Pan-ReDU

Welcome to Pan-ReDU!

What is Pan-ReDU

Finding and reusing data is hard. ReDU aims to make that easier. ReDU is a community-focused approach to find and reuse public data containing mass spectrometric data at the repository scale. It is a collection of metadata from MetaboLights, Metabolomics Workbench, and GNPS/MassIVE within a single table with harmonized nomenclature. Our goal is to empower researchers to contextualize their data with public data and explore questions using repository-scale public data.

Components

There are three main components of Pan-ReDU to understand:

1. Understanding and navigating public metadata

   • The Pan-ReDU dashboard is available here. Documentation on navigating the dashboard can be found on the following pages.
   • Explanations of metadata categories can be found here.
   • Allowed terms for each category are available here.

2. Contributing public metadata

   • Tools for validating and submitting metadata are explained on the following pages.

3. Downloading raw data

   • Given a dataset accession id (e.g. MSV000083665, MTBLS284 or ST002962) download raw data file-by-file through the GNPS2 Dataset Explorer from any supported repository, as explained on the following pages.
   • Given a universal spectrum identifier (USI) (e.g. mzspec:MSV000083756:ccms_peak/Blank-3ACN-3IPA-2H2O_RE11_196.mzML) download raw data file-by-file through the GNPS Dashboard from any supported repository, as explained on the following pages.
   • Given a list of USIs download raw data in batch using our downloadpublicdata tool from any supported repository, as explained on the following pages.

Page Contributions

Yasin El Abiead (UCSD) and Mingxun Wang (UCR)