diag_2` <= (
			SELECT `code_to`
            FROM `diabetes_dwh_staging`.`icd9_index`
            LIMIT i, 1
		)
	);
    
    -- Transform "diag_3" values
	UPDATE `diabetes_dwh_staging`.`dataset_modified` SET `diag_3` = (
		SELECT `disease`
        FROM `diabetes_dwh_staging`.`icd9_index`
        LIMIT i, 1
	)
    WHERE `diag_3` REGEXP '^[0-9]+\\.?[0-9]*$' AND (
		`diag_3` >= (
			SELECT `code_from`
			FROM `diabetes_dwh_staging`.`icd9_index`
			LIMIT i, 1
        ) AND
		`diag_3` <= (
			SELECT `code_to`
			FROM `diabetes_dwh_staging`.`icd9_index`
			LIMIT i, 1
        )
	);
  SET i = i + 1;
END WHILE;

END;;

DELIMITER ;
CALL `diabetes_dwh_staging`.`TRANSFORM_ICD9`();

4.2 Transform Admission Type, Discharge Disposition, Admission Source with given mapping data set.

One procedure will takes around 15 seconds to execute with all take around 45 seconds.

DROP PROCEDURE IF EXISTS `diabetes_dwh_staging`.`TRANSFORM_ADMISSION_TYPE`;
DROP PROCEDURE IF EXISTS `diabetes_dwh_staging`.`TRANSFORM_ADMISSION_SOURCE`;
DROP PROCEDURE IF EXISTS `diabetes_dwh_staging`.`TRANSFORM_DISCHARGE_DISPOSITION`;
DELIMITER ;;

-- Admission Type
CREATE PROCEDURE `diabetes_dwh_staging`.`TRANSFORM_ADMISSION_TYPE`()
BEGIN

DECLARE n INT DEFAULT 0;
DECLARE i INT DEFAULT 1;

SET n = (SELECT COUNT(*) FROM `diabetes_dwh_staging`.`admission_type`);
-- Add the column
ALTER TABLE `diabetes_dwh_staging`.`dataset_modified`
ADD COLUMN `admission_type` VARCHAR(150);

WHILE i <= n DO
	UPDATE `diabetes_dwh_staging`.`dataset_modified`
    SET `admission_type` = (
		SELECT `description` FROM `diabetes_dwh_staging`.`admission_type` WHERE `id` = i
    )
    WHERE `admission_type_id` = i;
    SET i = i + 1;
END WHILE;

ALTER TABLE `diabetes_dwh_staging`.`dataset_modified`
DROP COLUMN `admission_type_id`;
END;;

-- Admission Source
CREATE PROCEDURE `diabetes_dwh_staging`.`TRANSFORM_ADMISSION_SOURCE`()
BEGIN

DECLARE n INT DEFAULT 0;
DECLARE i INT DEFAULT 1;

SET n = (SELECT COUNT(*) FROM `diabetes_dwh_staging`.`admission_source`);
-- Add the column
ALTER TABLE `diabetes_dwh_staging`.`dataset_modified`
ADD COLUMN `admission_source` VARCHAR(150);

WHILE i <= n DO
	UPDATE `diabetes_dwh_staging`.`dataset_modified`
    SET `admission_source` = (
		SELECT `description` FROM `diabetes_dwh_staging`.`admission_source` WHERE `id` = i
    )
    WHERE `admission_source_id` = i;
    SET i = i + 1;
END WHILE;

ALTER TABLE `diabetes_dwh_staging`.`dataset_modified`
DROP COLUMN `admission_source_id`;
END;;

-- Discharge Disposition
CREATE PROCEDURE `diabetes_dwh_staging`.`TRANSFORM_DISCHARGE_DISPOSITION`()
BEGIN

DECLARE n INT DEFAULT 0;
DECLARE i INT DEFAULT 1;

SET n = (SELECT COUNT(*) FROM `diabetes_dwh_staging`.`discharge_disposition`);
-- Add the column
ALTER TABLE `diabetes_dwh_staging`.`dataset_modified`
ADD COLUMN `discharge_disposition` VARCHAR(150);

