Ontologies Intro v04

A Practical
Introduction to
Ontologies & OWL
In association with:
The CO-ODE and HyOntUse projects

(www.co-ode.org)
Protégé
(protege.stanford.edu)
Advanced Knowledge Technologies

(www.aktors.org)
NorthWest Institute for Bio-Health Informatics

(www.nibhi.man.ac.uk)
funded by:
Semantic Mining Network of Excellence
http://www.semanticmining.org
The Joint Information Systems Council

(www.jisc.ac.uk)
The Engineering and Physical Sciences Research Council

(www.epsrc.ac.uk)
Info
Document version v.4
Document date 5th July 2005
Nick Drummond
Compiled By
www.cs.man.ac.uk/~drummond/
All materials (this document, slides,

www.co-ode.org/resources/tutorials/intro/
exercises) available at
Tutorial details available at www.co-ode.org/events/tutorials/escience02/
Copyright
Material published by The University of Manchester for this event is copyright The
University of Manchester and may not be reproduced without permission. Copyright exists
in all other original material published by staff of The University of Manchester and may
belong to the author or to The University of Manchester depending on the circumstances
of publication.
All Material © 2005, The University of Manchester

Contents
Introduction 5
Program 6
Day 1 6
Day 2 7
Course Slides 8
Introduction to Ontologies 8
OWL Overview 24
Hands On: Protégé-OWL part 1 44
Knowledge Acquisition 73
Ontology Engineering 83
Hands On: Protégé-OWL part 2 100
Formal Modelling Issues 119
Ontology Applications 140
COHSE 150
Instance Store 163
Intelligent Curation Using Ontologies 163
Discussion Topics 178
Appendices 179
Appendix A: Terminology 180
Appendix B: Syntax 181
Appendix C: Resources 183
Appendix D: Application Overviews 184
Manchester Pizza Finder overview 184
COHSE overview 185
Instance Store overview 186
Intelligent Curation through ontologies 187
Appendix E: Hands On: Protégé-OWL part 3 188
Acknowledgements 199
A Practical Introduction to Ontologies & OWL © 2005 The University of Manchester
Introduction
The University of Manchester, Bio-Health Informatics and Information Management Group
together with Advanced Knowledge Technologies (AKT) from Southampton University
welcome you to this two day tutorial and workshop.
With several years experience in teaching OWL and its predecessors to various audiences,
we are now providing a program that will take steps through ontology principles,
knowledge acquisition and modelling, quality, right through to the beginnings of ontology
driven applications.
The major goal of this tutorial is to provide the attendees with both the theoretical
foundations of ontology design and hands-on experience in the construction of ontologies
as well as an understanding of how this technology can be applied to various problem
domains. In particular, attendees will:
• Learn the basic principles of OWL based ontologies using styles developed at
Manchester and in the Semantic Web Best Practice Working Party
• Gain hands-on experience with ontology development using the Protégé-OWL tools
• Learn how to use the expressive power of OWL and to take advantage of its
inferencing capabilities to build robust, reusable models
• Learn several knowledge acquisition techniques and use them to model a subject
domain
• Be introduced to the skills needed to participate in the growing community of
users/developers of OWL
• Be exposed to real examples of ontology driven applications, and understand some
of the architectures that may be employed to solve domain problems
5
Program: Day 1
10:00 Registration & Coffee
10:30 Participants Introductions
10:45 Introduction to Ontologies
Alan Rector
• Motivation
• Simple Ontology Application examples
11:30 Break
11:45 OWL overview
Matthew Horridge
• "Ontology" Languages
• Ontology Paradigms
• OWL Constructs
12:30 Lunch
13:30 Hands On: Protégé-OWL tutorial part 1
Nick Drummond, Matthew Horridge
• Tool overview
• Constructing a taxonomy
• Disjointness & Introduction to the Reasoner
• Primitive Classes
• Conditions & Restrictions
15:45 Break
16:00 Ontology Engineering
Jeremy Rogers
• How to start
• Naming & Metadata
• Issues of Scope and Complexity
16:30 Discussion and Q&A
17:00 Finish
6
Program: Day 2
09:00 Coffee
09:30 Knowledge Acquisition
Robert Stevens
• Ontology Lifecycle
• Elicitation Techniques
• Laddering
10:00 Hands On: Protégé-OWL tutorial part 2
Nick Drummond, Matthew Horridge
10:45 • Defined Classes

break • Using the reasoner to build more complex hierarchies
• Class Expressions
• Open World Assumption
12:00 Formal Modelling Practice
Alan Rector
• Why Classify?
• Untangling Ontologies
12:45 Lunch
13:45 Ontology Applications
Sean Bechhofer, Daniele Turi, Matthew Horridge
• General themes / Architectures

• Case Study: COHSE
• Case Study: OWL Instance Store
• Simple Example: Pizza Finder application architecture
14:45 Break
15:00 Discussion and Q&A
• Suggested Topics
• Course Feedback
15:30 Finish for those that need to leave - Open discussion for those that wish to stay.
7
Introduction
Alan Rector
8
A Practical
Introduction to
Ontologies & OWL
Alan Rector
O p enG A LEN
BioHealth
Informatics
Group 1 Copyright © 2005 Univ. of Manchester
Speakers
►Alan Rector – Medical Informatics
►Robert Stevens - BioInformatics
►Sean Bechhofer – OntoGrid, COHSE
►Matthew Horridge – CO-ODE
►Nick Drummond – CO-ODE
►Jeremy Rogers - OpenGALEN
►Daniele Turi – IMG, Instance Store
►Katy Wolstencroft – Phosphabase, mygrid
2 Copyright © 2005 Univ. of Manchester
9
Overview (day 1)
►Introduction and Motivation

►plus example app
►OWL Language Overview

►The Web Ontology Language and constructs
►Hands On: Protégé-OWL 1

►Constructing a taxonomy and introduction to reasoning
►Knowledge acquisition
►Elicitation methodologies
►Q&A
Overview (day 2)
►Ontology Engineering
►Hands On: Protégé-OWL 2
►Using a reasoner for computing a classification
►Formal Modelling Issues

►Why classify?
►Untangling
►Applications
►Architecture and case studies
►Q&A, Open Discussion

►Feedback
10
The Car
The Car
Automobile
Voiture
Coche
Araba
11
Hard Work using the

Syntactic Web…
Find images of Peter Patel-Schneider, Frank van
Harmelen and Alan Rector…
Rev. Alan M.
Gates,
Associate
Rector of the
Church of the
Holy Spirit, Lake
Forest, Illinois
Impossible (?) using the

Syntactic Web…
► Complex queries involving background knowledge
► Find information about “animals that use sonar but are not either bats
or dolphins”, e.g., Barn owl
► Locating information in data repositories

► Travel enquiries
► Prices of goods and services
► Results of human genome experiments
► Finding and using “web services”

► Visualise surface interactions between two proteins
► Delegating complex tasks to web “agents”

► Book me a holiday next weekend somewhere warm, not too far
away, and where they speak French or English
12
What is the Problem?
Consider a typical web page:

Markup consists of:
rendering
information (e.g.,
font size and
colour)
Hyper-links to
related content
Semantic content is
accessible to humans
but not (easily) to
computers…
What information can we

see…
WWW2002
The eleventh international world wide web conference
Sheraton waikiki hotel
Honolulu, hawaii, USA
7-11 may 2002
1 location 5 days learn interact
Registered participants coming from
australia, canada, chile denmark, france, germany, ghana, hong kong, india,
ireland, italy, japan, malta, new zealand, the netherlands, norway, singapore,
switzerland, the united kingdom, the united states, vietnam, zaire
Register now
On the 7th May Honolulu will provide the backdrop of the eleventh international
world wide web conference. This prestigious event …
Speakers confirmed
Tim berners-lee
Tim is the well known inventor of the Web, …
Ian Foster
Ian is the pioneer of the Grid, the next generation internet …
13
What information can a

machine see…
Solution: XML markup with

“meaningful” tags?
<name>
</name>
<location>
</location>
<date> </date>
<slogan> </slogan>
<participants>
</participants>
< introduction>
</introduction>
<speaker> </speaker>
<bio> </ bio>…
14
But What About…
<conf>
</conf>
<place>
</place>
<date> </date>
<slogan> </slogan>
<participants>
</participants>
<introduction>
</introduction>
<speaker> </speaker>
<bio> …
Machine sees…
< >
</ >
< >
</ >
< > </ >
< > </ >
< >
</ >
< >
</ >
< > </ >
< > </ >
< > </ >
< > </ >
15
Need to Add “Semantics”
► External agreement on meaning of annotations

