Uploading Data

KBase includes an extensive collection of data imported from various public sources; it also offers the ability to upload your own data for analysis. Please refer to this section of the Narrative Interface User Guide for general information about loading data into your Narratives. This Data Guide focuses on the details of how to upload specific types of data.

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.

The first step in uploading your data is to locate the Data Panel along the left side of the Narrative Interface window and click either the “Add Data” button, the red “+” button, or the right arrow at the upper right of the panel to access the slideout Data Browser. The Data Browser has several tabs that allow you to access data already in KBase, as well as the “Import” tab for importing your own data. 

Import Data

In the Import tab, use the pulldown list under “DATA TYPE” to choose the data type you want to upload (and then click the “Next” button). The following data types can be uploaded into KBase with the specified file extensions.

Note: the “.txt” file extension is not currently recognized by any of the uploaders. If you download a data file from another site (for example, a sequence file from GenBank), it may end up with an extra “.txt” extension (seqname.fna.txt, for example). You will need to remove that extension from the filename before trying to upload the file into KBase.

Data Type Available Upload Formats and Recognized File Extensions
Contigs FASTA (.fasta, .fna, .fa)
FBA Model SBML (.sbml, .xml) TSV (.tsv) EXCEL (.xls)
Genome GENBANK (.gbk, .gb, .genbank, .gbf, .gbff)
Media TSV (.tsv)
Short Reads FASTA (.fasta, .fna, .fa) FASTQ (.fastq, .fnq, .fq)
Transcript FASTA (.fasta, .fna, .fa)
Phenotype Set TSV (.tsv)
Expression Matrix TSV (.tsv or .tab)

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:

Upload

Once you have completed all of the required fields, click the Import button to begin the process of transferring your data into KBase. Notice that the status of the import job is displayed at the bottom of the window.

To close the Import panel and return to the Narrative Interface, simply click the “Close” button on the bottom right of the import panel. 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).

After you have successfully imported a data set and it appears in your Data Panel, you can import another data set by clicking the “Back” button in the Import panel and then repeating the upload instructions.

The next sections of this guide describe the specific steps involved in uploading the currently supported data types, and show examples for each type.

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 Narrative menu).

You can find out more about using the new (beta) Bulk Upload interface in the Bulk Upload Guide.