To execute a keyword search, enter some text related to the data you are looking for. For example, try entering the keyword “arabidopsis” in the search box and click the search icon (the magnifying glass) or press Enter. This searches for your keyword across all categories of searchable data and returns the number of results found in each category (if any).
In this example, the search string “arabidopsis” matches some objects in three data categories, which are listed with a count of objects found.
Search Tip: OR vs. AND
If your search string includes multiple words (e.g., “Bacillus subtilis”), then by default the search will return all objects that have ANY of the words in any field. In other words, there is an implicit OR between “Bacillus” and “subtilis.” To find only the results that contain ALL the words in your search string, use the keyword AND: “Bacillus AND subtilis”, or surround the text you’re looking for with quotation marks to find only exact matches to that phrase (“Bacillus subtilis”, for example, would not match the text “Bacillus” or the text “subtilis Bacillus”).
Search results can be refined by the category of data and filtered according to taxonomic information, genome features, publication information, or type of biological model, depending on the data object type. Clicking on a category name will display a list of search results for that category. For example, notice the Genomes category contains four data objects for the “arabidopsis” query. Click on this category to view these genomes on the results page (see image below).
Key components of the search results page include:
- Summary table of results — Search results are listed in a table with several columns of information. The column headers vary depending on the data category. For Genomes, they are the Genome ID (a unique ID number assigned to each data object by KBase), Scientific Name, Domain, %GC (GC Content,) Contigs, Genes, and DNA Size. Each column can be sorted by clicking on the column header.
- Category navigation options — These options (shown on the left side below the header “Show Results for”) allow you to return to seeing all categories. Also, if subcategories exist for the data category you are exploring, those subcategories will appear here and are clickable, allowing you to move up or down in the category hierarchy. For instance, the Metabolic Models category has a subcategory for Flux Balance Analysis Models. A quick way to tell what category your results are in is by finding the green text in the category navigation options. In the screenshot above, notice that the word “Genomes” (under “Back to Any Category”) is green, meaning you are currently in the Genomes category.
- Filters — The results page for each data category has one or more filters that can be selected to refine the search results. Each type of filter can be expanded to show possible values for that filter type. Genomes, for example, can be filtered by taxonomy.
- Viewing options — There are two groups of buttons above the search results: “Views” and “Items per page.” The default number of results displayed per page is 10. You can increase this number to 25, 50, or 100 by clicking one of the “Items per page” buttons at the top right, a useful option when you have many search results and want to browse them quickly.
The Views buttons display results in either a compact view (default) or an expanded view with additional information in light blue boxes below each result (see image). To see the expanded view of the Arabidopsis genome results, click the second “Views” button. For the Genomes category, the additional information is the Taxonomy lineage for each organism.