WHILE i <= n DO
	UPDATE `diabetes_dwh_staging`.`dataset_modified`
    SET `discharge_disposition` = (
		SELECT `description` FROM `diabetes_dwh_staging`.`discharge_disposition` WHERE `id` = i
    )
    WHERE `discharge_disposition_id` = i;
    SET i = i + 1;
END WHILE;

ALTER TABLE `diabetes_dwh_staging`.`dataset_modified`
DROP COLUMN `discharge_disposition_id`;
END;;

DELIMITER ;
CALL `diabetes_dwh_staging`.`TRANSFORM_ADMISSION_TYPE`();
CALL `diabetes_dwh_staging`.`TRANSFORM_ADMISSION_SOURCE`();
CALL `diabetes_dwh_staging`.`TRANSFORM_DISCHARGE_DISPOSITION`();

Step 05 - Create Schema for Data Warehouse

Exucute following query to create database and tables for Data Warehouse as in the Dimensional Model

DROP SCHEMA IF EXISTS `diabetes_dwh` ;

CREATE SCHEMA IF NOT EXISTS `diabetes_dwh` DEFAULT CHARACTER SET utf8 COLLATE utf8_general_ci ;
USE `diabetes_dwh` ;

CREATE TABLE IF NOT EXISTS `diabetes_dwh`.`dim_patient` (
  `patient_sk` INT NOT NULL AUTO_INCREMENT COMMENT '',
  `patient_number` VARCHAR(45) NOT NULL COMMENT '',
  `race` VARCHAR(45) NULL COMMENT '',
  `gender` VARCHAR(45) NULL COMMENT '',
  `age` VARCHAR(45) NULL COMMENT '',
  PRIMARY KEY (`patient_sk`)  COMMENT '')
ENGINE = InnoDB;

CREATE TABLE IF NOT EXISTS `diabetes_dwh`.`dim_junk_admissionDetails` (
  `admissionDetail_sk` INT NOT NULL AUTO_INCREMENT COMMENT '',
  `admission_type` VARCHAR(200) NULL COMMENT '',
  `admission_source` VARCHAR(200) NULL COMMENT '',
  `medical_speciality` VARCHAR(200) NULL COMMENT '',
  PRIMARY KEY (`admissionDetail_sk`)  COMMENT '')
ENGINE = InnoDB;

CREATE TABLE IF NOT EXISTS `diabetes_dwh`.`dim_discharge` (
  `discharge_sk` INT NOT NULL AUTO_INCREMENT COMMENT '',
  `discharge_disposition` VARCHAR(150) NULL COMMENT '',
  `readmitted` VARCHAR(45) NULL COMMENT '',
  `payer_code` VARCHAR(45) NULL COMMENT '',
  PRIMARY KEY (`discharge_sk`)  COMMENT '')
ENGINE = InnoDB;

CREATE TABLE IF NOT EXISTS `diabetes_dwh`.`dim_test_results` (
  `test_results_sk` INT NOT NULL AUTO_INCREMENT COMMENT '',
  `glucose_serum_test_result` VARCHAR(45) NULL COMMENT '',
  `a1c_test_results` VARCHAR(45) NULL COMMENT '',
  PRIMARY KEY (`test_results_sk`)  COMMENT '')
ENGINE = InnoDB;

CREATE TABLE IF NOT EXISTS `diabetes_dwh`.`dim_medication` (
  `medication_sk` INT NOT NULL AUTO_INCREMENT COMMENT '',
  `change_of_medication` VARCHAR(45) NULL COMMENT '',
  `diabetes_medicatin` VARCHAR(45) NULL COMMENT '',
  `metformin` VARCHAR(45) NULL COMMENT '',
  `repaglinide` VARCHAR(45) NULL COMMENT '',
  `nateglinide` VARCHAR(45) NULL COMMENT '',
  `chlorpropamide` VARCHAR(45) NULL COMMENT '',
  `glimepiride` VARCHAR(45) NULL COMMENT '',
  `acetohexamide` VARCHAR(45) NULL COMMENT '',
  `glipizide` VARCHAR(45) NULL COMMENT '',
  `tolbutamide` VARCHAR(45) NULL COMMENT '',
  `pioglitazone` VARCHAR(45) NULL COMMENT '',
  `rosiglitazone` VARCHAR(45) NULL COMMENT '',
  `acarbose` VARCHAR(45) NULL COMMENT '',
  `miglitol` VARCHAR(45) NULL COMMENT '',
  `troglitazone` VARCHAR(45) NULL COMMENT '',
  `tolazamide` VARCHAR(45) NULL COMMENT '',
  `examide` VARCHAR(45) NULL COMMENT '',
  `citoglipton` VARCHAR(45) NULL COMMENT '',
  `insulin` VARCHAR(45) NULL COMMENT '',
  `glyburide-metformin` VARCHAR(45) NULL COMMENT '',
  `glipizide-metformin` VARCHAR(45) NULL COMMENT '',
  `glimepiride-pioglitazone` VARCHAR(45) NULL COMMENT '',
  `metformin-rosiglitazone` VARCHAR(45) NULL COMMENT '',
  `metformin-pioglitazone` VARCHAR(45) NULL COMMENT '',
  PRIMARY KEY (`medication_sk`)  COMMENT '')
ENGINE = InnoDB;

