Uploading investigation data to the CSSI DCC Portal allows you to curate, manage, and reuse datasets in a standards-compliant way. The ISA-Tab specification 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.
An ISA-Tab archive file is a compressed (.zip) file containing multiple text files and data files. Each tab-delimited text file in an ISA-Tab file 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. During registration, you must also select the I would like to upload Investigation data checkbox and be approved. For more information, refer to Registering to Use the CSSI DCC Portal.
You can upload a single ISA-Tab archive file and save it to a folder. If you need an administrator to delete an investigation version from a folder, click the Contact Us link at the bottom of the screen.
Uploading ISA-Tab Files
Uploading Large Files with Globus
Understanding Upload Errors
If your ISA archive does not meet those standards and conventions, you may encounter an error when you upload it to the CSSI DCC Portal. Your ISA archive will likely process successfully but the application will detail the error in the Status column. You may then want to address the error and upload again. A sample error message follows: CSSI DCC looks for errors in three types of files that are commonly in an ISA archive: After the upload completes, the error message appears in the Status column of the File Upload area on the Upload Single ISA Archive tab. It provides an overview of the error and a link to the details. Click the link in the status message. A page opens that details the status of the three types of files in the uploaded ISA archive. The Missing Files section details each missing data file referenced in the metadata of the assays: The Additional Files sections details files you uploaded that you didn't reference in the archive's metadata. The External File References section lists external file references in your uploaded archive and notes whether they are verified or not. If the portal can detect that the URL is valid without authenticating it, it appears in this list as “Verified.” In all other cases, it appears as “Not Verified.” File size is not tallied for external file references.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).
Controlling Access to Investigation Data
You must have the role of uploader or higher to control data access. Your administrator determines your role. When you assign access, you assign it to one or more groups rather than individual users, though a single group could contain a single user. Anyone with upload privileges can create and manage these groups, but you must create the group(s) before you upload. The following page family describes how to control access to investigation data.
Making an Investigation Open Access
Editing or Removing the Embargo Date for an Investigation
In the Comments field, provide any comments you want to associate with this request. Click Submit. The system changes the status of the investigation version to Request pending as of <date time>. An administrator processes your new request. When that administrator has approved your new request, the system changes the status of the investigation version (on the Upload ISA Archives page) back to Open Access approved, Embargoed. When system has made the investigation version open access, the system sends you an email notification with "CSSI DCC Portal Investigation Granted Open Access" as the subject line.