1. Logics for Data and Knowledge Representation
Ontology Building using Protégé : A Tutorial
Fausto Giunchiglia and Biswanath Dutta

2. Outline Introduction Ontology OWL Constructors Protégé and Protégé-OWL
Ontology Building
Class Hierarchy (subsumption)
Disjoint
Consistency Check
Property
Graphical representation
Restriction
Polyhierarchy
Individuals
Changed 2

3. Description Logic (DL) Family
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There are many varieties of DL and there is an informal naming convention, roughly describing the operators allowed.
OWL Mapping to equivalent DL
OWL Lite closely corresponds to SHIF(D)
OWL DL closely corresponds to SHOIN(D) 3

4. Terminology Box (TBox)
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A terminology box (or TBox) is a set of definitions and specializations
Can be seen as a set of “schema” axioms (sentences)
Terminological axioms express constraints on the concepts of the language, i.e. they limit the possible models
The TBox is the set of all the constraints on the possible models
Equivalence
TBOX
Equality axiom
Definition
PhD ≡ Postgraduate ⊓ ≥3Publish.Paper
Parent ≡ Person ⊓ ∃hasChild.Person
hasGrandChild ⊑ hasChild
Inclusion axiom
Specialization
Subsumption 4

5. Assertion Box (ABox) Student(paul) Professor(fausto)
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In an ABox one introduces individuals, by giving them names, and one asserts properties about them.
We denote individual names as a, b, c,…
An assertion with concept C is called concept assertion (or simply assertion) in the form:
C(a), C(b), C(c), …
An assertion with Role R is called role assertion in the form:
R(a, b), R(b, c), …
So, an ABox is a set of “data” axioms (ground facts)
Student(paul)
Professor(fausto)
Teaches(Fausto, LDKR) 5

6. Knowledge Base (KB) A Knowledge Base (KB) = TBox + Abox 6
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A Knowledge Base (KB) = TBox + Abox 6

7. Ontology
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An ontology describes the concepts and relationships that are important in a particular domain, providing a vocabulary for that domain as well as a computerized specification of the meaning of terms used in the vocabulary
Ontologies are ranges from:
taxonomies and classifications,
database schemas,
to fully axiomatized theories
Used in many business and scientific communities as a way to share, reuse and process domain knowledge
Central to many applications such as, scientific knowledge portals, information management and integration systems, electronic commerce, semantic web services, and so forth 7

8. Ontology : Basic Principle
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Ontology building is a fun!!!
Before starting modelling an ontology, we need an application in our mind 8

9. Naming Conventions There are no such standard conventions
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There are no such standard conventions
Different practices are found, like,
HumanBeing
humanBeing
Human_being
Use whatever you like
Important: try to be consistent 9

10. OWL Constructs: Classes
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Classes (concept, category) are sets of Individuals
Membership of a class is depend on its logical description, NOT on its name
Classes do not have to be named – they can be logical expressions – e.g., book with yellow cover page
A class is to be described in a way that it is possible for it to contain Individuals, except that you have some specific requirement where it is to represent the empty class
E.g., Human being, Person, Building, Personal moment, Vacation, Religious residence 10

11. OWL Constructs: Properties
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OWL defines the properties,
Object property- relate individuals to other individuals (e.g., isTaughtBy, supervises, isStudentOf, isLocatedIn)
Datatype property- relate individuals to datatype values (e.g. , author, title, phone, age, etc.)
Annotation property- use to add uninterpreted information (e.g., versioning information, comment) to classes, properties and individuals
Relationships in OWL are binary
N-ary relations???
Note: constraints, like, domains and ranges, can be given for object and datatype properties, but not for annotation properties
Note: ontologies can also have the ontology properties (provide uninterpreted information) as annotations, just like annotation properties, except that they relates ontologies to other ontologies. For example, owl:imports can be used to import other ontologies. 11

12. OWL Constructs: Individuals
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Individuals (Instance, Object) are the objects in the domain
An individual may be (and are likely to be) a member of multiple Classes
E.g., me, you, this tutorial, this room, this university, my house 12

