Much of the time, structural edits to your ontology will be accomplished via the Ontology Tree Editor panel:
Some components can also make structural changes to the ontology, but most of your day-to-day changes will be done here or in the Graph Editor.
Whenver you make a structural change in the ontology tree editor panel, that structural change operates on some collection of sources and targets. The sources are some collection of relationships (usually your current selection) and the target is a single link (often a link you've clicked or the final destination of a drag and drop gesture).
Some structural changes are only available with certain sources and targets. For example, the Delete operation has no target. The Merge operation is only available when there is a single source relationship and a target relationship has been specified. The Change Type drag and drop operation only works when there is a single source relationship, a target relationship has been defined, AND the child of the source relationship is a Property.
Some structural changes may be applied to several sources at once. For example, the Add child operation allows several relationships to be added at once.
The Delete operation behaves slightly differently with multiple sources: if any of the selected terms has children, it will not be deleted, and a message will pop up warning the user that the term(s) with children will not be deleted.
Drag and drop is the simplest, and most often used, editing method in OBO-Edit. To use drag and drop, first select the terms you would like to drag. This selection will be your source relationships. Click and drag your selection. A drag graphic will appear:
Drag the sources over your desired target relationship. When the sources are above a potential target, a yellow box will appear around the target:
When the mouse button is released, the sources will be dropped, and a menu of possible editing options will appear:
The menu of editing options will only contain options that make sense given the sources you dragged and the target you dropped onto.
To cancel a drag and drop operation in mid-drag, drop the sources onto an empty part of the screen (make sure no target is highlighted). To dismiss the drag and drop popup menu, click somewhere on the screen other than the menu (on some platforms, the drag and drop menu is automatically dismissed when the mouse is moved off the menu).
Not all editing operations are available via drag-and-drop (for example, adding new terms and deleting terms can only be achieved via menu-based editing methods - see below).
When a panel is focused, you can press a hotkey to assign a "drag mode". This allows you to edit faster, without having to see additional popup menus when you drop your selection. The hotkeys are:
Command+X Move
Command+C Copy
Command+Shift+M Merge
Command+D Default mode
When you press a hotkey, a dropdown box appears showing the current drag mode, and allowing you to pick a different drag mode with the mouse if you wish. The dropdown box appears at the top of the panel by default, but you can drag it to the bottom or either side if you prefer.
The Move and Copy drag modes display a special popup menu of relationship types when you complete the drag and drop operation. See the details for individual editing operations for further details.
By default, when you complete an editing operation, the drag mode reverts back to default mode. This behavior is configurable in the configuration screen - you can decide when the hotkey dropdown is visible (always, never, or "on hotkey"), and you can decide whether to revert back to the default drag mode when an editing operation is complete.
Editing operations can also be done by bringing up a right-click menu. The right-click menu is displayed by right-clicking (or command-clicking on MacOS) the mouse.
The currently selected relationships are used as the sources for the editing operation. If you right-click a certain term, that term is used as the target for the editing operation.
The right-click menu will display all the currently available editing operations. If an operation cannot be performed on the current target or sources, the operation will be grayed out. The right-click menu contains more than just editing operations; the right-click menu also allows you to configure display options for the current ontology tree editor panel.
The edit menu is available on the main OBO-Edit menu bar:
When using the edit menu, the currently selected relationships are used as the sources. It is not possible to select a target with the edit menu. As a result, all operations that require a target will be grayed out on the edit menu.