6 
 
Chapter 2 Requirements and the Protégé User Interface 
 
In order to follow this tutorial, you must have Protégé 5, which is available from the Protégé website,1 
and some of the Protégé Plugins which will be described in more detail below. For now, just make sure 
you have the latest version of Protégé. At the time this is being written the latest version is 5.5 although 
the tutorial should work for later versions as well.  
The Protégé user interface is divided up into a set of major tabs. These tabs can be seen in the 
Window>Tabs option. This option shows all the UI tabs that are currently loaded into the Protégé 
environment. Any tabs that are currently opened have a check mark next to them. To see a tab that is not 
visible just select it from the menu and it will be added to the top with the other major tabs and its menu 
item will now be checked. You can add additional major tabs to your environment by loading plugins. For 
example, when we load the SHACL4Protégé plugin the SHACLEditor will be added to the menu.  
Each major tab consists of various panes or as Protégé calls them views. Each view can be resized or 
closed using the icons in the top right corner of every view. The views can also be nested as sub-tabs 
within each major tab. When there could potentially be confusion between a tab that is a screen all its own 
(is under the Window>Tabs option) and a view that is a sub-tab we will call the screen tab a major tab.  
There are many views that are not in the default version of Protégé that can be added via the 
Window>Views option. The additional views are divided into various categories such as 
Window>Views>Individual views. Section 5.2 will show an example of adding a new view to a major 
tab.  
Chapter 3 What are OWL Ontologies? 
 
Ontologies are used to capture knowledge about some domain of interest. An ontology describes the 
concepts in the domain and also the relationships that hold between those concepts. Different ontology 
languages provide different facilities. The most recent development in standard ontology languages is 
OWL from the World Wide Web Consortium (W3C).  A good primer on the basic concepts of OWL can 
be found at: https://www.w3.org/TR/owl2-primer/  
OWL makes it possible to describe concepts in an unambiguous manner based on set theory and logic. 
Complex concepts can be built up out of simpler concepts. The logical model allows the use of a reasoner 
which can check whether all of the statements and definitions in the ontology are mutually consistent and 
can also recognize which concepts fit under which definitions. The reasoner can therefore help to 
maintain the hierarchy correctly. This is particularly useful when dealing with cases where classes can 
have more than one parent. The reasoner can also infer additional information. For example, if two 
properties are inverses only one value needs to be asserted by the user and the inverse value will be 
automatically inferred by the reasoner.  
3.1 Components of OWL Ontologies 
An OWL ontology consists of Classes, Properties, and Individuals. OWL ontologies are an 
implementation of Description Logic (DL) which is a decidable subset of First Order Logic. A class in 
OWL is a set, a property is a binary relation, and an individual is an element of a set. Other concepts from 
set theory are also implemented in OWL such as Disjoint sets, the Empty set (owl:Nothing), inverse 
 
1 http://protege.stanford.edu