13. Special Properties owl:TransitiveProperty (transitive property)
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owl:TransitiveProperty (transitive property)
E.g. “has better grade than”, “is ancestor of”
owl:SymmetricProperty (symmetry)
E.g. “has same grade as”, “is sibling of”
owl:FunctionalProperty defines a property that has at most one value for each object
E.g. “age”, “height”, “directSupervisor”
owl:InverseFunctionalProperty defines a property for which two different objects cannot have the same value
Note: Not all of these can be specified for a particular object property as to retain the decidability of OWL DL properties (e.g., an object property specified as transitive, and their super-properties and their inverses cannot have their cardinality restricted, either via a the functional part of property axioms or in cardinality restrictions) 13

14. Restriction Types       Existential, someValuesFrom
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Existential, someValuesFrom
“Some”, “At least one” 
Universal, allValuesFrom
“Only” 
hasValue
“equals x” 
Cardinality
“Exactly n” 
Max Cardinality
“At most n” 
Min Cardinality
“At least n” 14

15. Protégé
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Is developed by Stanford Medical Informatics (
Is a free, open-source software
Has large and growing user community base
Implements a rich set of knowledge-modeling structures
Supports the creation, visualization, and manipulation of ontologies in various representation formats
In core, Protégé is based on Frames (object oriented) modelling
Supports OWL through the Protégé-OWL plugin
Can be customized to provide domain-friendly support for creating knowledge models and entering data
Supports development of plugins to allow backend / interface extensions 15

16. Protégé-OWL The Protégé-OWL editor enables users to:
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The Protégé-OWL editor enables users to:
Load and save OWL and RDF ontologies
Edit and visualize classes, properties, and SWRL (Semantic Web Rule Language) rules
Define logical class characteristics as OWL expressions
Execute reasoners such as description logic classifiers
Edit OWL individuals for Semantic Web markup
Protégé supports SHOIN(D) 16

17. Saving OWL Files Two files:
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Two files:
.pprj – the project file stores information about the GUI and the workspace
.owl – the OWL file actual ontology is stored in RDF/OWL format 17

18. Protégé-OWL : Metadata Window
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Protégé-OWL : Metadata Window
Ontology URI
Ontology property
Ontology(ies)
Default Namespaces
Namespaces 18

19. Protégé-OWL : Class Building Window
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Asserted hierarchy as asserted by the ontology engineer
Class description widget
owl:Thing, a root class
Subsumption hierarchy
Asserted Conditions Widget
Class-specific tools (find usage etc)
Disjoint widget 19

20. Ontology Building Basic infrastructure (recall!) Classes/ concepts
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Ontology Building
Basic infrastructure (recall!)
Classes/ concepts
Properties/ roles
Object property
Datatype property
Annotation property [optional]
Individuals/ objects/ instances [mandatory ???] 20

21. Basic Things Step 1: Open Protégé Create a new project
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Step 1:
Open Protégé
Create a new project
Select OWL/RDF files as Project type
Define the Ontology URI
Select OWL DL as Language profile
Click to Finish
Save the project
Important: it is always good to save the ontology after each operation you do while building the ontology 21

22. Class Hierarchy (subsumption)
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Step 2:
Go to the OWL Classes tab
Create the following two classes:
Agent, MindProduct (as subClass of owl:Thing)
Add the following subClasses under the class Agent
Developer, Producer, Programmer
Add the following subClasses under the class MindProduct
Document, Music, Program, Song
Under Document, create the following subClasses
Book, Magazine 22

23. Disjoint
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In the previous slide, we organized the kind-of classes in a hierarchy (subsumption)
Note: human mind can easily process that, say, classes, Agent and MindProduct are not the same kind- of objects (and that’s why we kept them separately)
Step 3: We explicitly mention say the same, i.e., Agent and MindProduct are disjoint classes in our ontology using the disjoint wizard
Select class Agent
Click on Add all siblings in the Disjoints wizard
Select Mutually between all siblings 23

24. Disjoint
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Similarly we make classes, i.e., Developer, Producer, Programmer as disjoint classes
In a similar way, we make the classes, Document, Music, Program, Song as disjoint classes
Also make the classes, Book and Magazine as disjoint classes
E.g., 24

