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