► E.g., Dublin Core
►Agree on the meaning of a set of annotation tags
► Problems with this approach
►Inflexible
►Limited number of things can be expressed
► Use Ontologies to specify meaning of annotations

► Ontologies provide a vocabulary of terms
► New terms can be formed by combining existing ones
► Meaning (semantics) of such terms is formally specified
► Can also specify relationships between terms in multiple
ontologies
Ontology: Origins and

History
Ontology in Philosophy
a philosophical discipline—a branch of philosophy that
deals with the nature and the organisation of reality
► Science of Being (Aristotle, Metaphysics, IV, 1)
► Tries to answer the questions:
What characterizes being?
Eventually, what is being?
16
Ontology in Linguistics
Concept
Relates to
activates
Form Referent
Stands for
“Tank“
[Ogden, Richards, 1923]
?
Ontology in Computer
Science
► An ontology is an engineering artifact:
► It is constituted by a specific vocabulary used to describe a certain
reality, plus
► a set of explicit assumptions regarding the intended meaning of the
vocabulary.
► Thus, an ontology describes a formal specification of a certain

domain:
► Shared understanding of a domain of interest
► Frmal and machine manipulable model of a domain of interest
“An explicit specification of a conceptualisation” [Gruber93]
17
Structure of an Ontology
Ontologies typically have two distinct components:

► Names for important concepts in the domain
► Elephant is a concept whose members are a kind of animal
► Herbivore is a concept whose members are exactly those animals
who eat only plants or parts of plants
► Adult_Elephant is a concept whose members are exactly those
elephants whose age is greater than 20 years
► Background knowledge/constraints on the domain
► Adult_Elephants weigh at least 2,000 kg
► All Elephants are either African_Elephants or Indian_Elephants
► No individual can be both a Herbivore and a Carnivore
[Mike Uschold, Boeing Corp]
A semantic continuum
Pump: “a device for (pump has

moving a gas or liquid (superclasses (…))
from one place or
container to another”
Shared Semantics Semantics
human Text hardwired; processed and
consensus descriptions used at runtime used at runtime
Implicit Informal Formal Formal

(explicit) (for humans) (for machines)
Further to the right

• Less ambiguity
• Better inter-operation
• More robust – less hardwiring
• More difficult
18
A simple ontology: Pizzas
Pizza Pizza
Topping Pizza_base
Vegetarian Vegetable Deep

Pizza topping dish base
Cheese
topping Regular
Margherita Tomato
topping base
Pizza
Spicy Beef Mozzarella
Pizza topping
Ontology Design and

Deployment
► Given key role of ontologies in the Semantic Web,
it will be essential to provide tools and services to
help users:
► Design and maintain high quality ontologies, e.g.:
►Meaningful — all named classes can have instances
►Correct — captured intuitions of domain experts
►Minimally redundant — no unintended synonyms
►Richly axiomatised — (sufficiently) detailed descriptions
► Store (large numbers) of instances of ontology classes, e.g.:
Annotations from web pages
► Answer queries over ontology classes and instances, e.g.:
►Find more general/specific classes
►Retrieve annotations/pages matching a given description
► Integrate and align multiple ontologies
19
Example Ontology
Many languages use “object

oriented” model based on:
► Objects/Instances/Individuals
► Elements of the domain of discourse
► Equivalent to constants in FOL
► Types/Classes/Concepts
► Sets of objects sharing certain characteristics
► Equivalent to unary predicates in FOL
► Relations/Properties/Roles
► Sets of pairs (tuples) of objects
► Equivalent to binary predicates in FOL
► Such languages are/can be:
► Well understood
► Formally specified
► (Relatively) easy to use
► Amenable to machine processing
20
Aside: Set Based Model Theory

Many logics (including standard First Order Logic) use a model theory based on
Zermelo-Frankel set theory
The domain of discourse (i.e., the part of the world being modelled) is
represented as a set (often refered as ∆)
Objects in the world are interpreted as elements of ∆
Classes/concepts (unary predicates) are subsets of ∆
Properties/roles (binary predicates) are subsets of ∆ £ ∆ (i.e., ∆2)
Ternary predicates are subsets of ∆2 etc.
The sub-class relationship between classes can be interpreted as set inclusion
Doesn’t work for RDF, because in RDF a class (set) can be a member (element)
of another class (set)
In Z-F set theory, elements of classes are atomic (no structure)
Why it’s hard (1)
► Clash of intuitions
► Subject Matter Experts motivated by custom & practice
►Prototypes & Generalities
► Logicians motivated by logic & computational tractability
►Definitions and Universals
► Transparency & predictability vs

Rigour & Completeness
► Neophytes (you?) caught in the muddled middle
21
Why it’s hard (2)
► Conflation of Models
► Meaning: Correctness of Classification & retrieval
► Indexing: Task of discovery, search, or finding
► Use: Task of data entry, decision support, …
► Acquisition: Task of capturing knowledge
► Assuring quality & managing change

► Quality assurance: Criteria for whether it is ‘correct’
► Evolution Coping with change
► Regression testing Controlling changes & maintaining
Quality
Why its hard (3)
► Confusion of terminology and usage

► Religious wars over words and assumptions
► The intersection of
► Linguistics
► Cognitive science
► Software engineering
► Philosophy
► Human Factors
► A jumble of syntaxes
22
Vocabulary
► “Class” ≈ “Concept” ≈ “Category” ≈ “Type”

► “Instance” ≈ “Individual”
► “Entity” ≈ “object”, Class or individual
► “Property” ≈ “Slot” ≈ “Relation” ≈ “Relationtype” ≈
“Attribute” ≈ Semantic link type” ≈ “Role”
► but be careful about “role”
►Means “property” in DL-speak
►Means “role played” in most ontologies
►E.g. “doctor_role”, “student role” …
An Ontology should be just

the Beginning
Declare Databases
Ontologies structure
Knowledge
bases
The
Provide
domain “Semantic
description Web”
Software
agents Problem-
solving
methods Domain-
independent
applications
23
OWL Overview
Matthew Horridge
24
An Introduction to RDF(S) and a Quick

Tour of OWL
BioHealth
Open GALEN Informatics
Group
1 Ontology Tutorial
Ontology
- Borrowed from philosophy - the study of “The nature of

being”
- “A specification of a conceptualisation” [Gruber]
- In general, an ontology provides a mechanism to

capture information about the objects and the
relationships that hold between them in some domain
of interest.
2 Ontology Tutorial
25
RDF - Resource Description

