Web App To Quickly Know Proteins Associated With Diseases

Business Case

The scientists in our company (customers) require a web application to view protein, gene and disease information as well as generate customized reports.

This information is otherwise retrieved manually from multiple resources specified below.

Focus

prod_p2p is a web application that provides this information and allows to generate customized reports. I developed this web application by engineering a MySQL database from the below data sources and utilizing PHP, HTML & CSS.

Data Sources

• The Universal Protein Resource (UniProt)
• HUGO Gene Nomenclature Committee at the European Bioinformatics Institute (HGNC)
• Online Mendelian Inheritance in Man (OMIM)
• Disease Ontology (DO)

I selected a few diseases and utilized the associated protein and gene data. All data belongs to these entities.

Process

• Noted business requirements in detail (iterative process)

• Collected data from the 4 data sources

• Performed Data Modeling

  • Conceptual Data Model
  • Logical Data Model
  • Physical Data Models

• Applied Data Normalization

  • First Normal Form
  • Second Normal Form
  • Third Normal Form

• Engineered a MySQL Database

  • Transformed & Loaded Data (local .csv to MySQL database)
  • Validated foreign keys among tables & created SQL Views
  • Built custom Functions & Stored Procedures to include in reports

• Optimized MySQL Performance

  • Database structure
  • SQL statements

• Developed the Website

  • PHP
  • HTML & CSS

Home Page

Entity-Relationship Diagram

Implementation

Tools

Browser       Chrome or any other
Servers       Web server, database server, PHP server
XAMPP         5.6.32/PHP 5.6.32 or newer
MySQL         MySQL Workbench
Text Editor   VS Code or any other

Deployment

Instructions to successfully deploy my web application:

• Run Apache server and MySQL server on XAMPP
• Unzip webapp_p2p.zip contents into htdocs sub-folder within the installed xampp folder
• Launch MySQL Workbench and create a DBA user by running the following code in MySQL Workbench:

-- username: DBAuser & password: Xampp64097
CREATE USER 'DBAuser'@'localhost' IDENTIFIED BY 'Xampp640697';

-- to use custom username & password: change content in DbConnection.php file using a text editor

-- grant database administrator privileges to the created DBAuser
GRANT ALL PRIVILEGES ON * . * TO 'DBAuser'@'localhost';

• Open the script prod_p2p_bk from the contents of the unzipped folder
• Run the script on MySQL Workbench to import the prod_p2p database
• The restored prod_p2p database has views, functions and stored procedures required to generate reports from the web application
• To check if the database is properly connected open: http://localhost/webapp_p2p/DbConnection.php
• A successful deployment of the database shows a blank screen as below:

• If you do not see a blank screen:

  • Open the DbConnection.php file from the contents of the unzipped folder
  • Verify if details such as username & password are correct

• If you see a blank screen:

  • visit the home page: http://localhost/webapp_p2p/ProjectPresentation.php
  • use other aspects of my web application

Reports

Report 1: Gene Details

Report 2: Protein Synonym Information

Reports 3 to 6: Protein, Disease & Database data reports

App Documentation

I included further details about data set, deployment & usage instructions, practical applications and future work here.

Connect With Me

Prakash Dontaraju LinkedIn Twitter Medium