The GO Database View
When downloading the GO database, a new object called GO database (
) is created in the Navigation Area.
The GO Database element has a default hierarchical tree view (See figure 19.1). Here it is possible to search the different ontology terms, and see their relations.
It should be noted that the Gene Ontology is not a tree, but a directed acyclic graph - this means that a GO-term may have multiple parents, and thus appear different places in the tree view. Likewise, when searching for a specific GO-term, multiple locations in the tree might be highlighted, even though they refer to the same GO-term.
Figure 19.1: The GO Database View
In figure 19.2 an example of a search result is shown. Here, there are multiple GO terms matching the search query 'carbon'. The Previous and Next buttons can be used to navigate to the matching GO terms. Notice, that this particular GO-term (GO:0106148) is shown multiple times in the tree ('23 instances in tree'). In order to view the different locations in the tree for a matching GO-term, the arrow buttons at the bottom of the view can be used to focus on the different selected elements (see figure 19.3) - note, that this does not change the selection, it only changes the focused area of the tree.
Figure 19.2: Searching for GO terms.
Figure 19.3: Scrolling through different selected items in the GO view.
The Filter sidepanel section, can be used to restrict to the view to various subsets of the full database ("Slim" subsets). It is also possible to restrict the tree to only the terms that are currently selected.
When clicking on a GO term, the Property viewer in the side panel will show the description, relations, synonyms, and all related links.
It is possible to Select Names in Other Views and Copy Names to Clipboard (see figure 19.3). Selecting names in other views will match names in other editors that support this - currently, this is only supported in the Differential Abundance element view.