Organize Your Files

Alright, so you’ve got your metadata, you’ve got your experimental data. And now, it’s time to get organized!

The SPARC Dataset Structure (SDS) is a required organizational system with required naming conventions to promote consistency and ease of use. So if you opted out of using SODA in the previous step, please read through this page thoroughly.

And, if you did use SODA for the metadata files, guess what?! You can skip this page, and move on to the final step. Because SODA will guide you through all the information below! Be sure to check that link before Disseminating Your Data, as it has some last minute checks for you!

If you will organize your datasets yourself, templates can be found on this page.

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Checklist

Open Checklist

But first, let’s check to make sure you’ve done everything up to this point:

• Talked to curation team
• Requested access to the appropriate Pennsieve workspace
• Experimental protocol has been created on Protocols.io
• All required metadata files have been completed
  • Temporary link to unpublished protocol has been added to dataset_description file
• All folders/metadata files are named as set forth in the SDS file system
• All subject & sample names are CONSISTENT across all references in the SDS
  • All human subjects have been de-identified
• All data, metadata and associated files/info have been organized into the SDS file system
• All experimental data has been organized by subject and sample in the Primary Folder
• All required top-level folders include required manifest files
• Dataset has been uploaded onto Pennsieve
• Verify the completeness of the upload
• Dataset has been submitted for review

Completed all the checked boxes? Continue onward!

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Organizing Your Files with SODA

Alright, if you used SODA (and are still here), then it’s time to go back, upload your experimental data, and confirm your folders! Then, before Disseminating Your Data, visit the Upload Your Data page for the final step. See you soon, friend.

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Organizing Your Files without SODA

If you did NOT use guided mode in SODA to create your metadata files, then you will need to organize your experimental data, and all accompanying files, into the appropriate folders of your downloaded SDS template.

Follow these steps to do just that:

1. Organize your experimental data in the Primary Folder by subject and sample, as discussed here.
2. Include any accompanying files that are required for your dataset (as discussed here) by putting them into the appropriate folder.
3. Create a manifest file for every top-level folder.
   1. if you’re using SODA, it automatically creates a list of files for a manifest during the upload. Hmm, another reason to use SODA…
   2. But, if you are uploading datasets manually, you will need to create this file yourself. In your SDS template, you will have a spreadsheet template for this. <!--
   3. just copy and paste this template into every folder you are sending, and fill it out according to the contents of that folder. -->

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Additional Resources

A list of additional resources you may find useful while organizing your files:

• If you have any questions, please don’t hesitate to reach out to us:
  • Zoom Office Hours (details here)
  • Email: [email protected]
• For further details about the SDS structure, feel free to refer to this page
• Technical users can view the schema used to validate SDS here.
• For Tools and General Resources on SPARC, click here.

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Next Step

Finished organizing your files? Then the next step is STAND UP AND FIST PUMP! Because you’re a legend, first and foremost. And second, because you’re ready to upload your data!

Which you can do by clicking right here!