A Practical Introduction to Ontologies & OWL

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O p en G A L E N

A Practical Introduction to Ontologies & OWL

Session 1: Primitive Classes in OWL

Nick Drummond & Matthew Horridge

Copyright © 2005, The University of Manchester

Overview

► Pizzas – Card Sorting

► Protégé Introduction

► Subsumption

► Creating a Class Hierarchy

► Consistency

► Disjointness

► Relationships & Properties

► Restrictions

► Polyhierarchies - Issues


Our Domain

►Pizzas have been used in Manchester tutorials for years.

►Pizzas were selected as a domain for several reasons:► They are fun

► They are internationally known

► They are highly compositional

► 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!


You are the Expert

►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

►Having access to experts is critical for most domains

►Luckily, we are all experts in Pizzas, so we just need some material to verify our knowledge…


Reference Materials

►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


Our Ontology

► 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

Let us know your ideas for extending the application


Our Application

www.co-ode.org/downloads/pizzafinder/


Exercise 1: Card Sorting


Card Sorting - Issues

► different viewpoints

► Tomato – Vegetable or Fruit?

► culinary vs biological

► Ambiguity

► words not concepts

► 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


OWL Constructs

Person Country

Class (concept)

Animal

Individual (instance)

Belgium

Paraguay

China

Latvia

Elvis

Hai

Holger

Kylie

S.Claus

Rudolph

Flipper arrow = relationship

label = Property

lives_in

lives_in

lives_in

has_pet

has_pet

has_

pet


OWL Constructs:Classes

Eg Mammal, Tree, Person, Building, Fluid, Company

► Classes are sets of Individuals

► aka “Type”, “Concept”, “Category”

► Membership of a Class is dependent on its logical description, not its name

► Classes do not have to be named – they can be logical expressions – eg things that have colour Blue

► A Class should be described such that it is possible for it to contain Individuals (unless the intention is to represent the empty class)

► Classes that cannot possibly contain any Individuals are said to be inconsistent


OWL Constructs: Properties

Eg hasPart, isInhabitedBy, isNextTo, occursBefore

► Properties are used to relate Individuals

► We often say that Individuals are related along a given property

► Relationships in OWL are binary:

Subject predicate Object

Individual a hasProperty Individual b

nick_drummond givesTutorial Manchester_ProtegeOWL_tutorial_29_June_2005

► N-ary relationships can be modelled with workarounds in OWL, but this design pattern will not be discussed today


OWL Constructs: Individuals

Eg me, you, this tutorial, this room

► Individuals are the objects in the domain

► aka “Instance”, “Object”

► Individuals may be (and are likely to be) a member of multiple Classes


…

► Is a knowledge modelling environment

► Is free, open source software

► Is developed by Stanford Medical Informatics

► Has a large user community (approx 30k)


► core is based on Frames (object oriented) modelling

► has an open architecture that allows other modelling languages to be built on top

► supports development of plugins to allow backend / interface extensions

► now supports OWL through the Protégé-OWL plugin

So let’s have a look…

…


Protégé-OWL


Class Hierarchy Subsumption hierarchy

Structure as asserted by the ontology engineer

owl:Thing is the root class


Subsumption

► Superclass/subclass relationship, “isa”

► All members of a subclass can be inferred to be members of its superclasses

owl:Thing: superclass of all OWL Classes

B

A

• A subsumes B

• A is a superclass of B

• B is a subclass of A

• All members of B are also members of A


Class EditorClass annotations (for class metadata)

Class name and documentation

Properties “available” to

Class

Disjoints widget

Conditions Widget

Class-specific tools (find usage etc)


Exercise 2: Create Class Hierarchy

Before you start:

► If you are borrowing a laptop, please take a note of the number on the top cover

► Please save all files to:My Documents\ontologies

► Because you will be needing your work again tomorrow


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


Saving OWL Files

1. Select File Save Project AsA dialog (as shown) will pop up

2. Select a file directly by clicking the button on the top rightYou will notice that 2 files are created.pprj – the project file

this just stores information about the GUIand the workspace

.owl – the OWL filethis is where your ontology is stored inRDF/OWL format

3. Select OK

OWL = easy to make mistakes = save regularly


Loading OWL files

1. If you only have an OWLfile:

- File New Project- Select OWL Files as the type- Tick Create from existing sources- Next to select the .owl file

2. If you’ve got a valid project file*:- File Open Project- select the .pprj file

* ie one created on this version of Protégé - the s/w gets updated once every few days, so don’t count on it unless you’ve created it recently– safest to build from the .owl file if in doubt


Consistency Checking

► We’ve just created a class that doesn’t really make sense

► What is a MeatyVegetableTopping?

