The Ontology Editor Panel

Once an ontology is loaded, there are a number of ways to view it. The ontology editor panel is the main view of the classes in your ontology.

Top Level Nodes

Whenever OBO-Edit loads an ontology, the ontology editor panel always contains three root nodes named "Classes", "Relations", and "Obsolete":

All of the classes (aka "terms") in your ontology are listed beneath the "Classes" nodes. Relations (aka relationship types) are listed beneath "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.

Expanding/Collapsing Nodes

The ontology 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 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 "cellular component unknown" in the image above), it means that there are no branches beneath that node.

Representing Relationships

The ontology editor panel displays the ontology as a tree, with "child" nodes appearing 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

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 Plugin for information on customizing these icons.)

Note that root classes, root relations, and obsolete terms do not have a relationship type where the 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.

Viewing Obsoletes

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-nitroproppane metabolism". The obsolete "26S proteasome" does not have an exact replacement, but the, depending on context, one of the terms "proteasome complex (sensu Eukaryota)", "proteasome core complex (sensu Bacteria)" and "proteasome regulatory particle (sensu Bacteria)" 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 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".

Working with Multiple ontology editor panels

There can be several ontology editor panels on screen at once (to learn how to add more ontology editor panels to your interface, see the "Display Controls" section below and the Customizing the Interface section).

If there is more than one ontology editor panel, each panel's display is entirely independent. Each panel may display a different section of the ontology, may be filtered differently, may have different rendering settings, and may have a different collection of terms selected (kind of - see Working with Selections for a clarification).

However, no matter how many ontology editor panels are on screen, each is displaying a different view of the same ontology. Edits that are executed on one ontology editor panel will affect the contents of all ontology editor panels.

Display Controls

There are a number of buttons at the bottom of each ontology editor panel:

Note that many of these display options can also be modified via the ontology editor panel right-click menu. Right-click (or command-click on MacOS) within the ontology editor panel to bring up the right-click menu.

Other Views of the Ontology

The ontology editor panel isn't the only way to view an ontology. See The DAG Viewer, The Graph Viewer Plugin and The Parent Plugin to learn more about other ways to look at your ontology.