Overview
► Pizzas – Card Sorting
A Practical Introduction to
Ontologies & OWL
Session 1: Primitive Classes in OWL
► Protégé Introduction
► Subsumption
► Creating a Class Hierarchy
► Consistency
► Disjointness
► Relationships & Properties
► Restrictions
► Polyhierarchies - Issues
O p enGA LEN
BioHealth
Informatics
Group
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Copyright © 2006, The University of Manchester
Our Domain
Introduction to Ontologies Tutorial
You are the Expert
► Pizzas have been used in Manchester tutorials for years.
► Pizzas were selected as a domain for several reasons:
► They are fun
► Most often it is not the domain expert that formalises their
knowledge – because of the complexity of the modelling it
is normally a specialist “knowledge engineer”
Hopefully, as tools get easier to use, this will change
► They are internationally known
► Having access to experts is critical for most domains
► They are highly compositional
► Luckily, we are all experts in Pizzas, so we just need some
material to verify our knowledge…
► They have a natural limit to their scope
► They are fairly neutral
► Although arguments still break out over representation
► Even pizzas can do this - its an inevitable part of knowledge modelling
► ARGUING IS NOT BAD!
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Introduction to Ontologies Tutorial
Copyright © 2006, The University of Manchester
Introduction to Ontologies Tutorial
Reference Materials
Our Ontology
► Having references to validate decisions, and act as
provenance can be useful for maintaining an ontology
► Mistakes, omissions and intentions can be more easily
traced if a reference can be made
► When building, we highly recommend documenting your model as you go – keeping
provenance information is a good way of doing this
► We have provided you with a pizza menu and several cards
with ingredients on
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Introduction to Ontologies Tutorial
Our Application
► When building an ontology we need an application in mind – ontologies
should not be built for the sake of it
► Keep the application in mind when creating concepts – this should help
you scope the project
► The PizzaFinder application has been developed so that you can plug
your ontology in at the end of the day and see it in action
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Introduction to Ontologies Tutorial
Exercise 1: Card Sorting
► You have been given a selection of pizza toppings from a
takeway menu
► Group the toppings into several piles
► What similarities and differences are there between the different piles?
► Are there any concepts missing?
► If you can, regroup the toppings into different piles
► Feel free to add you own toppings to the cards
www.co-ode.org/downloads/pizzafinder/
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Introduction to Ontologies Tutorial
Copyright © 2006, The University of Manchester
Introduction to Ontologies Tutorial
Card Sorting - Issues
…
► different viewpoints
► Tomato – Vegetable or Fruit?
► Is a knowledge modelling environment
► culinary vs biological
► Is free, open source software
► Ambiguity
► Is developed by Stanford / Manchester
► words not concepts
► Has a large user community (approx 30k)
► Missing Knowledge
► What is peperonata?
► multiple classifications (2+ parents)
► lots of missing categories (superclasses?)
► competency questions
► What are we likely to want to “ask” our ontology?
► bear the application in mind
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Introduction to Ontologies Tutorial
Copyright © 2006, The University of Manchester
Introduction to Ontologies Tutorial
Protégé-4
…
► Protégé 4 (alpha) Built solely on OWL modelling language
► Supports development of plugins to allow backend /
interface extensions
So let’s have a look…
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Introduction to Ontologies Tutorial
Copyright © 2006, The University of Manchester
Introduction to Ontologies Tutorial
Class Hierarchy
Subsumption
Subsumption hierarchy
Structure as asserted by the ontology engineer
► Superclass/subclass relationship, “is-a”
► All members of a subclass can be inferred to be members of its
superclasses
Thing: superclass of all OWL Classes
A
B
• A subsumes B
• A is a superclass of B
• B is a subclass of A
• All members of B are also
members of A
Thing is the root class
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Introduction to Ontologies Tutorial
Exercise 2: Create Class
Hierarchy
Using your groups from exercise 1, create your class
hierarchy in Protégé following the steps shown in the
demo.
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Introduction to Ontologies Tutorial
Exercise 2: Create Class
Hierarchy
► You will notice that we use naming conventions for our
ontology entities
► Typically, we use CamelNotation with a starting capital for
Classes
► Use whatever conventions you like
► It is helpful to be consistent – especially when trying to find
things in your ontology
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Introduction to Ontologies Tutorial
Copyright © 2006, The University of Manchester
Introduction to Ontologies Tutorial
Create a Class Hierarchy
Saving OWL Files
OWL = easy to make mistakes = save regularly
► Start with your empty ontology…
1.
Select File Æ Save Project As
A dialog (as shown) will pop up
2.
