Introduction to repository submission

Overview

Teaching: 5 min
Exercises: 0 min

Questions

• Why submit my data to a repository?

• What is data?

• How do I find a suitable repository?

Objectives

• Explain why data should be publicly available and what the term data means.

• Explain different types of repositories and how to find a suitable one.

Why submit your datasets to a repository?

Why should I share my data?

• Open Science & FAIR
• Reproducibility
• Trail of evidence
• 3rd party access
• Archival
• Publication of paper requires it

What is data?

There are different types of data

• Raw: straight from the instrument eg fastq, bam, cram
• Processed: normalization, removal of outliers, expression measurements, statistics
• Metadata: minimum information to reproduce the data, sample information, precise protocols

How to find a suitable repository

Types of repositories

• Domain specific:
  • Best choice if suitable, long-term plan, typically free of charge, maximum reach.
  • E.g. ENA, ArrayExpress, PRIDE
• General purpose:
  • Second best, long-term plan, might cost (now or in future), good reach but less specific in metadata → more difficult for future users to judge if a dataset will be useful
  • E.g. Zenodo, Figshare, Dryad
• In house/institutional
  • For archive/backup purpose mainly, might cost, limited reach unless also published in data catalogue

How find a domain specific repository?

• EBI wizard - guide depending on data type
• ELIXIR deposition databases - core resources with long-term data preservation and accessibility plans
• FAIRsharing.org/databases - catalogue of many repositories, with possibility to filter on e.g. domain.

Key Points

• Benefits of sharing data are several e.g. reproducibility purposes, follow the Open Science directive, meet requirement from publishers.

• There are different types of data e.g. raw, processed and metadata.

• If possible, use a domain-specific repository since it has maximum reach in the research community.