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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 specification
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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 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.
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 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. If you need an administrator to delete an investigation version from a project, click the Contact Us link at the bottom of the screen.
Uploading ISA-Tab Files
Before uploading a file to the CSSI DCC portal, consult the ISA-Tab specification
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ISA-Tab files that you upload must be in .zip format. Use Globus to upload files larger than 100 GB.
To upload ISA-Tab files
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Click New Project.
The Project Properties page appears.
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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. |
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Click Save Project.
The new project is listed under Investigation Projects.
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If the File Upload section of the page is not visible, click Open next to the project name to show it. |
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If needed now or later, click Edit to change the project name. Depending on your privileges, you may not see the Delete button. |
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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:
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.
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If the file is 100 GB or smaller, click Upload selected files. If the file is larger than 100 GB, use Globus instead.
The file begins processing and the status moves through the following stages:
- 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
Once an administrator approves the upload request, the uploaded file appears as a new project version in the Investigation Projects section of the page. It is not yet published, so you must now publish it to use it in CSSI DCC. For instructions on previewing and publishing it, refer to Publishing ISA-Tab Files to the CSSI DCC Portal.
Uploading Large Files with Globus
Globus is a service that enables large file transfers securely. You must have an account with Globus before you use it to upload investigation files to CSSI DCC. If you do not already have an account, you are prompted to create one when you start the upload process.
To upload files using Globus
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On the Upload ISA TAB Files page, click .
If you have not yet logged into Globus, a log in page appears.
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For more information about using Globus, consult their documentation
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After you successfully log in, the Globus Transfer Files page appears. One of the Endpoints you configured is already populated, though you can change it.
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Select the starting endpoint (on the left) where the file(s) you want to upload reside(s). Narrow down to the path if necessary.
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Confirm or change the destination endpoint (on the right).
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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Since you have not yet published the uploaded file, you must publish it to use it in CSSI DCC. For instructions on previewing and publishing it, refer to Publishing ISA-Tab Files to the CSSI DCC Portal.
Understanding Upload Errors
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Controlling Access to Investigation Data
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Publishing ISA-Tab Files to the CSSI DCC Portal
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Viewing Publish History
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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.
To unpublish an ISA-Tab file
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