Framework
- RDF is a graphical language used for representing
information about resources on the web. It is a basic
ontology language.
- Resources are described in terms of properties and

property values using RDF statements.
- Statements are represented as triples, consisting of a

subject, predicate and object. [S, P, O]
3 Ontology Tutorial
RDF Example
hasColleague
Nick Matthew
- Subject: Nick
- Predicate: hasColleague
- Object: Matthew
4 Ontology Tutorial
26
Naming Resources In RDF
- RDF uses URIs - Unique Resource Identifiers to

identify resources.
Actually, to be more precise RDF uses URIRefs to identify

resources.
A URIRef consists of a URI and an optional Fragment

Identifier separated from the URI by the hash symbol #.
http://www.co-ode.org/people#hasColleague
coode:hasColleague
5 Ontology Tutorial
Vocabularies
- A set of URIRefs is known as a vocabulary
- The RDF Vocabulary - The set of URIRefs used in

descibing the RDF concepts e.g. rdf:Property,
rdf:Resource, rdf:type.
- The RDFS Vocabulary - The set of URIRefs used in

describing the RDF Schema langauge e.g.
rdfs:Class, rdfs:domain
- The ‘Pizza Ontology’ Vocabulary - pz:hasTopping,

pz:Pizza, pz:VegetarianPizza
6 Ontology Tutorial
27
Linking Statements
- The subject of one statement may be the object of

another statement.
- A set of linked statements (triples) forms an RDF

Graph.
7 Ontology Tutorial
An RDF Graph Example
"Matthew Horridge"
http://www.co-ode.org/people#hasName
http://www.co-ode.org/people#mh
http://www.co-ode.org/people#hasColleague
http://www.co-ode.org/people#hasHomePage
http://www.co-ode.org/people#nd
http://www.cs.man.ac.uk/~horridgm
http://www.co-ode.org/people#hasName
"Nick Drummond"
8 Ontology Tutorial
28
RDF Serialisation
RDF/XML
<?xml version="1.0"?>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xmlns:coode="http://www.co-ode.org/people#"
xml:base="http://www.co-ode.org/people">
<rdf:Description rdf:ID="mh">
<coode:hasHomepage rdf:resource="http://www.cs.man.ac.uk/~horridgm"/>
<coode:hasName>Matthew Horridge</coode:hasName>
</rdf:Description>
<rdf:Description rdf:ID="nd">
<coode:hasName>Nick Drummond</coode:hasName>
<coode:hasColleage rdf:resource="#mh"/>
</rdf:Description>
</rdf:RDF>
<rdf:RDF
xmlns:coode="http://www.co-ode.org/people#"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xml:base="file:/Users/matthewhorridge/Desktop/Test.rdf">
<rdf:Description rdf:about="http://www.co-ode.org/people#nd">
<coode:hasName>Nick Drummond</coode:hasName>
<coode:hasColleage>
<rdf:Description rdf:about="http://www.co-ode.org/people#mh">
<coode:hasName>Matthew Horridge</coode:hasName>
<coode:hasHomepage rdf:resource="http://www.cs.man.ac.uk/~horridgm"/>
</rdf:Description>
</coode:hasColleage>
</rdf:Description>
</rdf:RDF>
9 Ontology Tutorial
Editing RDF(S)
- IsaViz RDF Editor
- Protege-OWL in RDF(S) mode

<rdf:RDF
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
xmlns="http://www.owl-ontologies.com/unnamed.owl#"
xml:base="http://www.owl-ontologies.com/unnamed.rdf">
<rdfs:Class rdf:ID="Person"/>
<rdf:Property rdf:ID="hasFather"/>
<Person rdf:ID="Matthew">
<hasFather>
<Person rdf:ID="Peter"/>
<rdf:RDF
</hasFather>
</Person>
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
</rdf:RDF>
xmlns="http://www.owl-ontologies.com/unnamed.owl#"
xml:base="http://www.owl-ontologies.com/unnamed.rdf">
<rdfs:Class rdf:ID="Person"/>
<rdf:Property rdf:ID="hasFather"/>
<Person rdf:ID="Matthew">
<hasFather>
<Person rdf:ID="Peter"/>
</hasFather>
</Person>
10
</rdf:RDF> Ontology Tutorial
29
RDF Schema (RDFS) - The RDF

Vocabulary Description Language
- RDF Schema ‘semantically extends’ RDF to enable us

to talk about classes of resources, and the properties
that will be used with them.
- It does this by giving special meaning to certain rdf

properties and resources.
- RDF Schema provides the means to describe

application specific RDF vocabularies.
11 Ontology Tutorial
Describing Classes with RDFS

- To describe classes we can use built in RDF Schema
resources:
- rdfs:Class
- rdfs:subClassOf
- These are used in conjunction with the rdf:type

property.
rdfs:subClassOf coode:Person
coode:Man
rdf:type rdf:type
rdfs:Class
coode:Matthew
30
Describing Properties with RDF(S)

- RDF Schema allows us to describe properties.
(Properties are instances of the class rdf:Property!)
- We can specify a domain using rdfs:domain.
- We can specify a range using rdfs:range.
coode:Person
rdf:type
rdfs:Class
rdf:Property rdfs:domain
rdfs:range
rdf:type
coode:hasColleage
Other RDFS Built-In Properties
- rdfs:subPropertyOf
- rdfs:comment
- rdfs:label
- rdfs:seeAlso
- rdfs:isDefinedBy
31
RDF(S) Summary
- RDF - The Resource Description Framework allows us

to describe resources by specifying their properties and
property values.
- RDF Statements are triples of the form [Subject,

Predicate, Object]
- A set of RDF triples forms an RDF Graph
- RDF Schema semantically extends RDF by providing a

means to describe RDF Vocabularies.
RDF(S) Summary
- RDF and RDF Schema provide basic capabilities for

describing vocabularies that describe resources.
However, certain other capabilities are desirable e.g.:
Cardinality constraints, specifying that properties are

transitive, specifying inverse properties, specifying the
‘local’ range and/or cardinality for property when used
with a given class, the ability to describe new classes by
combining existing classes (using intersections and
unions), negation (using ‘not’).
32
OWL
- Latest standard in ontology languages from the World

Wide Web Consortium (W3C).
- Built on top of RDF (OWL semantically extends RDF

(S)), and based on its predecessor language DAML
+OIL.
- OWL has a rich set of modelling constructors.
- Three ‘species’: OWL-Lite, OWL-DL and OWL-Full.
The “Layer Cake”
4RUST
0ROOF
$IGITAL3IGNATURE
,OGIC
/NTOLOGY6OCABULARY
2$&2$&3CHEMA
8-,.38-,3CHEMA
5NICODE 52)
33
Components of an OWL Ontology
- Individuals
Italy
Nick England
hasColl
- Properties
u ntr
y USA
ea
Co
s In
gu
- Classes live
e
Country
Matthew h as
Pe
t
Pet
Person Fluffy
Fido
Reasoning
- For ontologies that fall into the scope of OWL-DL, we

can use a reasoner to infer information that isn’t
explicitly represented in an ontology. Standard
‘reasoning services’ are:
- Subsumption testing
- Equivalence testing
- Consistency testing
- Instantiation testing
34
The Three Species of OWL
- OWL-Full - No restrictions on how/where language

constructs can be used. The union of OWL and RDF
(S). OWL-Full is not decidable.
- OWL-DL - Restricted version of OWL-Full.

Corresponds to a description logic. Certain restrictions
on how/where language constructs can be used in
order to guarantee decidability.
- OWL-Lite - A subset of OWL-DL. The simplest and

easiest to implement of the three species.
OWL Classes
- OWL is an ontology language that is primarily designed

to describe and define classes. Classes are therefore
the basic building blocks of an OWL ontology.
- OWL supports six main ways of describing classes -

