The search field of KnetMiner allows users to input any terms related to traits of interest. The terms can be high level descriptions of a phenotypic trait (e.g. heat tolerance) or more specific terms such as biological processes and protein families (e.g. defence response to fungi or LRR). Search terms can be combined with; “OR”, “AND” & “NOT” statements, or put into double quotations for exact searches, i.e. “pathogen” AND “disease”.
Additionally, as the user types a query, the number of resulting documents and genes related to the query are shown and constantly updated in real time. This is only active once the query term is greater than 3 characters in length, updating at each keyboard event. This 1) helps the user to detect spelling mistakes, 2) gives a hint if the query term is too general, or too specific prior to the user executing the search, and 3) motivates the user to examine their query and explore different spelling, language, or more complex query statements (“OR”, “AND” & “NOT”).
After beginning to type a query, a hint icon appears at the right end side of the search box to indicate that alternative search terms are available. Click the hint icon to open a tab-based Concept Selector; click it again and it will close (Figure 1). The shown terms are derived from the underlying knowledge network. The Concept selector helps users to refine their keywords by suggesting more specific or synonymous terms. For example, using the Concept Selector on the term “drought” suggests other terms such as “drought sensitivity” or “drought recovery”. The wizard allows adding, replacing or excluding the new terms. The real-time messaging directly updates when the keywords change to indicate if the new terms would lead to a different number of linked genes.
Searching with keyword, gene list and/or genome regions
You can search KnetMiner with keywords, gene list or genome regions (or a combination thereof). KnetMiner will provide different types of responses based on the given inputs. The keyword search will search the whole genome while the other two search modes will be restricted to the specified gene list or genomic regions, respectively.
If you’re only joining in here, you will find it useful to use the sidebar to navigate and read more about Gene List and Genome Region searches.