How to Contribute to ReDU

Required Items

> Data (.mzXML or .mzML) uploaded to MassIVE and made public
> ReDU-compliant sample information uploaded to corresponding MassIVE accession

Step-by-step Instructions

Step 1 - Data

1A - Convert to Open-Source File Formats

1B - Upload Data to GNPS/MassIVE and Create a MassIVE ID

  • Data can be uploaded to MassIVE or GNPS using a FTP client. A free account is necessary.
  • Launch the "Submit your data" workflow (MassIVE) to create a MassIVE ID
  • The title must beginning with "GNPS - "
  • We encourage the upload of vendor-specific raw data, e.g. .raw (Thermo) and .d (Bruker and Agilent), in addition to open-source file formats (.mzXML, .mzML, or .mgf).
  • You will receive an email when the workflow has completed.
  • Details on dataset creation can be found here.

1C - Prepare the MassIVE ID

  • The MassIVE ID must be made publicly avaliable by clicking the "make public" button.
  • Please click the "convert spectra" button to expedite inclusion in ReDU.

Step 2 - Sample Information

2A - Make a copy of the Sample Information Template

  • Navigate to the ReDU Sample Information Template
  • One template is required per MassIVE ID.
  • Save a copy of the sample information template by going to "File - Make a copy" into a personal google drive

Sample Template_Copy

2B - Fill the Sample Information Template

  • Fill in sample information using drop-downs when applicable (grey columns at the end of the template are automatically entered using formulae).
  • It is highly recommended to fill the template in Google Sheets to ensure validation.
  • When copying and pasting from another spreadsheet, please copy + special paste so as to not chance the cell formulae or formatting.
  • ReDU uses a controlled vocublary - the accepted terms are listed in the "ReDUMS2_controlled_vocabulary" tab per column. If you require terms that are not avaliable, please raise an issue on GitHub.

Sample Template_Fill

2C - Download the Sample Information Template

  • When complete, delete all extra rows of the template.
  • Download from Google Sheets as a tab separated text file using "File-Download as" and selecting "Tab-seperated values..."

Sample Template_DeleteRows

Step 3 - Validation

3A - Validate your Sample Information File

  • Navigate to the ReDU Sample Information Validator
  • Drag-and-drop or select your sample information file into the validator.
  • A message will indicate if the files passes or not.
  • Non-adherant information is displayed in the "Sample Information Validation Errors" panel - the row, column, and the accepted terms are listed.
  • If errors occur, then please correct the non-adherant information in the template and repeat from 2C

Sample Validate

3B - Rename the Sample Information File

  • Upon passing the validator, rename the file to be exactly "gnps_metadata.tsv"
  • The filename must be gnps_metadata.tsv - this step is critical
  • It is suggested to make a seperate directory on your computer to store each MassIVE IDs sample information template

Step 4 - Upload the validated Sample Information file named "gnps_metadata.tsv"

  • Navigate to the MassIVE ID created
  • Click on the "add files" button
  • Use the Drag-and-Drop upload option to add the validated sample information file named "gnps_metadata.tsv"
  • Place the validated sample information file into the "Supplementary file" folder and submit the update

That is it! Double check that your data make it into the ReDU file selector.

Notes

  • GNPS/MassIVE is search multiple times per day to find new or updated sample information files so it may take some time for your data to appear.
  • If corrections or updates are necessary, please make them accordingly and upload the new validated sample information file named "gnps_metadata.tsv". ReDU will automatically import the most recent version of the "gnps_metadata.tsv" file (files cannot be deleted by users from MassIVE).
  • Any conflict between identically named files will result in their exclusion.
  • The filename in the sample information file must match the data uploaded to MassIVE (.mzML or .mzXML) - we do not support vendor-specific formats.