The simplest of these is a Named Class. The other
types are: Intersection classes, Union classes,
Complement classes, Restrictions, Enumerated
classes.
35
Named Classes
Professor
Person
Intersection Classes
- Intersection Classes are formed by combining two or

more classes with the intersection (AND) operator.
In description logics (and in

Protege-OWL) we use the
intersection symbol !)
Human ! Female
Human Female
36
Union Classes
- 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 "
JavaProgrammer " CProgrammer
JavaProgrammer CProgrammer
Complement Classes
- 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
37
Restrictions
- Restrictions describe a class of individuals based on

the type and possibly number of relationships that they
participate in.
- Restrictions can be grouped into three main categories:
- Quantifier Restrictions (Existential , Universal )
- Cardinality Restrictions (Min !, Equal =, Max ")
- Has Value Restriction (#)
Existential Restrictions
- The most common type of restriction we will use is an

existential restriction, which has the symbol
(backwards E).
- The existential restriction means ‘some values from’, or

at least one.
- An existential restriction describes the class of

individuals that have at least one kind of relationship
along a specified property to an individual that is a
member of a specified class.
38
Existential Restrictions
hasColleague
hasColleague
has
Co lleag
ue
hasC
olleague
hasColleague Lecturer Lecturer
Universal Restrictions
- Universal - (upside down A) all values from , or

only. For a given property, all the individuals
must be members of a speciﬁed class.
39
UE
EAG
#O LL
AS
H
! hasColleague
has
Co lleag
ue
hasC
olleague
hasColleague Professor Professor
Other Restrictions
- Cardinality Restrictions - For a given property,
cardinality restrictions allow us to talk about the number
of relationships that a class of individuals participate in.
- Has Value Restrictions - Allow us to specify that class

of individuals that participate in a specified relationship
with a specific individual.
40
hasValue Restriction Example
HAS#OLLEAGUE
HAS#OLL
EAGUE
E
HAS#OLLEAGU
hasColleague # Matthew Person
Enumeration Classes
- An enumeration class is specified by explicitly and

exhaustively listing the individuals that are members of
the enumeration class.
To specify an enumerated
3PAIN class, the individuals that are
members of the class are listed
'ERMANY
inside curly brackets {...}
&RANCE
)TALY
{Spain Germany France Italy}
HolidayDestinations
41
Properties
- There are two main categories of properties: Object

properties and datatype properties.
- Object properties link individuals to individuals.
- Datatype properties link individuals to datatype values

(e.g. integers, floats, strings).
- Object properties my have an inverse property e.g. the

inverse of worksFor might be employs.
- Properties can have as specified domain and range.
Property Characteristics
- We can specify certain property characteristics.
- Functional - For a given individual, the property

takes only one value.
- Inverse functional - The inverse of the property is

functional.
- Symmetric - If a property links A to B then it can be

inferred that it links B to A.
- Transitive - If a property links A to B and B to C then

it can be inferred that it links A to C.
42
OWL Summary
- OWL is the latest standard in ontology languages.
- It is layered on top of RDF and RDFS, and has a rich

set of constructs.
- There are three species of OWL: OWL-Lite, OWL-DL

and OWL-Full.
- We can perform automated reasoning over ontologies

that are written in OWL-Lite and OWL-DL.
More Information
- W3C OWL Web Site
- http://www.w3.org/2004/OWL/
- CO-ODE Web Site
- http://www.co-ode.org
- Protege-OWL Web Site
- http://protege.stanford.edu/plugins/owl
43
Protégé-OWL part 1
Nick Drummond
Matthew Horridge
44
A Practical Introduction to
Ontologies & OWL
Session 1: Primitive Classes in OWL
Nick Drummond & Matthew Horridge
O p enG A LEN
BioHealth
Informatics
Group
Overview
► Pizzas – Card Sorting

► Protégé Introduction
► Subsumption
► Creating a Class Hierarchy
► Consistency
► Disjointness
► Relationships & Properties
► Restrictions
► Polyhierarchies - Issues
Copyright © 2005, The University of Manchester
45
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…
46
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
47
Our Application
www.co-ode.org/downloads/pizzafinder/
Exercise 1: Card Sorting
48
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
_in
Person lives Country
Elvis Belgium
Holger lives_in
Paraguay
Kylie
Class (concept)
Latvia
S.Claus China
Hai
lives_in
Individual (instance)
ha
s_
pe
ha
et
arrow = relationship
s_
Flipper
has_p
pe
t
label = Property
Animal
Rudolph
49
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 Æ predicate Æ Object
Individual a Æ hasProperty Æ Individual b
nick_drummond Æ givesTutorial Æ 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
50
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)
51
…
► 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
52
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
A
• A subsumes B
B • A is a superclass of B
• B is a subclass of A
• All members of B are also
members of A
53
Class Editor
Class 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
54
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
OWL = easy to make mistakes = save regularly

1. Select File Æ Save Project As
A dialog (as shown) will pop up
2. Select a file directly by clicking the button on the top right

You will notice that 2 files are created
.pprj – the project file
this just stores information about the GUI
and the workspace
.owl – the OWL file
this is where your ontology is stored in
RDF/OWL format
3. Select OK
55
Loading OWL files
1. If you only have an OWL

file:
- FileÆ 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 Æ 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)
56
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
57
Accessing the Reasoner
Classify taxonomy
(and check consistency)
Compute inferred types

(for individuals)
Just check consistency

(for efficiency)
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 the

reasoner 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
58
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
59
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…
60
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
61
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 hierarchy

eg 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
62
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
63
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
Delete Property
New Object Property:

Associates an individual to another individual
not used today:

- New Datatype Property (String, int etc)
- New Annotation Properties for metadata
- New SubProperty – ie create “under” the

current selection
64
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 pattern
eg 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
65
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 Types
Logical (Anonymous) Classes
Create Restriction (next)
Create Class Expression Add Named Superclass
66
Creating Restrictions
Restricted Property
Restriction
Type
Filler
Expression
Expression
Syntax
Construct
check
Palette
What does this mean?
► We have created a restriction: ∃ hasBase PizzaBase

on Class Pizza as a necessary condition
ase
hasB
Pizza ase PizzaBase
hasB
ase
hasB
hasB
ase
► “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”
► “Every individual of the Pizza class must have at least one base
from the class PizzaBase”
67

ase
hasB
Pizza ase PizzaBase
hasB
ase
hasB
hasB
ase
► “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”
Why?

ha
sB
ase
hasB
a
se
ase PizzaBase
hasB
∃ hasBase
PizzaBase ase
hasB
hasB
ase
hasBas
e
► Each Restriction or Class Expression describes the set of all

individuals that satisfy the condition
68
Why? Necessary conditions

ha
sB
ase
hasB
a
se
Pizza PizzaBase
ase
hasB
∃ hasBase
PizzaBase ase
hasB
hasB
ase
hasBas
e
► Each necessary condition on a class is a superclass of that class

► 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
69
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
70
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
► 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
let the reasoner do it!

71
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
72
Knowledge
Acquisition
Jeremy Rogers
73
Informal Modelling
Jeremy Roberts
O p enG A LEN
BioHealth
Informatics
Group 1 Ontology Tutorial, © 2005 Univ. of Manchester
Steps in Developing an
Ontology
1. Establish the purpose
► Without purpose, no scope, requirements, evaluation,
2. Informal/Semiformal knowledge elicitation

► Collect the terms
► Organise terms informally
► Paraphrase and clarify terms to produce informal concept
definitions
► Diagram informally
3. Refine requirements & tests
2 Ontology Tutorial, © 2005 Univ. of Manchester
74
Steps in Implementing an
Ontology
4. Implementation
► Paraphrase and comment at each stage before implementing
► Develop normalised schema and skeleton
► Implement prototype recording the intention as a paraphrase
► Keep track of what you meant to do so you can compare with what happens
► Implementing logic-based ontologies is programming
► Scale up a bit
► Check performance
► Populate
► Possibly with help of text mining and language technology
5. Evaluate & quality assure

► Against goals
► Include tests for evolution and change management
► Design regression tests and “probes”
6. Monitor use and evolve
► Process not product!
Purpose & Scope of the

Animals Ontology
► To provide an ontology for an index of a

children’s book of animals including
► Where they live
► What they eat
►Carnivores, herbivores and omnivores
► How dangerous they are
► How big they are
► A bit of basic anatomy
►numbers of legs, wings, toes, etc.
75
Eliciting Knowledge
http://www.epistemics.co.uk/Notes/63-0-0.htm
► Most knowledge is in the heads of experts

