From Platform to Repository

About This Lesson

FAIR principle A1 states that data should be retrievable by its identifier using a standardised protocol. In practice, this means depositing your data in a recognised public repository where it gets a persistent identifier (DOI or accession number) and is discoverable by the global research community.

This lesson covers the journey from platform to repository. You will learn how the platform's RO-Crate packaging, FAIR score assessment, and export tools help you prepare data for deposition in repositories like the European Nucleotide Archive (ENA), Gene Expression Omnibus (GEO), and Zenodo.

What You'll Learn

• Why public repository deposition matters (funder mandates, journal requirements, discoverability)
• How RO-Crate packages your analysis results with full provenance metadata automatically
• How to use the FAIR score card to identify gaps before submission
• How to export data for repository submission (CSV, ZIP, RO-Crate)
• Which repositories to use: SRA/ENA for sequencing reads, GEO for expression data, Zenodo for general research outputs
• How to link repository accession numbers back to the platform for complete traceability

Key Concepts

• RO-Crate: A Research Object Crate — a standardised package that bundles your data, metadata, and provenance into a single, portable unit. Every completed analysis run generates one automatically.
• FAIR Score: A per-investigation assessment that scores your data across the four FAIR dimensions (Findable, Accessible, Interoperable, Reusable) and suggests improvements.
• Persistent Identifier: A DOI, accession number, or other identifier that will resolve to your data permanently, even if URLs change.
• Accession number: An identifier assigned by a repository (e.g. PRJNA123456 from SRA, GSE12345 from GEO) that uniquely identifies your deposited dataset.