Data Submission Walkthrough Intro

Learn about the requirements and steps to submit a dataset to the SPARC Portal

Welcome!

SPARC is an open data repository specializing in hosting and publishing multi-modal FAIR data on the peripheral nervous system and its CNS-end organ interactions.

Before getting started, please contact our curation team at [email protected] to ensure this is a good home for your data and to learn about the specific requirements for your data type. They will be your number-one resource throughout this process!


This document is part of a series related to the Data Submission to SPARC Process:

Getting Started

In the next few pages, we will walk you through every step of submitting your data.

But first, there are some important things you need to know. Please read this section thoroughly, as we can assure you it will save you much time and effort! Trust us – it’s worth it.

General Requirements

One of the value propositions for SPARC is that we curate data to a consistent set of standards to make it easier to browse, search and reuse. As such, there are some general requirements that you will need to keep in mind when submitting your dataset. Don’t worry, we have tools and humans to help you prepare your data for SPARC submission.

  • Datasets are required to follow the SPARC Data Structure (SDS), a standard for organizing and naming your data files.
  • SPARC requires your data to be accompanied by an experimental protocol publication with a corresponding Digital Object Identifier (DOI).
  • Projects funded by specific funding programs may have certain requirements - please contact the curation team to determine if this is true for your project.

SODA (Software to Organize Data Automatically) for SPARC

Throughout this walkthrough we will mention SODA frequently. SODA for SPARC is a free desktop software that will greatly simplify and expedite the data submission process. Case in point - there are four main steps in the submission process. SODA helps automate three of the four.

Sound too good to be true? It isn’t! So download it here before we get started. We’ll discuss how to use it in the subsequent pages.

A few more things about SODA:

  • It guides you through organizing data files according to the required SPARC Data Structure (SDS).
  • It automatically prepares required manifest files.
  • It uploads all your files to Pennsieve.
    • You’ll need this agent – just ignore the deprecation warning.
  • It helps you reinitiate the upload should it terminate unexpectedly, as may often happen with large datasets.
    • SODA does all checks of file integrity for you to get the upload back on track.

Pennsieve

You will be using the Pennsieve Data Management platform, managed by DAT-Core, to submit your dataset to the SPARC PORTAL. Fill out this Pennsieve Account Request form to request access to the correct workspace, such as the SPARC or RE-JOIN, and set up your account. We recommend doing that ASAP (i.e. now?) so you can have the access when you’re ready to submit.

For help with gaining access to these workspaces or setting up your Pennsieve account, contact [email protected].

Protocols.io

All datasets published on the SPARC Portal must have a published protocol with an associated Digital Object Identifier (DOI). We recommend using Protocols.io for this, as it will create the DOI for you.

A DOI makes your protocols citable, traceable, and reproducible. And, the protocol can be updated, which means it’s automatically updated in any publication citing it..


The Data Submission Process

So, assuming you’ve already spoken with the Curation Team… let’s get started!

Below, you will find the four chronological Steps of the process, with links that will lead you to separate pages. We highly recommend following these in order, as they will walk you through the completion of each step.

And while SODA automates a lot of this, we still recommend (highly!) referring to each page below, as they have important requirements and guidelines. Speaking of recommendations - we’ll mention again - use our curation team as a resource every step of the way.

  1. Create Your Protocol
    1. You will create your experimental protocol on Protocols.io, then include a temporary link when you submit your dataset for review.
    2. After curation review of your dataset, you will officially publish your protocol on Protocols.io and share the designated DOI with the SPARC Curation team.
  2. Prepare Your Metadata Files
    1. Your dataset will be accompanied by metadata files, which are descriptive files for your dataset.
  3. Organize Your Files
    1. All your data, metadata and accompanying files will be organized into the SPARC Data Structure (SDS) - a filing system that must be used for all submitted datasets.
  4. Upload Your Data
    1. You will upload your dataset to Pennsieve, either using the SODA application or directly on the Pennsieve platform.

Checklist

As you move through this walkthrough, you will see the checklist at the beginning of every step. This is the list of every major requirement you need to have completed to publish your data.

We will highlight what should be done every step of the way. As you can see, before moving on from this intro page, you should have completed the first two requirements.

  • 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

Additional Resources

Every step of the way, we will hit you with additional resources that may help you complete each task at hand. And to start:

  • If you have any questions, please don’t hesitate to reach out to us:
  • For Tools and General Resources on SPARC, click here.
  • For those funded by SPARC, further info on SPARC Material Sharing Policies, click here.
  • For detailed instructions on how to use SODA for SPARC, click here (but we will cover this in the walkthrough).

Next Step

Ready to publish your data? Well first things first – PAT YOURSELF ON THE BACK. Because providing your data for other investigators to use is pretty cool in our book.

And once you’ve done that, it’s time to create your protocol. And you can start by clicking here!