► Experts have vast amounts of knowledge
► Experts have a lot of tacit knowledge
► They don't know all that they know and use
► Tacit knowledge is hard (impossible) to describe
► Experts are very busy and valuable people
► Each expert doesn't know everything
…there are known knowns; there are things

we know we know. We also know there are
known unknowns; that is to say we know
there are some things we do not know. But
there are also unknown unknowns -- the ones
we don't know we don't know.
76
Elicitation Techniques
► Take experts off the job for short time periods

► Allow non-experts to understand the knowledge
► Focus on the essential knowledge
► Can capture tacit knowledge
► Allow knowledge to be collated from different experts
► Allow knowledge to be validated and maintained
Types of technique (1)
► Protocol-generation techniques
include various types of interviews (unstructured,
semi-structured and structured), reporting techniques
(such as self-report and shadowing) and observational
techniques
► Protocol analysis techniques

are used with transcripts of interviews or other text-
based information to identify various types of
knowledge, such as goals, decisions, relationships
and attributes. This acts as a bridge between the use
of protocol-based techniques and knowledge
modelling techniques.
77
► Hierarchy-generation techniques
such as laddering are used to build taxonomies or
other hierarchical structures such as goal trees and
decision networks.
► Matrix-based techniques
involve the construction of grids indicating such things
as problems encountered against possible solutions.
Important types include the use of frames for
representing the properties of concepts and the
repertory grid technique used to elicit, rate, analyse
and categorise the properties of concepts.
► Sorting techniques
are used for capturing the way people compare and
order concepts, and can lead to the revelation of
knowledge about classes, properties and priorities.
► Limited-information and constrained-processing tasks

are techniques that either limit the time and/or
information available to the expert when performing
tasks. For instance, the twenty-questions technique
provides an efficient way of accessing the key
information in a domain in a prioritised order.
78
► Diagram-based techniques
include the generation and use of concept maps, state
transition networks, event diagrams and process
maps. The use of these is particularly important in
capturing the "what, how, when, who and why" of
tasks and events.
Collect the concepts
► Card sorting is often the best way

► Write down each concept/idea on a card
► Organise them into piles
► Link the piles together
► Do it again, and again
► Works best in a small group
► In the lab we will provide you with some pre-printed cards and many
spare cards
►Work in pairs or triples
79
Example: Animals & Plants
► Dog Carnivore ► Dangerous

► Cat Plant ► Pet
► Cow ► Domestic Animal
Animal
► Person ► Farm animal
► Tree Fur ► Draft animal
► Grass Child ► Food animal
► Herbivore Parent ► Fish
► Male ► Carp
Mother
► Female ► Goldfish
Father
Organise the concepts

Example: Animals & Plants
► Dog Carnivore ► Healthy

► Cat Plant ► Pet
► Cow ► Domestic Animal
Animal
► Person ► Farm animal
► Tree Fur ► Draft animal
► Grass Child ► Food animal
► Herbivore Parent ► Fish
► Male ► Carp
Mother
► Female ► Goldfish
Father
80
Extend the concepts

“Laddering”
► Take a group of things and ask what they have in common
► Then what other ‘siblings’ there might be
► e.g.
► Plant, Animal Æ Living Thing
►Might add Bacteria and Fungi but not now
► Cat, Dog, Cow, Person Æ Mammal
►Others might be Goat, Sheep, Horse, Rabbit,…
► Cow, Goat, Sheep, Horse Æ Hoofed animal (“Ungulate”)
►What others are there? Do they divide amongst themselves?
► Wild, Domestic Æ Demoestication
►What other states – “Feral” (domestic returned to wild)
Vocabulary note:
“Sibling” = “brother or sister”
Choose Some Main Axes
► Add abstractions where needed

► e.g. “Living thing”
► identify relations
► e.g. “eats”, “owns”, “parent of”
► Identify definable things
► e.g. “child”, “parent”, “Mother”, “Father”
►Things where you can say clearly what it means
►Try to define a dog precisely – very difficult
►A “natural kind”
► make names explicit
81
Choose Some Main Axes

Add abstractions where needed; identify relations;
Identify definable things, make names explicit
► Living Thing ► Modifiers
Relations
► Animal eats
► domestic
►Mammal ► pet owns
►Cat ► Farmed
parent-of
►Dog ► Draft
►Cow ► Food …
►Person ► Wild Definable
►Fish ► Health Carinvore
►Carp ► healthy
Herbivore
►Goldfish ► sick
► Sex
Child
► Plant
►Tree ► Male Parent
►Grass
► Female Mother
► Age Father
►Fruit
► Adult
► Child
Food Animal
Draft Animal
Self_standing_entities
►Things that can exist on there own nouns

►People, animals, houses, actions, processes, …
►Roughly nouns
►Modifiers
►Things that modify (“inhere”) in other things
►Roughly adjectives and adverbs
82
Ontology Engineering
Jeremy Rogers
83
From hype to practicality

In which Eeyore reviews Ontology Engineering
Dr2 Jeremy Rogers

Manchester University
Jeremy.e.rogers@manchester.ac.uk
O p en G A LEN
BioHealth
Ontology Tutorial, © 2005 Univ. of Manchester
Informatics
Group
Outline
► Where do I start?
► Top level ontologies
► The naming of things

► Metadata and provenance
► Mission creep
► Reasoning
► Process, not product
► Innate complexity
84
Top ontologies
SHZZ
BA
BEAR
DA DZZT
NINNER
Top ontologies
SHOE
Brrrrr BADJOO DZZT
BOO TAKTOR
PLAY
DA
OSKA NO
NINNER TEDDY
OPA SHYA
JOO CAY ISKY PREE APA
DOW
85
Invasion of the
Philosophers
Previous efforts at ontology building have been conceived in
pragmatic terms, as an outgrowth of knowledge engineering or
artificial intelligence research or more generally as a project
deriving its motivation from the need to solve problems internal to
the development of computer systems.
ECOR, in contrast, looks beyond the realm of software artefacts,
starting out from the idea that the project of developing reference
ontologies can profit from the theories developed by philosophers
over 2500 years of ontological research.
Too many ontology builders have taken as their starting point
existing database systems or the conceptualizations used by the
practitioners within given domains, without sufficiently checking
whether these conceptualizations correspond with identifiable
entities and relations on the side of reality itself.
Top level ontologies

CYC
SUMO
GUM
Mikrokosmos
Phenomenon
DomainCategory
ModifierConcept
SENSUS
Feature
Collection
State Selector
Aspect Role
Unit
Modality
DOLCE
Generalised
Structure
Process Generalised
Substance
Status
Level Of
Specification
OCHRE
Heat
Energy Substance
Chemical
Substance
Body
Substance
NAMED
Substance
BFO
Light
Sound
Tissue NAMED Body Substance
GALEN
86
Outline
►Where do I start?
►Top level ontologies
►The naming of things

►Metadata and provenance
►Mission creep
►Reasoning
►Process, not product
►Innate complexity
Classes vs their Names
► Classes represent concepts not their names

► The class name can change, but still refer to the same
concept (e.g. First Disease = Measles)
► Synonym names for the same concept are not different
classes
► Class names usually given in singular (in English)
► Many arguments are about names not substance
► Are both concepts valid?
►Cough – sign or symptom?
► If so, may need new names – even if neologisms
►CoughSign, CoughSymptom
87
When to introduce…
a new class?
►Subclasses of a class usually have
► Additional properties
► Additional restrictions
► Narrowed restrictions
► Closure axioms
►New classes
► Leaf nodes – new things
► New definitions – new RE-USABLE abstractions
► High level primitives
► Organisational principles
When to introduce…
A new class or a property value?
How important is the distinction for the domain?
88
Outline

►Mission creep
►Reasoning
OWL Annotations
►Enable us to describe the class itself, e.g.

