Once an ontology is loaded, there are a number of ways to view it. The Ontology Tree Editor panel is the main view of the classes in your ontology.
See the "Component Toolbars" subsection of Components for explanations of the icons at the top of each Ontology Tree Editor panel.
Whenever OBO-Edit loads an ontology, the Ontology Tree Editor panel always contains three root nodes named "Classes", "Relations", and "Obsolete":
All of the classes (aka "terms") in your ontology are listed under the "Classes" nodes. Relations (aka relationship types) are listed under "Relations", and all obsolete objects (which may be classes, relations, or instances) will be listed under the Obsolete node.
These top level nodes do not represent objects in the ontology. They exist simply to help organize the display. You cannot select these top-level nodes or modify them in any way.
The Ontology Tree Editor panel displays the ontology as a tree. Branches of the tree can be expanded or collapsed, so that only a part of the tree is visible at any one time. The expand/collapse controls look like boxes containing a plus or minus sign:
If the expand/collapse control is marked with a plus, that means that there are other branches of the tree below, and clicking on the control will cause those branches to become visible. If the control is marked with a minus, it means that child branches are already visible, and clicking on the control will cause them to be collapsed. If a line in the display has no expand/collapse control (like "podosome" in the image above), it means that there are no branches beneath that node.
In the Ontology Tree Editor panel, "child" nodes appear beneath their "parent" nodes. Each node in the display represents a relationship between two terms. Consider this small piece of the display:
Here, "extracellular organelle" is beneath "organelle" and is indented to the right. This indicates that "extracellular organelle" is a child of organelle.
Each line of the display describes a relationship between a child term and its parents. The arrow is there as a reminder that these relationships are to be read from right-to-left. The symbol means that the relationship type is is_a, so the example above means:
extracellular organelle is_a organelle
We understand the relationships the same way if a node has multiple children:
The highlighed section means:
Relationship types are represented as icons that appear between a parent and child term:
A few icons for common relationship types are provided by OBO-Edit by default. (See the Configuration Manager for information on customizing these icons.)
Note that root classes, root relations, and obsolete terms do not have a relationship type where they connect to the root display nodes. For example, there is no relationship type icon between "biological process" and "Classes" in the above example. That is because relationship types only exist between entities in the ontology. Since the top level nodes are simply to organize the display, entities in the ontology have no named relationship to them.
Obsolete terms appear under the "Obsolete" node. Although obsolete terms cannot have parents or children, if an obsolete term has replacement or "consider" terms specified, they will appear underneath the obsolete term:
In this case, the view means that the obsolete term "2-nitropropane biosynthesis" has been replaced by "2-nitropropane metabolism". The obsolete "26S proteasome" does not have an exact replacement, but the term "proteasome complex" might be a valid replacement.
Note that "replaced by" and "consider" are not real relationship types. There is no relation named "replaced by" or "consider". These lines appear in the Ontology Tree Editor panel as a viewing convenience, but they do not represent real relationships in the ontology. They merely represent assignments to the OBO tags named "consider" and "replaced_by".
See Assigning Replacement Terms for more information about "consider" and "replaced_by".
You can display several Ontology Tree Editor panels at once (to learn how to add more Ontology Tree Editor panels to your interface, see the Components and Perspectives sections). If there is more than one Ontology Tree Editor panel, each panel can be independently set to global or local selection mode. In global selection mode, the Ontology Tree Editor will respond to external events in other panels (for example, clicking on search results), whereas in local selection mode it doesn't. Each panel that is in local selection mode may display a different section of the ontology, and may have a different term or collection of terms selected.
The selection mode can be toggled by the globe/house icon button in the titlebar. In the titlebar shown below, the globe icon (indicating that the panel is in global selection mode) is the fourth from the left.
When you're in local selection mode, you'll see the house icon instead of the globe, and the background of the Ontology Tree Editor will turn gray. By default, only one Ontology Tree Editor can be in global selection mode at a given time. This behavior can be controlled in the Configuration Manager.
Another way to prevent the OTE from changing when a new term is selected in a different window is with the "Lock View" command, available as a right-mouse menu option in the OTE. When you lock the view, the background of the OTE turns gray. You can unlock it with the "Unlock View" command.
Whether in global or local selection mode, panels may be filtered differently or may have different rendering settings. See Working with Selections for more information.
However, no matter how many Ontology Tree Editor panels are on screen, each is displaying a different view of the same ontology. Edits that are executed on one Ontology Tree Editor panel will affect the contents of all Ontology Tree Editor panels.
You can change the font used in this component via the "Font" tab in the Configuration Manager.
The Ontology Tree Editor panel isn't the only way to view an ontology. See The Tree Viewer, The Graph Viewer, The GraphViz Viewer and The Parent_Editor to learn more about other ways to look at your ontology.