Pan-ReDU Data Selection Dashboard User Guide¶

Welcome to the Pan-ReDU Dashboard! This guide will help you navigate the dashboard, filter data, download datasets, and utilize downstream tools for your metabolomics research.

Overview¶

The Pan-ReDU Dashboard is a comprehensive platform that aggregates metadata from public metabolomics repositories:

MetaboLights
Metabolomics Workbench
GNPS

By consolidating this data, the dashboard provides a unified interface for exploring and analyzing metabolomics datasets.

At the top of the dashboard, you'll find the navigation bar, which includes:

Pan-ReDU Logo: Click to return to the homepage.
Contribute Your Data: Link to submission page for your own metadata.
Pan-ReDU Dashboard - Documentation: Access detailed documentation about the dashboard.
Download Complete Pan-ReDU: Download the entire Pan-ReDU dataset.

Summary Statistics¶

On the left side of the dashboard, the Summary Statistics card provides quick insights:

Total Files: Number of files available.
Unique Datasets: Number of datasets.
Files by DataSource: Breakdown of files by their source repository.
Represented Taxonomies: Diversity of biological NCBI taxa represented.
Human/Mouse Data: Specific statistics for human and mouse samples (often of interest for biomedical studies).
Last Modified: Date when the dataset was last updated.

Filtering Data¶

Using Column Filters¶

Below the summary statistics, the main data table displays the dataset. Each column header includes a filter input:

Locate the Column Filter: Click on the filter input beneath the column name.
Enter Filter Criteria: Input your filter expression. You can use operators such as:
=: Equals (for numerical columns)
!=: Not equal (for numerical columns)
>: Greater than (for numerical columns)
<: Less than (for numerical columns)
>=: Greater than or equal to (for numerical columns)
<=: Less than or equal to (for numerical columns)
contains: Contains substring (for character columns; case-insensitive)
scontains: Contains substring (for character columns; case-sensitive)
Apply Multiple Filters: Combine filters using && (AND operator). For example:

Example: To find entries where "NCBITaxonomy" contains 'Homo sapiens' and "MassSpectrometer" contains 'Orbitrap':
```
{NCBITaxonomy} contains "Homo sapiens" && {MassSpectrometer} contains "Orbitrap"
```
Regular Expressions in Filters: Use regular expressions (regex) within the contains operator for complex filtering.

Example: To find entries where NCBITaxonomy contains either "Homo" or "Mus", but not "musculus":
```
{NCBITaxonomy} contains "(Homo|Mus)(?!.*musculus)"
```
Example: To find samples where UBERONBodyPartName contains "blood" and NCBITaxonomy contains "Rattus norvegicus":
```
{UBERONBodyPartName} contains "blood" && {NCBITaxonomy} contains "Rattus norvegicus"
```

Example Filters¶

The dashboard provides preset example filters for quick access. These filters are not meant to be exhaustive. For example, the Plant Samples filter will return all rows with value "plant" in the "SampleType" column rather than return all plant samples. For more complex filters (e.g., plant samples based on the NCBITaxonomy), download the whole dataset and do so locally or reach out to us:

Human Samples: Filters for samples from Homo sapiens.
Plant Samples: Shows samples categorized under plants.
Orbitrap Mass Spectrometer: Filters samples analyzed using an Orbitrap mass spectrometer (QExactive, Orbitrap, Astral substrings).
Homo sapiens and Mus but no Mus musculus: Advanced filter excluding Mus musculus.
Blood Samples from Rattus norvegicus: Filters for blood samples from Rattus norvegicus.

To use an example filter:

Click on the Filter Name: Under "Example Filters", click the desired filter button.
View Filtered Data: The data table will automatically update to reflect the filter.

Subset to mz(X)ML Files¶

To filter the table to only include files ending with .mzML or .mzXML:

Click "Subset Table to mz(X)ML files": This button is located under "Filter Table". Make sure the USI column is not toggled before clicking.
View Results: The data table will display only the relevant files while keeping your current filters.

Downloading Data¶

Download Filtered Data¶

After applying your filters, you can download the resulting dataset:

Click "ReDU Table": Located under "Download Filtered Subset".

USIs for Batch Processing/Download¶

Download USIs of filtered ReDU table which can be used for batch processing in various GNPS tools or raw data download.

Important Note:
This returns a TSV file: This link returns the USIs from your filtered selection in a TSV file.
How to Use:
Download Data: You'll download a TSV file with USIs of the filtered table. You can download raw data for those USIs in batch via the command-line tool. The tutorial for that tool can be found here and on the next pages of this documentation.
Batch Molecular Networking or MassQL search: You can paste downloaded USIs directly into the text fields of the workflows for MassQL or Molecular Networking. If you do not have a GNPS2 account yet, reach out to Prof. Mingxun Wang.

Download Complete Dataset¶

To download the entire ReDU dataset:

Click "Download Complete ReDU": Found in the navigation bar at the top.

Downstream Tooling¶

The dashboard offers direct links to tools for further analysis and data inspection:

View/Download Raw Data in Browser¶

View selected raw data files directly in your browser or download them to your PC.

Important Note:
Raw data download: If you wish to download raw data, scroll down to the 'File Summaries' section of the Dashboard.
How to Use:
Proceed to GNPS: You'll be redirected to the GNPS dashboard input page with the USIs already populated.

Molecular Networking/Library Matching¶

Generate Molecular Networks and molecule annotations for selected files.

Important Note:
Batch processing: If you wish to process more files than can be selected, download the (filtered) ReDU table, as described above, or the filtered USIs (via the "USIs for Batch Processing/Download" button) and copy the USIs directly into the text field of the workflow.
How to Use:
Proceed to GNPS: You'll be redirected to the GNPS workflow input page with the USIs already populated.

MassQL/Fragmentation Rule Search¶

Query mass spectrometry data using MassQL.

Important Note:
Batch processing: If you wish to process more files than can be selected, download the (filtered) ReDU table, as described above, or the filtered USIs (via the "USIs for Batch Processing/Download" button) and copy the USIs directly into the text field of the workflow.
How to Use:
Proceed to GNPS: You'll be taken to the MassQL workflow input page with the USIs already populated.