The Tree Viewer

You can show the Tree Viewer (which is not in the default layouts) with [Viewers] -> [Tree Viewer]. (Note that this component used to be called the DAG View.) The Tree Viewer displays all the possible paths to the currently selected term or terms:

This display shows a view of the ontology where every link that does not end in the selected term has been removed. Hence, every leaf in this tree is the currently selected term.

At the bottom left of the screen is a summary of the number of paths in the trimmed view. A path is a unique collection of links that leads from the selected term to the ontology root. In gthe example above, there are 6 paths to the root from "glycosome". Note that even if a term only has one parent, it may have multiple paths to the root if one of its ancestors has multiple parents. The sub-selection location is displayed in dark blue and all other locations of the term are shown in light blue. Right-clicking (alt-clicking on Mac) one of these light blue locations in the ontology will cause the sub-selection in the Ontology Tree Editor to be changed to the new location.

Configuring the Tree Viewer

To configure the Tree Viewer, press the wrech icon in the top right corner of the panel. A configuration window will appear:

Configuration options:

• Show paths to multiple selected terms- If this checkbox is unchecked, the Tree Viewer only displays paths to a single term (the current sub-selection). If this box is checked, the Tree Viewer will show paths to all the currently selected terms. Note that only the location of the primary sub-selected term in the Ontology Tree Editor will display in dark blue, all other terms will be in light blue.
• Show non-transitive paths - The Tree Viewer normally doesn't show paths that include non-transitive relationship types. If this box is selected, paths with non-transitive relationships will be shown. This often leads to a highly cluttered display, as in the following example.