► We’d like to be able to check the logical consistency of our model

► This is one of the tasks that can be done automatically by software known as a Reasoner

► 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)


Reasoners

► 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:► 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


Reasoners and Protégé

► 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 (eg some may be more optimised for speed/memory, others may have more features)

► 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


Accessing the Reasoner

Classify taxonomy

(and check consistency)

Just check consistency

(for efficiency)

Compute inferred types

(for individuals)


Reasoning about our Pizzas

► When we classify an ontology we could just use the “Check Consistency” button but we’ll get into the habit of doing a full classification as we’ll be doing this later

► The reasoner dialog will pop up while thereasoner works

► When the reasoner has finished, you will see an inferred hierarchy appear, which will show any movement of classes in the hierarchy

► If the reasoner has inferred anything about our model, this is reported in the reasoner dialog and in a separate results window

► inconsistent classes turn red► moved classes turn blue


Disjointness

► OWL assumes that classes overlap

MeatTopping VegetableTopping

= individual

► 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


Disjointness

► If we state that classes are disjoint

MeatTopping VegetableTopping

= 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


ClassesTab: Disjoints Widget

Add siblings as disjoint

Add new disjoint Remove disjoint siblings

List of disjoint classes


Exercise 3: Add Disjoints

► Run a reasoner locally on your machine

► Your reasoner may be found at…


Why is MeatyVegetableTopping Inconsistent?

► 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

► 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


Other Inconsistencies?

► Your ontology is likely to have several classes with multiple parents

► 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


What have we got?

► We’ve created a tangled graph (not a tree – multiple parents) of mostly disjoint classes

► Disjoints are inherited down the subsumption hierarchyeg 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)


What are we missing?

► This is not a semantically rich model

► Apart from “is kind of” (subsumption) and “is not kind of” (disjoint), we currently don’t have any other information of interest

► We want to say more about Pizza Individuals, such as their relationship with other Individuals

Pizza PizzaTopping

= individual


Relationships in OWL

► In OWL-DL, relationships can only be formed between Individuals or between an Individual and a data value.(In OWL-Full, Classes can be related, but this cannot be reasoned with)

► Relationships are formed along Properties

► 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


OWL Properties

► Object Property – relates Individuals

► Datatype Property – relates Individuals to data (int, string, float etc)

► Annotation Property – for attaching metadata to classes, individuals or properties


Properties Tab: Property Browser

Note that Properties can be in a hierarchy, although we are not going to be using this feature today


Creating Properties

not used today:

- New Datatype Property (String, int etc)

New Object Property:

Associates an individual to another individual

Delete Property

- New Annotation Properties for metadata

- New SubProperty – ie create “under” the current selection


Creating Properties

► We tend to name properties using camelNotation with a lowercase letter to begin

► We often create properties using 2 standard naming patterns:► has… (eg hasColour)

► is…Of (eg isTeacherOf) or other suffixes (eg …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 patterneg hasPart, isPartOf

► Our example hasBase fits into this(we will not create the inverse in this tutorial)


Associating Properties with Classes

► 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

► This comes in the form of Restrictions

► We create Restrictions using the Conditions widget

► Conditions can be any kind of Class – you have already added Named superclasses in the Conditions Widget. Restrictions are a type of Anonymous Class


Conditions Widget

Conditions asserted by the ontology engineer

Add different types of condition

Definition

of the class

(later)

Description

of the class

Conditions inherited from superclasses


Conditions TypesLogical (Anonymous) Classes

Add Named Superclass

Create Restriction (next)

Create Class Expression


Creating Restrictions

Restriction

Type

Restricted Property

Filler

Expression

Syntax

check

Expression

Construct

Palette


What does this mean?

► We have created a restriction: hasBase PizzaBaseon Class Pizza as a necessary condition

► “If an individual is a member of this class, it is necessary that it has at least one hasBase relationship with an individual from the class PizzaBase”

Pizza PizzaBase

hasBase

hasBase

hasBase

hasBase

► “Every individual of the Pizza class must have at least one base from the class PizzaBase”


What does this mean?


Pizza PizzaBase

hasBase

hasBase

hasBase

hasBase

► “There can be no individual, that is a member of this class, that does not have at least one hasBase relationship with an individual from the class PizzaBase”


hasBase PizzaBase

Why?


PizzaBase

hasBase

hasBase

hasBase

hasBase

hasBase

hasBase

► Each Restriction or Class Expression describes the set of all individuals that satisfy the condition


Pizza

Why? Necessary conditions


► Each necessary condition on a class is a superclass of that class

PizzaBase

hasBase

hasBase

hasBase

hasBase

hasBase

hasBase

hasBase PizzaBase

► ie The restriction hasBase PizzaBase is a superclass of Pizza

► As Pizza is a subclass of the restriction, all Pizzas must satisfy the restriction that they have at least one base from PizzaBase


Exercise 4: Properties & Restrictions


Restriction Types

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”


Primitive Classes

► All classes in our ontology so far are Primitive

► We describe primitive pizzas

► Primitive Class = only Necessary Conditions

► They are marked as plain orange circles in the class hierarchy

We condone building a disjoint tree of primitive classes


Polyhierarchies

► By the end of this tutorial we intent to create a VegetarianPizza

► Some of our existing Pizzas should be types of VegetarianPizza

► However, they could also be types of SpicyPizza or CheeseyPizza

► We need to be able to give them multiple parents in a principled way

► We could just assert multiple parents like we did with MeatyVegetableTopping (without disjoints)

BUT…


Asserted Polyhierarchies

We believe asserting polyhierarchies is bad

let the reasoner do it!

►We lose some encapsulation of knowledge► Why is this class a subclass of that one?

►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


Summary

You should now be able to:

► extract Knowledge (and act as an expert)

► identify components of the Protégé-OWL Interface

► create Primitive Classes

► create Properties

► create some basic Restrictions on a Class using Existential qualifiers

A Practical Introduction to Ontologies & OWL

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