BioDB_SQL_API_Project

Biological database integration project combining R + SQL + APIs to unify annotations from Ensembl, UniProt, KEGG, and miRBase.

Objective

Build a reproducible mini data-integration pipeline that:

1. retrieves biological entities from major resources,
2. standardizes identifiers,
3. stores harmonized records in a relational schema,
4. supports downstream querying and interpretation.

Repository Contents

• BD_assignment.R — R workflow for API retrieval, transformation, and integration
• BD_assignment.sql — relational schema and SQL components
• BD_asignment.pdf — coursework/report documentation

Skills Demonstrated

• API-driven biological data ingestion
• relational schema design for bioinformatics entities
• R-to-SQL integration workflows
• reproducible scripting and data transformation logic

Core Tools

• R (httr, jsonlite, biomaRt, RMySQL, clusterProfiler)
• MySQL
• REST APIs (UniProt, KEGG; Ensembl access patterns)

Run Concept (high-level)

1. Configure database credentials in R script.
2. Execute data retrieval and mapping functions.
3. Persist mapped outputs into normalized SQL tables.
4. Validate integrated tables with SQL queries and summary checks.

Recruiter-facing Note

This project highlights real-world integration thinking: moving from fragmented biological sources to a queryable, analysis-ready data model.