Access the Search Page

There are two ways to access the reference data contained in KBase. You can search KBase data even if you are not logged in through a KBase account. However, unless you are logged in you will not be able to save the results of your searches and transfer them to the Narrative Interface for analysis. From the kbase.us home page, locate the “Data & Tools” dropdown menu and select “Search Reference Data.” This option works even if you do not have a KBase account.

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Registered KBase users can also access the Data Search interface from the Narrative Interface via the “Search Data” menu option in the dropdown menu located in the top left corner.

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In this guide, we will assume that you have signed in to the Narrative Interface (narrative.kbase.us) with your KBase username and password. If you are not familiar with the Narrative Interface, you may wish to consult the Narrative Guide for an explanation of the major components, or the Narrative Quick Start for a quick overview.

When you access Data Search, it will conduct an initial query of all of the public data in KBase. After a few seconds you should see a short list of major data categories, each with a count showing how many data objects were found in that category. This represents a real-time query of all available reference data in KBase.

The Data Search tool will appear and conduct an initial query of the entire public data store.  After a few seconds you should see a short list of major data categories. This represents a real-time query of all available data.

Please note: This tool accesses public reference data that has been loaded into KBase. It does not yet include data uploaded by KBase users for use in Narratives, even if that data has been made publicly available.

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Key features of this page include:

  1. Search box — When you type a string (i.e., sequence of characters) into the search box and perform a search, you will get a list of all data objects found to have your search string in ANY field, such as “Scientific Name” or “Function.” The special wildcard symbol * (asterisk) represents any sequence of characters. For example, the search string *bac finds genome features for Rhodobacter sphaeroides and Bacillus subtilis, as well as data for Escherichia coli TW10509 and its associated WbaC protein.By default, an asterisk appears by itself in the search box, which matches all the searchable objects.
  2. Data categories — KBase currently has thousands of searchable metagenomes, genome features, genomes, and metabolic models. The number of data objects available for each category is listed in parentheses. Selecting one of these categories from the initial search page will display every data object in that category.
  3. Sign-in links — These links are located in the beige box at the left and also the top right corner. You will need to sign in if you want to copy your search results to a Narrative for further analysis. Once you sign in, you will see a Data Cart associated with your username on the left of the search page.

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