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4.2 Using a Reasoner 
You may notice that one or more of your classes is highlighted in red as in Figure 4.5. This is because we 
haven’t run the reasoner yet so Protégé has not been able to verify that our new classes have no 
inconsistencies. When just creating classes and subclasses in a new ontology there is little chance of an 
inconsistency. However, it is a good idea to run the reasoner often. When there is an inconsistency the 
sooner it is discovered the easier it is to fix. One common mistake that new users make is to do a lot of 
development and then run the reasoner only to find that there are multiple inconsistencies which can make 
debugging significantly more difficult. So let’s get into the good habit of running the reasoner often. 
Protégé comes with some reasoners bundled in and others available as plugins. Since we are going to 
write some SWRL rules later in the tutorial, we want to use the Pellet reasoner. It has the best support for 
SWRL at the time this tutorial is being written.  
Exercise 5: Install and Run the Pellet Reasoner 
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1. Check to see if the Pellet reasoner is installed. Click on the Reasoner menu. At the bottom of the menu 
there will be a list of the installed reasoners such as Hermit and possibly Pellet. If Pellet is visible in that 
menu then select it and skip to step 3.  
2. If Pellet is not visible then do File>Check for plugins and select Pellet from the list of available plugins 
and then select Install. This will install Pellet and you should get a message that says it will take effect the 
next time you start Protégé. Do a File>Save to save your work then quit Protégé and restart it. Then go to 
File>Open recent. You should see your saved Pizza tutorial in the list of recent ontologies. Select it to 
load it. Now you should see Pellet under the Reasoner menu and be able to select it so do so.  
3. With Pellet selected in the Reasoner menu execute the command Reasoner>Start reasoner. The 
reasoner should run very quickly since the ontology is so simple. You will notice that the little text 
message in the lower right corner of the Protégé window has changed to now say Reasoner active.   The 
next time you make a change to the ontology that text will change to say: Reasoner state out of sync with 
active ontology. With small ontologies the reasoner runs very quickly, and it is a good idea to get into the 
habit of running it often, as much as after every change.  
4. It is possible that one or more of your classes will still be highlighted in red after you run the reasoner. 
If that happens do: Window>Refresh user interface and any red highlights should go away. Whenever 
your user interface seems to show something you don’t expect the first thing to do is to try this command.  
There are no mandatory naming conventions for OWL entities.  In chapter 7, we will discuss 
names and labels in more detail. A best practice is to select one set of naming conventions and 
then abide by that convention across your organization. For this tutorial we will follow the 
standard where class and individual names start with a capital letter for each word and do not 
contain spaces. This is known as CamelBack notation. For example: Pizza, PizzaTopping, 
etc. Also, we will follow the standard that class names are always singular rather than plural. 
E.g., Pizza rather than Pizzas, PizzaTopping rather than PizzaToppings.