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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 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, see Uploading and Publishing Investigation Data.
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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
- Log in to the CSSI DCC Portal.
- Select Investigations > Upload.
The Upload ISA TAB Files page appears.
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.
- Enter a title for your new project. Note that this title and that of the ISA-Tab file that the project contains can be different.
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 title Changing the Project Name 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:
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. If the file is larger than 10 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, unpublished file appears 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.
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To view the publish history of an investigation file
- Browse or search for an investigation.
The Investigation Details page appears.
- Click History to show the timeline.
- The current version number appears above the timeline. You can hover over the version number to see the date when this version became the current version. In this example, Version 1 became current on 6/9/2017.
When a file has multiple versions, they appear on the timeline as well. The version that is currently selected is always green. In the example below, the current version is selected, so it appears in green. The current version is also open-ended to the future until you publish another version.
Info The white space between versions, as in the example below, indicate times when no version of the investigation file was published.
- To select a previous version, hover the mouse over the timeline. If the version you want to select is not immediately visible, move the scroll wheel on the mouse down to move left and up to move right until you see a previous version. In this example, a previous version was current only on 6/22/2017.
- Click the previous version to select it. The Investigation Details page appears, showing the selected version number at the top. You can download the full data or selected metadata of this previous version. You cannot download selected data of a previous version.
- The current version number appears above the timeline. You can hover over the version number to see the date when this version became the current version. In this example, Version 1 became current on 6/9/2017.
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