Using the old import tab

Looking for documentation about the NEW import tab?

The new (early 2018) Import tab lets you drag & drop data from your computer into your Staging Area to import into your Narrative. This page describes the old Import tab, which will be retired some time in early 2018. You can find documentation about the new Import tab here.

If you prefer the OLD Import tab in the Data Panel, you can use it to upload certain types of data from outside sources or from your computer.

In the Old Import tab, use the pulldown list under “DATA TYPE” to choose the data type you want to upload (and then click the “Next” button). Be sure to provide information for all of the required fields for importing a given data type. Required fields are marked by a red arrow to the right of the field. Once a required field has been satisfactorily filled in, a green check mark will appear in the place of the red arrow. Note that some fields have additional information that can be seen by hovering over the “i” to the right of the short description:

Importing a GenBank genome file

As an example, let’s import a genome from GenBank. 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 OLD 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.

Importing a FASTA formatted assembly file from your computer

For this example, we will use an Escherichia coli K12 MG1655 assembly file from NCBI as the source:

After downloading and unzipping the file, navigate to the Import tab in the Data Browser to perform the following steps.

  • Choose Assembly from the data type dropdown menu
  • Click the Next button
  • Select the UPLOAD FROM FASTA FILE tab
  • Select a FASTA file from a directory on your computer
  • Provide a name for the Assembly data object
  • Click the Import button; a cell will appear in the Narrative showing the import status
  • After the import process has completed, an Assembly object will be generated and appear in your Data Panel

Importing from FTP

Another way to import assembly files is by specifying a FTP or HTTP link. For this example, we will import the the same Escherichia coli K12 MG1655 as in the example above using the FTP importer.

Before following the steps below, right click and select “Copy Link Address” on this FTP link for the Escherichia coli K12 MG1655 assembly.

  • Choose Assembly from the data type dropdown menu
  • Click the Next button
  • Select the IMPORT FROM FTP tab
  • Copy and paste the FTP link for the desired FASTA file into the “FTP File” field
  • Provide a name for the Assembly data object
  • Click the Import button; a cell will appear in the Narrative showing the import status
  • After the import process has completed, the Assembly object will appear in your Data Panel

 
Please see the Data Upload and Download Guide for more detailed instructions about uploading different types of data to KBase.

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).

Looking for documentation about the NEW import tab?

The new (early 2018) Import tab lets you drag & drop data from your computer into your Staging Area to import into your Narrative. This page describes the old Import tab, which will be retired some time in early 2018. You can find documentation about the new Import tab here.