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titleContents of this Page
Table of Contents

Uploading investigation data to the CSSI DCC Portal allows you to curate, manage, and reuse datasets in a standards-compliant way. The ISA-TAB Tab specification

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describes this standard and how to structure your investigation data to create an Investigation-Study-Assay tab-delimited (ISA-TAB) archive file. This may involve configuring it using open-source software made for this purpose: http://isa-tools.org/ software
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 made for this purpose.

An ISA -TAB archive file is a compressed (.ZIPzip) file containing multiple text files and data files. Each tab-delimited text file in an ISA -TAB file archive describes the structure, meaning the column headers and row values when considered in spreadsheet format, of the investigation, study, and assay components of the archive. The data files correspond to each assay and are included in the archive in their native format, for example, Microsoft Excel. An ISA -TAB archive file may also contain images and other files.

Only users who have registered for and logged in to the CSSI DCC Portal can upload investigation data. 

Registering to Use the CSSI DCC Portal

Before you can log in for the first time, you must register.

To register on the CSSI DCC Portal

  1. Navigate to the CSSI DCC Portal.
    The home page appears.
    Image Removed
  2. Click Login.
    The Please Sign In page appears.
    Image Removed
  3. Click Register.
    The Registration page appears.
    Image Removed
  4. Provide information in all of the following required fields:
    • First name
    • Last name
    • Institution
    • Email address
    • Password
    • Confirm password
  5. If you want to upload investigation data to the CSSI DCC portal in the future, select the I would like to upload investigation data box. Doing so ensures that your future submissions are correctly tracked.
  6. Select the I'm not a robot box.
  7. Click Register.
    A message box appears.
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  8. Check your inbox for an email with the subject line "CSSI DCC Account Activation." Click the link in the email to complete account activation.
  9. Get started using the CSSI DCC Portal.

Logging In to the CSSI DCC Portal

Before you can upload investigation data, you must register and then log in.

You do not need to log in to browse, search, and download investigation data.

To log in to the CSSI DCC Portal

  1. Navigate to the CSSI DCC Portal.
    The home page appears.
    Image Removed
  2. Click Login.
    The Please Sign In page appears.
    Image Removed
  3. Enter your email address and password you specified when you registered.
  4. Click Sign In.
    The CSSI DCC Portal home page appears.

Uploading ISA-TAB Files

Note

Files that you upload to the portal must be in one of the following archive formats: .zip, .rar, .tar, or .gz. Each file must be no larger than 500 MB.

Also, before uploading files <ask about preparation, verification>

To upload ISA-TAB files

...

Click New Project.
The Project Properties page appears.

Info

A project is simply a container for the ISA-TAB file. It allows you to track multiple versions of ISA-TAB file uploads to this project.

It is a best practice for each investigation to have its own project.

...

Click Save Project.
The new project is listed under Investigation Projects.

Info

If the File Upload section of the page is not visible, click Open next to the project name to show it.

...

Info

If needed now or later, click Edit to change the project name. Depending on your privileges, you may not see the Delete button.

...

Select the file you want to upload to this project in one of the following ways:

  • Drag and drop the ISA-TAB archive file from your computer to the Drop your files here box surrounded by the dashed lines:
    Drop your files here or click to browseImage Removed

  • Click the Drop your files here box image and browse to where the file is stored.

    Info

    ISA-TAB files that you upload must be in .zip format. The file can be no larger than 20 GB.

...

  • Uploading
  •  Processing Queued  
  • Queued
  • Preparing uploaded files
  •  Parsing ISA TAB Metadata  
  • Preparing Data Files  
  • Validating assay files and file sizes  
  • File processed successfully  
  • Success: file processed successfully 

...

Refresh the page to see the new upload listed in the Investigation Projects section of the page.
 Project with uploaded file processed successfullyImage Removed

Info
titleVersioning ISA TAB Files

The first time you upload an ISA TAB file to a new project, it is the first version of that file.

While it is a best practice to associate only one investigation with a project, you can make changes to your investigation data, create a new ISA TAB file that reflects those changes, and then upload the new file to the original project. Each time you upload a new ISA TAB file to a project, the version number increases by one.

 You are now ready to publish the ISA-TAB file to CSSI DCC.

Publishing ISA-TAB Files to CSSI DCC

  1. Upload at least one ISA-TAB file to a project. 
  2. If you have uploaded multiple versions of the file to the project, decide which version of the ISA-TAB file you want to publish to CSSI DCC.  

  3. Click the Preview button next to that version.
    The Publish Preview page appears.
    Image Removed

  4. Review the uploaded file by exploring the investigation details.

Troubleshooting the Upload Process

...

Uploading investigation data requires a logged-in CSSI DCC user account with permission to upload. For details on requesting permission to upload data, refer to Managing Your Account. 

You can upload a single ISA archive and save it to a folder. If you need an administrator to delete an investigation version from a folder, contact the Center for Strategic Initiatives (CSSI) Data Coordinating Center (https://cssi-dcc.nci.nih.gov/cssiportal/contactus) or click the Contact Us link at the bottom of any DCC page.

The following page family describes how to upload investigation data and request open access for your uploaded data.

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Unpublishing ISA-Tab Files

After publishing a file, you may want to unpublish a version of it to remove that version completely from the CSSI DCC server.

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titleAccess Control and Unpublishing

When you unpublish a file, all access restrictions that may have been applied to it are removed from the investigation. If you decide to publish this investigation later, you must reapply any access restrictions you want.

To unpublish an ISA-Tab file

  1. Open a previously published file.
  2. Next to the version you want to unpublish, click Unpublish.
    The status of this version becomes Unpublication Request Pending. Once an administrator approves the request, the version returns to its unpublished state.