CREATE TABLE IF NOT EXISTS `diabetes_dwh`.`dim_junk_diagnosis` (
  `diagnosis_sk` INT NOT NULL AUTO_INCREMENT COMMENT '',
  `primary_diagnosis` VARCHAR(200) NULL COMMENT '',
  `secondary_diagnosis` VARCHAR(200) NULL COMMENT '',
  `additional_diagnosis` VARCHAR(200) NULL COMMENT '',
  PRIMARY KEY (`diagnosis_sk`)  COMMENT '')
ENGINE = InnoDB;

CREATE TABLE IF NOT EXISTS `diabetes_dwh`.`fact_admission` (
  `encounter_id` INT NOT NULL AUTO_INCREMENT COMMENT '',
  `patient_sk` INT NOT NULL COMMENT '',
  `test_sk` INT NOT NULL COMMENT '',
  `medication_sk` INT NOT NULL COMMENT '',
  `diagnosis_sk` INT NOT NULL COMMENT '',
  `date_sk` DATETIME NOT NULL COMMENT '',
  `time_in_hospital` VARCHAR(45) NULL COMMENT '',
  `num_lab_procedure` INT NULL COMMENT '',
  `num_procedures` INT NULL COMMENT '',
  `num_medication` INT NULL COMMENT '',
  `number_outpatient` INT NULL COMMENT '',
  `number_emergency` INT NULL COMMENT '',
  `number_inpatient` INT NULL COMMENT '',
  `number_diagnoses` INT NULL COMMENT '',
  PRIMARY KEY (`encounter_id`)  COMMENT '',
  UNIQUE INDEX `patient_sk_UNIQUE` (`patient_sk` ASC)  COMMENT '',
  UNIQUE INDEX `test_sk_UNIQUE` (`test_sk` ASC)  COMMENT '',
  UNIQUE INDEX `medication_sk_UNIQUE` (`medication_sk` ASC)  COMMENT '',
  UNIQUE INDEX `diagnosis_sk_UNIQUE` (`diagnosis_sk` ASC)  COMMENT '',
  UNIQUE INDEX `date_sk_UNIQUE` (`date_sk` ASC)  COMMENT '')
ENGINE = InnoDB;

Step 06 - Loading Data

6.1 Loading to Patient Dimension

There are 19808 distict values.

INSERT INTO `diabetes_dwh`.`dim_patient` (`patient_number`, `race`, `gender`, `age`)
SELECT DISTINCT `patient_nbr`, `race`, `gender`, `age`
FROM `diabetes_dwh_staging`.`dataset_modified`
ORDER BY `patient_nbr`, `age`;

SELECT COUNT(*) FROM `diabetes_dwh`.`dim_patient`;

6.2 Loading to Test Results Dimension

There are 7 distict values.

INSERT INTO `diabetes_dwh`.`dim_test_results` (`glucose_serum_test_result`, `a1c_test_results`)
SELECT DISTINCT `max_glu_serum`, `A1Cresult`
FROM `diabetes_dwh_staging`.`dataset_modified`;

SELECT COUNT(*) FROM `diabetes_dwh`.`dim_test_results`;

6.3 Loading to Discharge Dimension

There are 339 distict values.

