(The OBO-Edit Reasoner page discusses what a reasoner is.)
The reasoner is activated and deactivated via the Reasoner Manager. You can turn on the reasoner in OBO-Edit by showing the Reasoner Manager ([Reasoner] -> [Reasoner Manager]) and selecting a reasoner from the pulldown list. Once you make your choice, you can get rid of the Reasoner Manager panel However, because the reasoner uses so much memory, it is generally a good idea to turn it on only when you really need it, and turn it off when you're done. Be sure to save your work before you turn on the reasoner, in case OBO-Edit runs out of memory and dies.
Like most OBO-Edit components, the Reasoner Manager remembers its state when OBO-Edit is exited. This means that if the reasoner is on when you exit OBO-Edit, it will be on the next time you start OBO-Edit. The entire application runs more slowly when the reasoner is running, so usually it makes sense to turn off the reasoner before you exit OBO-Edit (you can always turn it back on next time if you need it).
When the reasoner is turned on, the titlebar of the OBO-Edit window says "(REASONER ON)" as a visual reminder.
The reasoner changes the way the ontology is displayed in the ontology editor panel. Some of the implied links discovered by the reasoner may be shown in the ontology editor panel. By default, these implied links are displayed with a wavy blue arrow:
Not all implied links are shown in the ontology editor panel, because doing so would quickly make the interface unmanagable. Consider our elephant ontology once more:
If every single implied link were shown, we would see:
It's easy to imagine how confusing this would get with an ontology of any complexity.
To reduce this complexity, OBO-Edit trims the ontology before displaying it. Trimming hides links that would unhelpfully clutter the display. The reasoner still knows about these links, but they are not shown to the user.
A link L is trimmed if it satisfies either of the following conditions:
There is one exception: user-created links are never trimmed. This means that redundant links are always visible, because all redundant links are user-created.