Bio BrowserPublic Space

Searching (screenshot)

Searching for caBIO domain objects is initiated by choosing the specific class of interest from the list within the search menu and entering search parameters in the resultant dialog.

• Good initial example: search for Genes with the gene symbol EPO.

Search Results (screenshot)

A search result will trigger changes in multiple places within the application, including:

• the status bar, which will report how many objects were found by the search;
• the tree view, which will present the results as an interactive tree;
• the document view that displays the underlying XML document.
  

Example, continued: The results of the EPO gene symbol search above can be seen in this screenshot.

Interactive Tree Navigation (screenshot)

The interactive tree contains different types of nodes differentiated by specific icons:

• Red circles: these nodes represent a specific instance of a domain model object returned by the search. Certain nodes (currently only Pathway objects) have context-sensitive menus. To access these menus, select the node and right click. The resulting menu contains operations specific to that object.
  
• Example: The Pathway context-sensitive menu contains an option to open a document containing its pathway diagram.
• Green arrows: these nodes represent relationships from the search result to other objects, or collections of objects. The node text describes the objects at the end of the relationship. Double clicking on these tree nodes will initiate a search for the related objects and the corresponding search result will overwrite the existing results.
  

Example, continued: See the navigation from an EPO gene to its related pathway collection, followed by the selection of a specific pathway and opening of a document containing the rendered pathway diagram, at screenshot.