How to Upload Data to TraceBase

This is a general introduction to the data submission process. For frequently asked specific questions, see the Uploading FAQ.

The submission process is designed to be as self-explanatory as possible.

To get started, click the upload button in the menu bar at the top of the page.

Note: uploading can be disabled, in which case there would be no upload option in the menu bar.

There are 4 tabs on the Upload Page that proceed from left to right:

Upon finishing any one page, you can leave and come back. Your work is saved in the downloaded Study Doc.

Step-by-Step Instructions

1. Start - Create a Study Doc

The simplest usage of the Study Doc template generation interface is to drop all of your peak annotation files using the drag and drop area and click "Download Template". The tool will automatically extract your samples and compounds and use them to pre-fill the downloaded Study Doc.

It creates a unique biological sample representative using the various sample headers spread across your various peak annotation files.

You can save yourself some time in the Fill In step by entering Mass Spec Run metadata associated with each peak annotation file.

For details on how best to leverage this feature, see 1 - How to Start an Upload.

2. Fill In - Enter data into the Study Doc using Excel

The "Fill In" tab contains specific pointers and tips on how to fill in data in the Study Doc (Excel spreadsheet). You can also find useful information in the header row comments, which will contain tips like the expected units, value format (e.g. date format), and a description of the values.

Generally, the process should be fairly self explanatory, and the validation page will ensure information is entered completely and correctly.

For some general tips to keep in mind that can ensure the process proceeds smoothly and for detailed information, see 2 - How To Fill In the Study Doc.

3. Validate - Check your Study doc for warnings and errors

Submit your filled-in study doc for validation.

It is not required for you to fix any reported issues, but pay particular attention to any warnings (displayed in yellow) because warnings are treated by curators as unnecessary fixes or are issues that are at the discretion of the researcher to resolve.

A curator will fix issues for you, but note that any efforts you make to fix errors will speed up the loading of your data, especially if the fixing of any error requires your domain knowledge.

After submission, a curator will keep a log of any changes they make for you to review and approve before the load.

As with the previous steps, the validation process is designed to be self explanatory, so feel free to jump right in and start validating. If you'd like to know more, check out the 3 - How to Validate a Study Doc page.

4. Submit - Organize your files and notify the curators

In short, compile all of your data in a shared drive and submit the short linked Google form.

Under the "Submit" tab, follow the directions on how to organize and where to deposit your data. Then click the "Submission Form" button and fill out the short Google form to let the curators know that your submission is done.

For details on organizing and submitting data, see 4 - How to Submit Data.

What happens next?

TraceBase curators will re-validate your study to ensure that everything will load smoothly. If there are any issues, you will be contacted to sort everything out. The study data will be loaded into TraceBase and you will be notified of the load completion via email so you can start browsing your data.

Contact us anytime if you would like to check in on the load status or if you have any questions, concerns, comments, or discover any post-load issues.