► Comments & Explanations
► Authorship
► Provenance –
► where it came from, previous versions, evidence, etc.
► what it is to be used for, scope, limitations, work arounds
► Editorial status
► External coding systems
► CUI/LUI, S-CT, MeSH, etc.
► Additional names
89
Outline

►Mission creep
►Reasoning
Ontology Engineering:
Mission Creep
►An ontology should not contain all the possible
information about the domain
► No need to specialize or generalize more than the application
requires
► No need to include all possible properties of a class
► Only the most salient properties
► Only the properties that the applications require
90
Limiting the Scope
►Ontology of wine, food, and their pairings probably

will not include
► Bottle size
► Label color
► My favorite food and wine
►An ontology of biological experiments will contain

► Biological organism
► Experimenter
►Is the class Experimenter a subclass of Biological

organism?
Outline

►Mission creep
►Reasoning
91
A Prac ca n roduc on o On o og es & OWL © 2005 The Un vers y o Manches er
topClass
I Certain infectious and parasitic diseases
II Neoplasms
III Diseases of the blood and blood-forming organs and certain disorders involving the immune mechanism
IV Endocrine, nutritional and metabolic diseases
V Mental and behavioural disorders
Goodbye to
VI Diseases of the nervous system
VII Diseases of the eye and adnexa
VIII Diseases of the ear and mastoid process
IX Diseases of the circulatory systems
X Diseases of the respiratory system
XI Diseases of the digestive system
XII Diseases of the skin and subcutaneous tissue
XIII Diseases of the musculoskeletal system and connective tissue
XIV Diseases of the genitourinary system
XV Pregnancy, childbirth and the puerperium
XVI Certain conditions originating in the perinatal period
XVII Congenital malformations, deformations and chromosomal abnormalities
XVIII Symptoms, signs and abnormal clinical and laboratory findings, not elsewhere classified
XIX Injury, poisoning and certain other consequences of external causes
XX External causes of morbidity and mortality
V01-V99 Transport accidents
combinatorial explosions
V01-V09 Pedestrian injured in transport accident
V10-V19 Pedal cyclist injured in transport accident
V10 Pedal cyclist injured in collision with pedestrian or animal
V10.0 Pedal cyclist injured in collision with pedestrian or animal, driver, nontraffic accident
V10.00 Pedal cyclist injured in collision with pedestrian or animal, driver, nontraffic accident, while engaged in sports activity
V10.01 Pedal cyclist injured in collision with pedestrian or animal, driver, nontraffic accident, while engaged in leisure activity
V10.02 Pedal cyclist injured in collision with pedestrian or animal, driver, nontraffic accident, while working for an income
V10.03 Pedal cyclist injured in collision with pedestrian or animal, driver, nontraffic accident, while engaged in other types of work
V10.04 Pedal cyclist injured in collision with pedestrian or animal, driver, nontraffic accident, while resting, sleeping, eating or engaging in other vital activities
V10.08 Pedal cyclist injured in collision with pedestrian or animal, driver, nontraffic accident, while engaged in other specified activities
V10.09 Pedal cyclist injured in collision with pedestrian or animal, driver, nontraffic accident, during unspecified activity
V10.1 Pedal cyclist injured in collision with pedestrian or animal, passenger, nontraffic accident
V10.10 Pedal cyclist injured in collision with pedestrian or animal, passenger, nontraffic accident, while engaged in sports activity
V10.11 Pedal cyclist injured in collision with pedestrian or animal, passenger, nontraffic accident, while engaged in leisure activity
V10.12 Pedal cyclist injured in collision with pedestrian or animal, passenger, nontraffic accident, while working for an income
V10.13 Pedal cyclist injured in collision with pedestrian or animal, passenger, nontraffic accident, while engaged in other types of work
V10.14 Pedal cyclist injured in collision with pedestrian or animal, passenger, nontraffic accident, while resting, sleeping, eating or engaging in other vital activities
V13 Pedal cyclist injured in collision with car, pick-up truck or van
V10.18 Pedal cyclist injured in collision with pedestrian or animal, passenger, nontraffic accident, while engaged in other specified activities
V10.19 Pedal cyclist injured in collision with pedestrian or animal, passenger, nontraffic accident, during unspecified activity V13.0 Pedal cyclist injured in collision with car, pick-up truck or van, driver, nontraffic accident V15.2 Pedal cyclist injured in collision with railway train or railway vehicle, unspecified pedal cyclist, nontraffic accident
V10.2 Pedal cyclist injured in collision with pedestrian or animal, unspecified pedal cyclist, nontraffic accident V13.00 Pedal cyclist injured in collision with car, pick-up truck or van, driver, nontraffic accident, while engaged in sports activity V15.20 Pedal cyclist injured in collision with railway train or railway vehicle, unspecified pedal cyclist, nontraffic accident, while engaged in sports activity
V10.20 Pedal cyclist injured in collision with pedestrian or animal, unspecified pedal cyclist, nontraffic accident, while engaged in sports activity
V13.01 Pedal cyclist injured in collision with car, pick-up truck or van, driver, nontraffic accident, while engaged in leisure activity V15.21 Pedal cyclist injured in collision with railway train or railway vehicle, unspecified pedal cyclist, nontraffic accident, while engaged in leisure activity
V10.21 Pedal cyclist injured in collision with pedestrian or animal, unspecified pedal cyclist, nontraffic accident, while engaged in leisure activity
V10.22 Pedal cyclist injured in collision with pedestrian or animal, unspecified pedal cyclist, nontraffic accident, while working for an income V13.02 Pedal cyclist injured in collision with car, pick-up truck or van, driver, nontraffic accident, while working for an income V15.22 Pedal cyclist injured in collision with railway train or railway vehicle, unspecified pedal cyclist, nontraffic accident, while working for an income
V10.23 Pedal cyclist injured in collision with pedestrian or animal, unspecified pedal cyclist, nontraffic accident, while engaged in other types of work V13.03 Pedal cyclist injured in collision with car, pick-up truck or van, driver, nontraffic accident, while engaged in other types of work V15.23 Pedal cyclist injured in collision with railway train or railway vehicle, unspecified pedal cyclist, nontraffic accident, while engaged in other types of work
V10.24 Pedal cyclist injured in collision with pedestrian or animal, unspecified pedal cyclist, nontraffic accident, while resting, sleeping, eating or engaging in other vital activities V13.04 Pedal cyclist injured in collision with car, pick-up truck or van, driver, nontraffic accident, while resting, sleeping, eating or engaging in other vital activities V15.24 Pedal cyclist injured in collision with railway train or railway vehicle, unspecified pedal cyclist, nontraffic accident, while resting, sleeping, eating or engaging in other vital activities
V10.28 Pedal cyclist injured in collision with pedestrian or animal, unspecified pedal cyclist, nontraffic accident, while engaged in other specified activities
V13.08 Pedal cyclist injured in collision with car, pick-up truck or van, driver, nontraffic accident, while engaged in other specified activities V15.28 Pedal cyclist injured in collision with railway train or railway vehicle, unspecified pedal cyclist, nontraffic accident, while engaged in other specified activities
V10.29 Pedal cyclist injured in collision with pedestrian or animal, unspecified pedal cyclist, nontraffic accident, during unspecified activity
V10.3 Pedal cyclist injured in collision with pedestrian or animal, while boarding or alighting V13.09 Pedal cyclist injured in collision with car, pick-up truck or van, driver, nontraffic accident, during unspecified activity V15.29 Pedal cyclist injured in collision with railway train or railway vehicle, unspecified pedal cyclist, nontraffic accident, during unspecified activity
V10.30 Pedal cyclist injured in collision with pedestrian or animal, while boarding or alighting, while engaged in sports activity V13.1 Pedal cyclist injured in collision with car, pick-up truck or van, passenger, nontraffic accident V15.3 Pedal cyclist injured in collision with railway train or railway vehicle, while boarding or alighting
V10.31 Pedal cyclist injured in collision with pedestrian or animal, while boarding or alighting, while engaged in leisure activity
V13.10 Pedal cyclist injured in collision with car, pick-up truck or van, passenger, nontraffic accident, while engaged in sports activity V15.30 Pedal cyclist injured in collision with railway train or railway vehicle, while boarding or alighting, while engaged in sports activity
