GEO uploader: simplifying the data deposition in the GEO repository

Area of Science:

• Genomics
• Bioinformatics
• Data Management

Background:

• Gene Expression Omnibus (GEO) submissions are complex, involving manual metadata preparation, FTP uploads, and MD5 validation.
• Current manual processes are time-consuming, error-prone, and demand significant bioinformatics expertise, hindering data sharing.

Purpose of the Study:

• To develop a user-friendly tool that automates the entire GEO submission workflow.
• To reduce the technical barriers and time required for researchers to submit their data to GEO.

Main Methods:

• Developed GEO Uploader, a web-based application with an intuitive interface.
• Implemented features for automated file uploads, MD5 calculations, and metadata template population.
• Included parallel processing, real-time progress tracking, and support for complex submission structures.

Main Results:

• GEO Uploader reduces submission initiation time from hours to under 20 seconds.
• Successfully deployed across 30+ users, handling 50+ upload sessions, including large datasets (>100 GB).
• Demonstrated practical utility and reliability in real-world research environments.

Conclusions:

• GEO Uploader significantly lowers the technical barrier for GEO submissions through comprehensive automation.
• Empowers researchers without specialized bioinformatics skills to independently submit data, enhancing data sharing.
• Promotes open science practices in genomics by improving accessibility to data sharing platforms.