Add Data to Your Narrative

Now that you are familiar with ways to find and explore data in KBase, you can select or upload data to analyze. Locate the Data Panel along the left side of the screen and click the Add Data button, the red “+” button, or the right arrow at the upper right of the panel to access the slideout Data Browser.

Any data that you upload to KBase is kept private unless you explicitly choose to share it. You can share any of your Narratives (including their associated data) with one or more specific users, or make it publicly available to all KBase users. Please see the Sharing page for more information about how to do that. The Terms and Conditions page describes the KBase data policy.

Let’s look closer at the five tabs of the Data Browser:

  • The My Data tab shows data objects that you have added to your project. You may need to refresh this tab to see your most recently added data.
  • The Shared With Me and Public tabs display datasets that others have loaded and made accessible to you (or to everyone). Data within each group is searchable and can be filtered. Since there are a large number of public datasets, you may wish to filter them by data type (using the pulldown selector on the left) or narrow the list by searching (in the “Search data” text box) for specific text in the data objects’ names.
  • The Example tab shows datasets that have been pre-loaded for use with particular apps. These can be handy for trying out the Narrative Interface.
  • Finally, the Import tab allows you to upload your own datasets for analysis. This capability is still under development. At the moment, it supports only a few data types (with more to be added soon).

Data available in KBase

If you hover your cursor over any data object under the first four tabs, options will appear allowing you to add that object to your Narrative or find out more about it.

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In the previous section, we described the process of adding a genome to your Narrative from the public data in KBase. Now let’s check out the different data types available under the Example tab. The icon to the left of each data object represents its data type.

 

As described in the previous section, the Add button next to these icons lets you add the data object to your Narrative. You can add more more data to your Narrative from the Example tab to try out various KBase apps.

Uploading data from external sources

Bulk Upload

Uploading large numbers of files, such as sequencing read sets, one at time through the Data Panel in the Narrative Interface can be time-consuming. To address this issue, KBase is expanding its data import functionality to support bulk upload of data, meaning that users can import multiple files simultaneously (or single very large files). Currently, KBase supports bulk upload of sequencing reads, genomes, and FASTA files through its bulk upload interface (accessible via the menu at the top left).

You can find out more about using the new (beta) Bulk Upload interface in the Bulk Upload Guide. The guide that you are currently looking at discusses how to upload data via the Narrative User interface.

You can use the Import tab in the Data Panel to upload certain types of data from outside sources or from your computer. The new Data Upload and Download Guide explains how you can add your own data of various types to your Narratives for analysis. As an example, let’s import a genome from GenBank.

Currently, you can import a genome into your Narrative by (1) uploading a GBK file stored locally on your computer or (2) importing a file from GenBank’s FTP site. This example will demonstrate the first option.

Under the Import tab, select Genome from the “Data Type” dropdown and then click Next.

You will be presented with a panel that has tabs called Upload GenBank File and Import from FTP. Make sure you have chosen the first tab and then click the blue Select file button to browse for a GenBank (GBK) file on your computer. Once you have located the file and see “100.0%” to its right,  type in a name for your genome object in the Genome Object ID field (being sure not to use any spaces or special characters in the name).

When completed properly, both required fields will have a green check mark next to them.

After entering the requested information, click the Import button at the bottom of the panel. A new Upload cell will open in your Narrative showing the progress of the import.

When the data has finished uploading, you should see the newly added genome in your Data Panel.

 

Close the Data Browser

When you’re done adding data objects to your Narrative, you’ll want to close the Data Browser slideout panel, since it covers part of your Narrative main panel. You can use the “Close” button at the lower right corner of the Data Browser, but if you have a small screen, you might not be able to see that button. Another way to close the Data Browser is to click the arrow on the top right of your Data Panel (the same one that opens the Data Browser slideout).

Coming Soon

KBase is rolling out new upload interfaces, including Bulk Upload (for large datasets), upload apps, and the ability to drag-and-drop data into your Narrative. We welcome your suggestions for future upload functionality, and bug reports on current uploaders.

Once you have added data–your own data or reference data that is already in KBase–to your Narrative, you will be ready for the exciting part: analyzing it! The next two sections describe how to choose and run an app to analyze your data.