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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

Before uploading a file to the CSSI DCC portal, consult the ISA-TAB specification

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. This specification describes 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
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 made for this purpose.

ISA-TAB files that you upload must be in .zip format. Use Globus to upload files larger than 10 GB.

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.
    The file is listed in the File Upload area and the status is listed as Ready.

...

If the file is smaller than 10 GB, click Upload selected files.
The file uploads and appears in the Investigation Projects section of the page. It is unpublished, so you must publish it to CSSI DCC.
Project with uploaded file processed successfullyImage Removed

Info

If the file is larger than 10 GB, use Globus instead.

Uploading with Globus

Globus is a service that enables large file transfers securely. You must have an account with Globus to use it to upload investigation files to CSSI DCC. If you do not already have an account, you will be prompted to create one.

To upload files using Globus

  1. Begin uploading by creating a project and selecting a file.

  2. Click Upload with Globus buttonImage Removed.
    If you have not yet logged into Globus, a log in page appears.
    Log in to use Globus web appImage Removed

    Info

    If you have trouble logging in, go to support.globus.org

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    or send an e-mail to support@globus.org.

     After you successfully log in, the Globus Transfer Files page appears.
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  3. Select the starting endpoint (on the left) where the file(s) you want to upload reside(s). Narrow down to the path if necessary.

  4. Select the destination endpoint (on the right).

  5. Click the arrow button to begin the transfer request.
    A message appears when the transfer request is submitted successfully.
    Image Removed

Validating the Upload

You may encounter an upload error. A sample error message follows:

Missing Data Files: File processed successfully. 1 files referenced in the assay(s) were not found. Click here to view the missing file lists (limited to 1000 entries each).

The CSSI DCC Portal validates uploaded ISA-TAB files using standards and conventions described in the ISA-TAB specification

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. The ISA tools site
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 provides additional technical information about validating ISA-TAB files.

Versioning ISA TAB Files

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

It is a best practice to associate only one investigation with a project. You can upload multiple versions of an ISA-TAB file to that project. You may want to do this if you change your investigation data or need to fix it due to an upload error. Each time you upload a new ISA TAB file to a project, the version number increases by one.

Publishing ISA-TAB Files to CSSI DCC

...

Click the Preview button next to that version.
The Publish Preview page appears.
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Review the uploaded file by exploring the investigation details. If you are satisfied with the content of this version, request its publication by clicking Publish this Version. If you are not satisfied or the upload generated an error, click Return to go back to your project and upload a new version of the ISA-TAB file.

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.

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