INSERT INTO `diabetes_dwh`.`dim_discharge` (`discharge_disposition`, `readmitted`, `payer_code`)
SELECT DISTINCT `discharge_disposition`, `readmitted`, `payer_code`
FROM `diabetes_dwh_staging`.`dataset_modified`;

SELECT COUNT(*) FROM `diabetes_dwh`.`dim_discharge`;

6.4 Loading to Medication Dimension

There are 633 distict values.

INSERT INTO `diabetes_dwh`.`dim_medication` (
	`change_of_medication`, `diabetes_medicatin`, `metformin`, `repaglinide`,
    `nateglinide`, `chlorpropamide`, `glimepiride`, `acetohexamide`, `glipizide`,
    `tolbutamide`, `pioglitazone`, `rosiglitazone`, `acarbose`, `miglitol`,
    `troglitazone`, `tolazamide`, `examide`, `citoglipton`, `insulin`,
    `glyburide-metformin`, `glipizide-metformin`, `glimepiride-pioglitazone`,
    `metformin-rosiglitazone`, `metformin-pioglitazone`
)
SELECT DISTINCT `change`, `diabetesMed`, `metformin`,
	`repaglinide`, `nateglinide`, `chlorpropamide`, `glimepiride`, `acetohexamide`,
    `glipizide`, `tolbutamide`, `pioglitazone`, `rosiglitazone`, `acarbose`,
    `miglitol`, `troglitazone`, `tolazamide`, `examide`, `citoglipton`, `insulin`,
    `glyburide-metformin`, `glipizide-metformin`, `glimepiride-pioglitazone`,
    `metformin-rosiglitazone`, `metformin-pioglitazone`
FROM `diabetes_dwh_staging`.`dataset_modified`;

SELECT COUNT(*) FROM `diabetes_dwh`.`dim_medication`;

6.5 Loading to Diagnosis Junk Dimension

Lets load all distinct values for the junk dimension. There are 2323 distict values.

INSERT INTO `diabetes_dwh`.`dim_junk_diagnosis` (`primary_diagnosis`, `secondary_diagnosis`, `additional_diagnosis`)
SELECT DISTINCT `diag_1`, `diag_2`, `diag_3`
FROM `diabetes_dwh_staging`.`dataset_modified`;

SELECT COUNT(*) FROM `diabetes_dwh`.`dim_junk_diagnosis`;

6.6 Loading to Admission Junk Dimension

Lets load all distinct values for the junk dimension. There are 391 distict values with including NULL values.

INSERT INTO `diabetes_dwh`.`dim_junk_admissionDetails` (`admission_type`, `admission_source`, `medical_speciality`)
SELECT DISTINCT `admission_type`, `admission_source`, `medical_specialty`
FROM `diabetes_dwh_staging`.`dataset_modified`;

SELECT COUNT(*) FROM `diabetes_dwh`.`dim_junk_admissionDetails`;

6.7 Loading to Fact

SELECT `stg`.`encounter_id`,
	`patient`.`patient_sk`, `test`.`test_results_sk`,
    `stg`.`time_in_hospital`, `stg`.`num_lab_procedures`
FROM `diabetes_dwh_staging`.`dataset_modified` as `stg`,
	`diabetes_dwh`.`dim_patient` as `patient`, 
    `diabetes_dwh`.`dim_test_results` as `test`,
    `diabetes_dwh`.`dim_discharge` as `discharge`,
    `diabetes_dwh`.`dim_medication` as `medication`,
    `diabetes_dwh`.`dim_junk_diagnosis` as `diag`,
    `diabetes_dwh`.`dim_junk_admissionDetails` as `adm_details`
WHERE `stg`.`patient_nbr` = `patient`.`patient_number` AND `stg`.`age` = `patient`.`age`
	AND `test`.`glucose_serum_test_result` = `stg`.`max_glu_serum` AND `test`.`a1c_test_results` = `stg`.`A1Cresult`
    AND `stg`.`discharge`.`discharge_disposition` = `discharge_disposition` AND `stg`.`readmitted` = `discharge`.`readmitted` AND `srg`.`payer_code` = `discharge`.`payer_code`;

Data Mining

Transforming for Data Mining

Transform age to an integer value. (eg transform "[40-50)" to 45)