V10.32 Pedal cyclist injured in collision with pedestrian or animal, while boarding or alighting, while working for an income
V10.33 Pedal cyclist injured in collision with pedestrian or animal, while boarding or alighting, while engaged in other types of work V13.11 Pedal cyclist injured in collision with car, pick-up truck or van, passenger, nontraffic accident, while engaged in leisure activity V15.31 Pedal cyclist injured in collision with railway train or railway vehicle, while boarding or alighting, while engaged in leisure activity
V10.34 Pedal cyclist injured in collision with pedestrian or animal, while boarding or alighting, while resting, sleeping, eating or engaging in other vital activities V13.12 Pedal cyclist injured in collision with car, pick-up truck or van, passenger, nontraffic accident, while working for an income V15.32 Pedal cyclist injured in collision with railway train or railway vehicle, while boarding or alighting, while working for an income, while working for an income
V10.38 Pedal cyclist injured in collision with pedestrian or animal, while boarding or alighting, while engaged in other specified activities V13.13 Pedal cyclist injured in collision with car, pick-up truck or van, passenger, nontraffic accident, while engaged in other types of work V15.33 Pedal cyclist injured in collision with railway train or railway vehicle, while boarding or alighting, while engaged in other types of work
V10.39 Pedal cyclist injured in collision with pedestrian or animal, while boarding or alighting, during unspecified activity
V13.14 Pedal cyclist injured in collision with car, pick-up truck or van, passenger, nontraffic accident, while resting, sleeping, eating or engaging in other vital activities V15.34 Pedal cyclist injured in collision with railway train or railway vehicle, while boarding or alighting, while resting, sleeping, eating or engaging in other vital activities
V10.4 Pedal cyclist injured in collision with pedestrian or animal, driver, traffic accident
V10.40 Pedal cyclist injured in collision with pedestrian or animal, driver, traffic accident, while engaged in sports activity V13.18 Pedal cyclist injured in collision with car, pick-up truck or van, passenger, nontraffic accident, while engaged in other specified activities V15.38 Pedal cyclist injured in collision with railway train or railway vehicle, while boarding or alighting, while engaged in other specified activities
V10.41 Pedal cyclist injured in collision with pedestrian or animal, driver, traffic accident, while engaged in leisure activity V13.19 Pedal cyclist injured in collision with car, pick-up truck or van, passenger, nontraffic accident, during unspecified activity V15.39 Pedal cyclist injured in collision with railway train or railway vehicle, while boarding or alighting, during unspecified activity
V10.42 Pedal cyclist injured in collision with pedestrian or animal, driver, traffic accident, while working for an income
V13.2 Pedal cyclist injured in collision with car, pick-up truck or van, unspecified pedal cyclist, nontraffic accident V15.4 Pedal cyclist injured in collision with railway train or railway vehicle, driver, traffic accident
V10.43 Pedal cyclist injured in collision with pedestrian or animal, driver, traffic accident, while engaged in other types of work
V10.44 Pedal cyclist injured in collision with pedestrian or animal, driver, traffic accident, while resting, sleeping, eating or engaging in other vital activities V13.20 Pedal cyclist injured in collision with car, pick-up truck or van, unspecified pedal cyclist, nontraffic accident, while engaged in sports activity V15.40 Pedal cyclist injured in collision with railway train or railway vehicle, driver, traffic accident, while engaged in sports activity
V10.48 Pedal cyclist injured in collision with pedestrian or animal, driver, traffic accident, while engaged in other specified activities V13.21 Pedal cyclist injured in collision with car, pick-up truck or van, unspecified pedal cyclist, nontraffic accident, while engaged in leisure activity V15.41 Pedal cyclist injured in collision with railway train or railway vehicle, driver, traffic accident, while engaged in leisure activity
V10.49 Pedal cyclist injured in collision with pedestrian or animal, driver, traffic accident, during unspecified activity V13.22 Pedal cyclist injured in collision with car, pick-up truck or van, unspecified pedal cyclist, nontraffic accident, while working for an income V15.42 Pedal cyclist injured in collision with railway train or railway vehicle, driver, traffic accident, while working for an income
V10.5 Pedal cyclist injured in collision with pedestrian or animal, passenger, traffic accident
V13.23 Pedal cyclist injured in collision with car, pick-up truck or van, unspecified pedal cyclist, nontraffic accident, while engaged in other types of work V15.43 Pedal cyclist injured in collision with railway train or railway vehicle, driver, traffic accident, while engaged in other types of work
V10.50 Pedal cyclist injured in collision with pedestrian or animal, passenger, traffic accident, while engaged in sports activity
V10.51 Pedal cyclist injured in collision with pedestrian or animal, passenger, traffic accident, while engaged in leisure activity V13.24 Pedal cyclist injured in collision with car, pick-up truck or van, unspecified pedal cyclist, nontraffic accident, while resting, sleeping, eating or engaging in other vital activities V15.44 Pedal cyclist injured in collision with railway train or railway vehicle, driver, traffic accident, while resting, sleeping, eating or engaging in other vital activities
V10.52 Pedal cyclist injured in collision with pedestrian or animal, passenger, traffic accident, while working for an income V13.28 Pedal cyclist injured in collision with car, pick-up truck or van, unspecified pedal cyclist, nontraffic accident, while engaged in other specified activities V15.48 Pedal cyclist injured in collision with railway train or railway vehicle, driver, traffic accident, while engaged in other specified activities
V10.53 Pedal cyclist injured in collision with pedestrian or animal, passenger, traffic accident, while engaged in other types of work
V13.29 Pedal cyclist injured in collision with car, pick-up truck or van, unspecified pedal cyclist, nontraffic accident, during unspecified activity V15.49 Pedal cyclist injured in collision with railway train or railway vehicle, driver, traffic accident, during unspecified activity
V10.54 Pedal cyclist injured in collision with pedestrian or animal, passenger, traffic accident, while resting, sleeping, eating or engaging in other vital activities
V10.58 Pedal cyclist injured in collision with pedestrian or animal, passenger, traffic accident, while engaged in other specified activities V13.3 Pedal cyclist injured in collision with car, pick-up truck or van, while boarding or alighting V15.5 Pedal cyclist injured in collision with railway train or railway vehicle, passenger, traffic accident
V10.59 Pedal cyclist injured in collision with pedestrian or animal, passenger, traffic accident, during unspecified activity V13.30 Pedal cyclist injured in collision with car, pick-up truck or van, while boarding or alighting, while engaged in sports activity V15.50 Pedal cyclist injured in collision with railway train or railway vehicle, passenger, traffic accident, while engaged in sports activity
V10.9 Pedal cyclist injured in collision with pedestrian or animal, unspecified pedal cyclist, traffic accident V13.31 Pedal cyclist injured in collision with car, pick-up truck or van, while boarding or alighting, while engaged in leisure activity V15.51 Pedal cyclist injured in collision with railway train or railway vehicle, passenger, traffic accident, while engaged in leisure activity
V10.90 Pedal cyclist injured in collision with pedestrian or animal, unspecified pedal cyclist, traffic accident, while engaged in sports activity
V13.32 Pedal cyclist injured in collision with car, pick-up truck or van, while boarding or alighting, while working for an income V15.52 Pedal cyclist injured in collision with railway train or railway vehicle, passenger, traffic accident, while working for an income
V10.91 Pedal cyclist injured in collision with pedestrian or animal, unspecified pedal cyclist, traffic accident, while engaged in leisure activity
V10.92 Pedal cyclist injured in collision with pedestrian or animal, unspecified pedal cyclist, traffic accident, while working for an income V13.33 Pedal cyclist injured in collision with car, pick-up truck or van, while boarding or alighting, while engaged in other types of work V15.53 Pedal cyclist injured in collision with railway train or railway vehicle, passenger, traffic accident, while engaged in other types of work