25. What is Next? So, what we have done till now: So, what we do next
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So, what we have done till now:
Created a new project file
Gave a name to this new ontology and save into our local system
Created the class hierarchies
Explicitly stated the not-kind of classes (disjointness)
So, what we do next
We first check the consistency of our ontology by running the reasoner
Before check the consistency we do another step (see next slide) 25

26. Consistency Check
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Add named classes
Step 4: We add a new class, called, InconsistentClass_1 under the class Agent
Make InconsistentClass_1 as disjoint class with all its siblings
As per the inheritance rule, InconsistenceClass_1 has a parent Agent
Now make this class such that it has multi-parents
To do this,
Select class InconsistentClass_1
Click on the Add named classes from the Asserted Conditions widget
Select the class Development from list
Press Ok 26

27. Consistency Check Now run the consistency check
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Consistency Check
Now run the consistency check
To do this we use the Pellet reasoner (integrated with the Protégé-OWL editor)
Classify taxonomy
(and check consistency)
Check consistency (for efficiency)
Compute inferred types
(for individuals) 27

28. Consistency Check
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Now make the classes InconsistentClass_1 and Developer as non-disjoint classes
How to do this?
Select the class InconsistentClass_1
Go to the Disjoints widget and select the class Developer
Click on “Delete selected row”
Save the ontology
Run the consistency check again 28

29. Next step? So, what is next? Step 5 : we add the following properties
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So, what is next?
Step 5 : we add the following properties
Object property
write, download, produce
Datatype property
name, dateOfBirth, title
Annotation property
dc:title, dc:creator, dc:date
Set the domain and range of those properties
Assign the special properties to those properties (wherever needed) 29

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Object Property
Range
Domain
Important: properties can also be built in a hierarchy (not shown here) 30

31. Datatype Property Range Domain 31
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Datatype Property
Range
Domain 31

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Annotation Property 32

33. Graphical View of the Asserted Classes
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The (Asserted) class hierarchy view
OWL Viz 33

34. Restrictions Next, we add class restrictions… (Step 6)
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Next, we add class restrictions… (Step 6)
This we do from the Asserted Conditions widget 34

35. Restrictions Restricted property Restriction Filler Create restriction
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Restricted property
Restriction
Filler
Create restriction
Expression construct palette 35

36. Restrictions : Necessary Conditions
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We create the following condition:
Programmer ⊑ ∃write.Programs
Producer ⊑ ∀produce.(Music ⊔ Song)
Program ⊑ ∀download.Developer
Important:
Restrictions are a type of Anonymous Class
Each class restrictions on a class become a superclass to that class
In the above picture, produce(Music or Song) become a superclass of class Produce 36

37. What is Next?
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Now assume that, we have some few more agents, like, Hacker, Tracker, Computer Guru, Inventor
We add these agents by creating a new class, called MixedAgent
Why we are considering them as mixed, because of their following features
Hackers and Trackers are basically the Programmer
Computer Guru - an authority on computers and computing
Inventor - who is the first to think of or make something 37

38. Class Restrictions
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Now, from the newly added class description (see previous slide), we see that the classes, Hacker and Tracker are the programmers, which
implies that they write Program
We explicitly state this knowledge into our ontology in the form of restrictions 38

39. Polyhierarchy
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Now it is obvious that since Hacker and Tracker are the programmers, we can say that these two classes are also be the child of class Programmer
This leads to the polyhierarchy
BUT, we do not state this knowledge manually
We will use reasoner to do this for us
Let reasoner infer this knowledge automatically
To get this job done by the reasoner, we need to do one more step 39

40. Polyhierarchy
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We make the following Necessary Condition as Necessary and Sufficient Condition
Programmer ⊑ ∃write.Programs
How to make this?
Click on the class Programmer
Select the following Necessary Condition (in the Asserted Condition widget)
Drag and drop it to the Necessary and Sufficient Condition block 40

41. Polyhierarchy Now run the reasoner You see the following
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Now run the reasoner
You see the following
In the Inferred Hierarchy window, classes with blue colors represent the newly REorganized classes
Classify taxonomy (and check consistency) 41

42. REorganized Class Hierarchy
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Individuals 43