🧬 BioDB_SQL_API_Project

This repository contains the Biological Database Integration Project developed as part of MSc Bioinformatics coursework.
It demonstrates the integration of multiple biological data sources — Ensembl, UniProt, KEGG, and miRBase — using a combination of R scripts and SQL relational design.

---

📂 Repository Contents

File	Description
BD_assignment.pdf	Project report documenting the R–SQL integration workflow, methodology, and results.
BD_assignment.R	Main R script performing data retrieval and integration using REST APIs, BioMart, and MySQL.
BD_assignment.sql	MySQL schema defining the relational structure for genes, proteins, pathways, and miRNAs.

---

⚙️ Overview

The project builds an automated data pipeline to:

1. Retrieve gene and protein data from Ensembl and UniProt via API.
2. Map KEGG pathways and perform functional enrichment using clusterProfiler.
3. Integrate miRNA information from miRBase.
4. Store all data in a structured MySQL database for downstream querying and analysis.

---

🧩 Key Technologies

• R – for scripting, data retrieval, and enrichment analysis
• MySQL – for database design and relational integration
• REST APIs – for accessing UniProt and KEGG resources
• biomaRt, RMySQL, httr, jsonlite, clusterProfiler – main R packages used

---

🧠 Learning Outcomes

• Designing relational schemas for biological data
• Accessing bioinformatics APIs programmatically
• Integrating heterogeneous biological datasets
• Applying R-based functional and pathway analysis
• Bridging R dataframes and SQL tables

---

📊 Database Schema Summary

Tables included:

• gene_annotations – Ensembl gene information
• kegg_data – KEGG pathway enrichment results
• mirna_data – miRNA mapping
• summary – combined relational table joining all datasets