This document is part of a series related to the Data Submission to SPARC Process:
And with that, you’re ready to start preparing your metadata! Which means the time is finally nigh…Whether you’re preparing your metadata files using SODA guided mode or manually, you will need to follow these requirements:The next step in the process is to prep your metadata files. These required assets are descriptive files for your data, subjects, samples, etc., and will be submitted with your dataset.
This page will guide you through exactly what those files are. Please read through it fully, as it has requirements/guidelines you’ll need to know. Then, you’ll find two links to choose from for the preparation – one for SODA, and one for manual file formatting.
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- Temporary link to unpublished protocol has been added to Dataset_description file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!
To start, let’s talk about the SPARC Dataset Structure (SDS).
The SDS is the organizational file system required for all dataset submissions. This promotes consistency and ensures other investigators can easily understand your data. Part of that ease comes from the organization itself, and part of it comes from the metadata files incorporated in it.
If you use SODA guided mode for this step, it will guide you through the preparation of your metadata files and automatically organize them in the SDS format. If you choose to do it manually, you will fill out spreadsheet templates provided in our SDS zip folder, which can be downloaded here.
Either way, you will see multiple kinds of metadata files. So let’s talk about which ones are required.
Submissions to the SPARC Portal must include certain metadata files. Some are universally required, while others are only required if your data calls for it.
- Dataset_description - contains the study metadata to describe the dataset.
- Samples - contains information on the samples involved in the data collection.
- Subjects - contains information on the subjects involved in the data collection.
- Submission - contains information on the submission and related milestones.
- Performances - contains information on the performances, i.e. a run, session or execution of one type of experimental protocol.
- Resources – contains information on resources used in the data collection, such as reagents, equipment, nucleotide sequences, etc.
- README - contains an introduction and background for the dataset, may include how to open files, what special software/equipment is necessary to read the data, any suggestions as to how to use data, etc.
- Manifest* – required for every top-level folder and includes a brief description for every file in the folder.
Please note, Manifest Files are best created AFTER your top-level folders are organized, as they describe the contents of the folder. So don’t worry about completing those in this step – we will cover that in the “Organize Your Files” step.
Of course, it’s worth mentioning - SODA will automatically make the required manifest files and prompt you to add a description of each file in a systematic way if (when!) you upload through that platform. When you move files around using SODA the manifest will be updated automatically for you.
The following files are only required under certain parameters:
- Code_description – only required if code was used in the generation of the data.
- Code_parameters – only required if code was used in the generation of the data.
- Changes – only required if there’s necessary information on the history of the dataset or any changes to the dataset since an initial publication.
Whether you’re preparing your metadata files using SODA Guided Mode or manually, you will need to follow these requirements:
- Do not rename the key folders and files provided in the template folder.
- The Dataset_description template should not be changed at all.
- Do not add, edit, or delete required columns/rows.
- Blue and green fields are mandatory and should not be altered.
- Yellow fields are optional and can be altered.
- Do not change any column headings in any Excel file.
- To add additional metadata in the Subject and Sample files, please append new columns to the right side.
- Leave fields empty when there is no information available at the time of submission.
- Reference “Naming Conventions” section of Organize Your Files for naming requirements.
And with that, you’re ready to start preparing your metadata! Which means the time is finally nigh…
For you to use SODA! The moment we’ve all been waiting for. At the following link, you will find true joy in the form of documentation that walks you through preparing your metadata on SODA.
And once you’re done doing that, you can actually skip the next step of Organizing Your Files, because SODA Guided Mode will walk you through that step as well! So once you’ve prepped your metadata AND organized it and your experimental data into the appropriate folders, you can move on to the final step: Upload Your Data.
Be sure to check out that page for all last minute checks before Disseminating Your Data on SODA. See you soon friend.
A list of additional resources you may find useful while preparing your metadata:
- Should you have any questions or issues with the process:
- SPARC Optical Microscopy Imaging Data and Imaging Metadata Standard (1.0). Zenodo. https://doi.org/10.5281/zenodo.5347993.
- To read more about SDS, click here.
- Technical users can view the schema used to validate SDS here.
- More info about each metadata file can be found here.
- For Tools and General Resources on SPARC, click here.
Finished prepping your metadata? The next step then is to BRUSH YOUR SHOULDERS OFF! Because it’s always good to celebrate a win.
And now, it’s time to Organize Your Files, which you can start by clicking right here.
Updated 7 months ago