Select a directory by using the Browse button
An OWL file is created in the specified directory
.owl – the OWL file
this is where your ontology is stored in
RDF/OWL format
3.
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Introduction to Ontologies Tutorial
Labels – so what?
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Introduction to Ontologies Tutorial
Disjointness
► Humans might be able to interpret what the labels mean
and how they are defined, but the computer cannot.
► OWL assumes that classes overlap
MeatTopping
Pizza
A
Click OK
B
PizzaBase
C
PizzaTopping
VegetableTopping
= individual
D
► This means an individual could be both a MeatTopping and a
VegetableTopping at the same time
► We want to state this is not the case
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Introduction to Ontologies Tutorial
Copyright © 2006, The University of Manchester
Introduction to Ontologies Tutorial
Disjointness
Consistency Checking
► We’ve just created a class that doesn’t really make sense
► If we state that classes are disjoint
MeatTopping
► What is a MeatyVegetableTopping?
VegetableTopping
► We’d like to be able to check the logical consistency of our model
= individual
► This means an individual cannot be both a MeatTopping and
a VegetableTopping at the same time
► We must do this explicitly in the interface
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Introduction to Ontologies Tutorial
Reasoners
► Being able to use a reasoner is one of the main advantages of using
a logic-based formalism such as OWL (and why we are using
OWL-DL)
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Introduction to Ontologies Tutorial
Reasoners and Protégé
► Reasoners are used to infer information that is not explicitly contained within
the ontology
► You may also hear them being referred to as Classifiers
► Standard reasoner services are:
► Protégé-OWL supports the use of reasoners implementing the DIG
interface
► This means that the reasoner you choose is independent of the
ontology editor, so you can choose the implementation you want
depending on your needs (e.g., some may be more optimised for
speed/memory, others may have more features)
► Consistency Checking
► Subsumption Checking
► Equivalence Checking
► Instantiation Checking
► Reasoners can be used at runtime in applications as a querying mechanism (esp
useful for smaller ontologies)
► We will use one during development as an ontology “compiler”. A well
designed ontology can be compiled to check its meaning is that intended
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► This is one of the tasks that can be done automatically by software
known as a Reasoner
Introduction to Ontologies Tutorial
► These reasoners typically set up a service running locally or on a
remote server – Protégé-OWL can only connect to reasoners over an
http:// connection
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Introduction to Ontologies Tutorial
Why is MeatyVegetableTopping
Inconsistent?
Other Inconsistencies?
► Your ontology is likely to have several classes with multiple parents
► We have asserted that a MeatyVegetableTopping is a subclass of two
classes we have stated are disjoint
► The disjoint means nothing can be a MeatTopping and a
VegetableTopping at the same time
► This means that MeatyVegetableTopping can never contain any
individuals
► We call this a tangle
► As we have seen, a class cannot have 2 disjoint parents – it will be
inconsistent
► To remove other inconsistencies you will have to be careful about
where your disjoints are – remove disjoints between multiple parents
by hand
► This is obviously an awkward thing to manage – we will later show you
how to manage your tangle to simplify these issues
► The class is therefore inconsistent
► This is what we expect!
► It can be useful to create classes we expect to be inconsistent to “test”
your model – often we refer to these classes as “probes” – generally it is a
good idea to document them as such to avoid later confusion
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Introduction to Ontologies Tutorial
What have we got?
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Introduction to Ontologies Tutorial
Relationships in OWL
► We’ve created a tangled graph (not a tree – multiple parents) of mostly
disjoint classes
► In OWL-DL, relationships can only be formed between
Individuals or between an Individual and a data value.
► Disjoints are inherited down the subsumption hierarchy
► Relationships are formed along Properties
(In OWL-Full, Classes can be related, but this cannot be reasoned with)
e.g., something that is a TomatoTopping cannot be a Pizza because its
superclass, PizzaTopping, is disjoint from Pizza
► You should now be able to select every class and see its siblings in the
disjoints widget (if it has any)
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Introduction to Ontologies Tutorial
► We can restrict how these Properties are used:
► Globally – by stating things about the Property itself
► Or locally – by restricting their use for a given Class
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Introduction to Ontologies Tutorial
OWL Properties
Types of Properties
► Object Property – relates Individuals
hasParent
► Inverse
► Datatype Property – relates Individuals to data (int, string,
float etc)
Matthew
Dorothy
hasChild
► Functional
hasBir
er
thMoth
Peggy
Implies that Peggy and
Margaret are the same
individual
Dorothy
hasBirthMothe
r
Margaret
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Introduction to Ontologies Tutorial
Copyright © 2006, The University of Manchester
Introduction to Ontologies Tutorial
Types of Properties
► Inverse Functional
r Of
Mothe
isBirth
Peggy
isBirthMotherO
f
Margaret
Peter
► Antisymmetric
isChildOf
isChildOf
David
Robert
William
Ian
isChildOf
hasAncestor
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Gemma
hasSibling
hasAncestor
hasAncestor
Matthew
Matthew
Implies that Peggy and
Margaret are the same
individual
Dorothy
► Transitive
hasSibling
► Symmetric
X
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Introduction to Ontologies Tutorial
Properties cntd.