DROP PROCEDURE IF EXISTS `diabetes_dwh_staging`.`transform_for_datamining`;
DELIMITER ;;

CREATE PROCEDURE `diabetes_dwh_staging`.`transform_for_datamining`()
BEGIN

DECLARE i INT DEFAULT 0;
DECLARE age_str VARCHAR(10);
DECLARE age_str_int INT;

ALTER TABLE `diabetes_dwh_staging`.`dataset_modified`
ADD COLUMN `age_int` INT;

WHILE i < 10 DO
	SET age_str = CONCAT('[', i * 10, '-', (i+1) * 10, ')');
    SET age_str_int = i * 10 + 5;
    
    UPDATE `diabetes_dwh_staging`.`dataset_modified`
    SET `age_int` = age_str_int
    WHERE `age` = age_str;
    
    SET i = i+1;
END WHILE;

END;;

DELIMITER ;
CALL `diabetes_dwh_staging`.`transform_for_datamining`();

Export CSV file for Data Mining

Lets export diabetes_dwh_staging.dataset_modified table to csv file. Then it can be used with weka for data mining. Replace <dataset_directory> directory in the query with the absolute path of the file. Use '/' as path seperator.

SELECT 'race', 'gender', 'age', 'admission_type',
	'discharge_disposition', 'admission_source', 'time_in_hospital', 'payer_code',
    'medical_specialty', 'num_lab_procedures', 'num_procedures', 'num_medications',
    'number_outpatient', 'number_emergency', 'number_inpatient', 'diag_1', 'diag_2',
    'diag_3', 'number_diagnoses', 'max_glu_serum', 'A1Cresult', 'metformin', 'repaglinide',
    'nateglinide', 'chlorpropamide', 'glimepiride', 'acetohexamide', 'glipizide',
    'glyburide', 'tolbutamide', 'pioglitazone', 'rosiglitazone', 'acarbose', 'miglitol',
    'troglitazone', 'tolazamide', 'examide', 'citoglipton', 'insulin', 'glyburide-metformin',
    'glipizide-metformin', 'glimepiride-pioglitazone', 'metformin-rosiglitazone',
    'metformin-pioglitazone', 'change', 'diabetesMed', 'readmitted'
UNION
SELECT `race`, `gender`, `age_int`, `admission_type`,
	`discharge_disposition`, `admission_source`, `time_in_hospital`, `payer_code`,
    `medical_specialty`, `num_lab_procedures`, `num_procedures`, `num_medications`,
    `number_outpatient`, `number_emergency`, `number_inpatient`, `diag_1`, `diag_2`,
    `diag_3`, `number_diagnoses`, `max_glu_serum`, `A1Cresult`, `metformin`, `repaglinide`,
    `nateglinide`, `chlorpropamide`, `glimepiride`, `acetohexamide`, `glipizide`,
    `glyburide`, `tolbutamide`, `pioglitazone`, `rosiglitazone`, `acarbose`, `miglitol`,
    `troglitazone`, `tolazamide`, `examide`, `citoglipton`, `insulin`, `glyburide-metformin`,
    `glipizide-metformin`, `glimepiride-pioglitazone`, `metformin-rosiglitazone`,
    `metformin-pioglitazone`, `change`, `diabetesMed`, `readmitted`
FROM `diabetes_dwh_staging`.`dataset_modified`
INTO OUTFILE 'D:/data_set.csv'
FIELDS TERMINATED BY ',' ENCLOSED BY '"'
LINES TERMINATED BY '\r\n';

Now we can import this data set to Weka.

Name		Name	Last commit message	Last commit date
Latest commit History 51 Commits
data_cleansing		data_cleansing
data_loading		data_loading
data_mining		data_mining
data_transforming		data_transforming
dataset		dataset
dimensional_modeling		dimensional_modeling
.gitignore		.gitignore
LICENSE.md		LICENSE.md
README.md		README.md
data_warehouse.mwb		data_warehouse.mwb
export_for_data_mining.sql		export_for_data_mining.sql
process.png		process.png
process.xml		process.xml
staging_area.mwb		staging_area.mwb

License

renuka-fernando/diabetes_data_warehouse

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