know
s Of
► Reflexive
Describing Classes using
Properties
►
We now have a property we want to use to describe Pizza
individuals
►
To do this, we must go back to the Pizza class and add some
further information
knowsOf
George
► Irreflexive
Simon
►
This comes in the form of Restrictions
►
We create Restrictions using the Class Description Frame
►
Conditions can be any kind of Class – you have already added Named
superclasses in the Class Description Frame. Restrictions are a type of
Anonymous Class
motherOf
Georgina
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Simon
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Creating Properties
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Introduction to Ontologies Tutorial
Existential Restrictions
► We tend to name properties using camelNotation with a lowercase letter to
begin
► We often create properties using 2 standard naming patterns:
► has… (e.g., hasColour)
Existential, someValuesFrom “Some”, “At least one”
Describe classes of individuals that participate in at least one
relationship along a specified property to individuals that are
members of a specified class.
► is…Of (e.g., isTeacherOf) or other suffixes (e.g., …In …To)
► This has several advantages:
► It is easier to find properties
► It is easier for tools to generate a more readable form
(see tooltips on the classes in the hierarchy later)
► Inverses properties typically follow this pattern
e.g., hasPart, isPartOf
► Our example hasBase fits into this
(we will not create the inverse in this tutorial)
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Introduction to Ontologies Tutorial
Copyright © 2006, The University of Manchester
Introduction to Ontologies Tutorial
Domain and Range
Named Classes
► Properties link individuals from the domain to individuals
from the range.
hasTopping
PizzaTopping
Pizza
= individual
Professor
Professor
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Introduction to Ontologies Tutorial
Intersection Classes
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Introduction to Ontologies Tutorial
Union Classes
►Intersection Classes are formed by combining two or
more classes with the intersection (AND) operator.
►Union Classes are formed using the union (OR) operator
with two or more classes.
In description logics (and in
Protege-OWL) we use the
union symbol ⊔
In description logics (and in
Protege-OWL) we use the
intersection symbol ⊓)
Human ⊓ Female
JavaProgrammer ⊔ CProgrammer
JavaProgrammer
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Person
Person
Introduction to Ontologies Tutorial
Copyright © 2006, The University of Manchester
CProgrammer
Introduction to Ontologies Tutorial
Complement Classes
Exercise 4: Properties &
Restrictions
►A complement class is specified by negating another class.
It will contain the individuals that are not in the negated
class.
In Description Logics
(and in Protege-OWL)
the negation symbol ¬
is used.
¬ Professor ⊓ Woman
Woman
Professor
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Introduction to Ontologies Tutorial
Primitive Classes
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Introduction to Ontologies Tutorial
Asserted Polyhierarchies
We believe asserting polyhierarchies is bad
► All classes in our ontology so far are Primitive
► We lose some encapsulation of knowledge
► We describe primitive pizzas
► Why is this class a subclass of that one?
► Primitive Class = only Necessary Conditions
► They are marked as plain orange circles in the class hierarchy
► Difficult to maintain
► Adding new classes becomes difficult because all subclasses
may need to be updated
► Extracting from a graph is harder than from a tree
We condone
building a
disjoint tree
of primitive
classes
let the reasoner do it!
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Introduction to Ontologies Tutorial
Copyright © 2006, The University of Manchester
Introduction to Ontologies Tutorial
Summary
Polyhierarchies
► By the end of this tutorial we intent to create a VegetarianPizza
You should now be able to:
► Some of our existing Pizzas should be types of VegetarianPizza
► However, they could also be types of SpicyPizza or CheeseyPizza
► extract Knowledge (and act as an expert)
► identify components of the Protégé-OWL Interface
► We need to be able to give them multiple parents in a principled way
► create Primitive Classes
► We could just assert multiple parents like we did with
MeatyVegetableTopping (without disjoints)
► create Properties
► create some basic Restrictions on a Class using Existential
qualifiers
BUT…
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Introduction to Ontologies Tutorial
Copyright © 2006, The University of Manchester
Introduction to Ontologies Tutorial