V10.93 Pedal cyclist injured in collision with pedestrian or animal, unspecified pedal cyclist, traffic accident, while engaged in other types of work V13.34 Pedal cyclist injured in collision with car, pick-up truck or van, while boarding or alighting, while resting, sleeping, eating or engaging in other vital activities V15.54 Pedal cyclist injured in collision with railway train or railway vehicle, passenger, traffic accident, while resting, sleeping, eating or engaging in other vital activities
V10.94 Pedal cyclist injured in collision with pedestrian or animal, unspecified pedal cyclist, traffic accident, while resting, sleeping, eating or engaging in other vital activities
V13.38 Pedal cyclist injured in collision with car, pick-up truck or van, while boarding or alighting, while engaged in other specified activities V15.58 Pedal cyclist injured in collision with railway train or railway vehicle, passenger, traffic accident, while engaged in other specified activities
V10.98 Pedal cyclist injured in collision with pedestrian or animal, unspecified pedal cyclist, traffic accident, while engaged in other specified activities
V10.99 Pedal cyclist injured in collision with pedestrian or animal, unspecified pedal cyclist, traffic accident, during unspecified activity V13.39 Pedal cyclist injured in collision with car, pick-up truck or van, while boarding or alighting, during unspecified activity V15.59 Pedal cyclist injured in collision with railway train or railway vehicle, passenger, traffic accident, during unspecified activity
V11 Pedal cyclist injured in collision with other pedal cycle V13.4 Pedal cyclist injured in collision with car, pick-up truck or van, driver, traffic accident V15.9 Pedal cyclist injured in collision with railway train or railway vehicle, unspecified pedal cyclist, traffic accident
V11.0 Pedal cyclist injured in collision with other pedal cycle, driver, nontraffic accident V13.40 Pedal cyclist injured in collision with car, pick-up truck or van, driver, traffic accident, while engaged in sports activity V15.90 Pedal cyclist injured in collision with railway train or railway vehicle, unspecified pedal cyclist, traffic accident, while engaged in sports activity
V11.00 Pedal cyclist injured in collision with other pedal cycle, driver, nontraffic accident, while engaged in sports activity
V13.41 Pedal cyclist injured in collision with car, pick-up truck or van, driver, traffic accident, while engaged in leisure activity V15.91 Pedal cyclist injured in collision with railway train or railway vehicle, unspecified pedal cyclist, traffic accident, while engaged in leisure activity
V11.01 Pedal cyclist injured in collision with other pedal cycle, driver, nontraffic accident, while engaged in leisure activity
V11.02 Pedal cyclist injured in collision with other pedal cycle, driver, nontraffic accident, while working for an income V13.42 Pedal cyclist injured in collision with car, pick-up truck or van, driver, traffic accident, while working for an income V15.92 Pedal cyclist injured in collision with railway train or railway vehicle, unspecified pedal cyclist, traffic accident, while working for an income
V11.03 Pedal cyclist injured in collision with other pedal cycle, driver, nontraffic accident, while engaged in other types of work V13.43 Pedal cyclist injured in collision with car, pick-up truck or van, driver, traffic accident, while engaged in other types of work V15.93 Pedal cyclist injured in collision with railway train or railway vehicle, unspecified pedal cyclist, traffic accident, while engaged in other types of work
V11.04 Pedal cyclist injured in collision with other pedal cycle, driver, nontraffic accident, while resting, sleeping, eating or engaging in other vital activities
V13.44 Pedal cyclist injured in collision with car, pick-up truck or van, driver, traffic accident, while resting, sleeping, eating or engaging in other vital activities V15.94 Pedal cyclist injured in collision with railway train or railway vehicle, unspecified pedal cyclist, traffic accident, while resting, sleeping, eating or engaging in other vital activities
V11.08 Pedal cyclist injured in collision with other pedal cycle, driver, nontraffic accident, while engaged in other specified activities
V11.09 Pedal cyclist injured in collision with other pedal cycle, driver, nontraffic accident, during unspecified activity V13.48 Pedal cyclist injured in collision with car, pick-up truck or van, driver, traffic accident, while engaged in other specified activities V15.98 Pedal cyclist injured in collision with railway train or railway vehicle, unspecified pedal cyclist, traffic accident, while engaged in other specified activities
V11.1 Pedal cyclist injured in collision with other pedal cycle, passenger, nontraffic accident V13.49 Pedal cyclist injured in collision with car, pick-up truck or van, driver, traffic accident, during unspecified activity V15.99 Pedal cyclist injured in collision with railway train or railway vehicle, unspecified pedal cyclist, traffic accident, during unspecified activity
V11.10 Pedal cyclist injured in collision with other pedal cycle, passenger, nontraffic accident, while engaged in sports activity V13.5 Pedal cyclist injured in collision with car, pick-up truck or van, passenger, traffic accident V16 Pedal cyclist injured in collision with other nonmotor vehicle
V11.11 Pedal cyclist injured in collision with other pedal cycle, passenger, nontraffic accident, while engaged in leisure activity
V13.50 Pedal cyclist injured in collision with car, pick-up truck or van, passenger, traffic accident, while engaged in sports activity V16.0 Pedal cyclist injured in collision with other nonmotor vehicle, driver, nontraffic accident
V11.12 Pedal cyclist injured in collision with other pedal cycle, passenger, nontraffic accident, while working for an income
V11.13 Pedal cyclist injured in collision with other pedal cycle, passenger, nontraffic accident, while engaged in other types of work V13.51 Pedal cyclist injured in collision with car, pick-up truck or van, passenger, traffic accident, while engaged in leisure activity V16.00 Pedal cyclist injured in collision with other nonmotor vehicle, driver, nontraffic accident, while engaged in sports activity
V11.14 Pedal cyclist injured in collision with other pedal cycle, passenger, nontraffic accident, while resting, sleeping, eating or engaging in other vital activities V13.52 Pedal cyclist injured in collision with car, pick-up truck or van, passenger, traffic accident, while working for an income V16.01 Pedal cyclist injured in collision with other nonmotor vehicle, driver, nontraffic accident, while engaged in leisure activity
V11.18 Pedal cyclist injured in collision with other pedal cycle, passenger, nontraffic accident, while engaged in other specified activities
V13.53 Pedal cyclist injured in collision with car, pick-up truck or van, passenger, traffic accident, while engaged in other types of work V16.02 Pedal cyclist injured in collision with other nonmotor vehicle, driver, nontraffic accident, while working for an income
V11.19 Pedal cyclist injured in collision with other pedal cycle, passenger, nontraffic accident, during unspecified activity
V11.2 Pedal cyclist injured in collision with other pedal cycle, unspecified pedal cyclist, nontraffic accident V13.54 Pedal cyclist injured in collision with car, pick-up truck or van, passenger, traffic accident, while resting, sleeping, eating or engaging in other vital activities V16.03 Pedal cyclist injured in collision with other nonmotor vehicle, driver, nontraffic accident, while engaged in other types of work
V11.20 Pedal cyclist injured in collision with other pedal cycle, unspecified pedal cyclist, nontraffic accident, while engaged in sports activity V13.58 Pedal cyclist injured in collision with car, pick-up truck or van, passenger, traffic accident, while engaged in other specified activities V16.04 Pedal cyclist injured in collision with other nonm
V11.21 Pedal cyclist injured in collision with other pedal cycle, unspecified pedal cyclist, nontraffic accident, while engaged in leisure activity V13.59 Pedal cyclist injured in collision with car, pick-up truck or van, passenger, traffic accident, during unspecified activity
V11.22 Pedal cyclist injured in collision with other pedal cycle, unspecified pedal cyclist, nontraffic accident, while working for an income
V13.9 Pedal cyclist injured in collision with car, pick-up truck or van, unspecified pedal cyclist, traffic accident
V11.23 Pedal cyclist injured in collision with other pedal cycle, unspecified pedal cyclist, nontraffic accident, while engaged in other types of work
V11.24 Pedal cyclist injured in collision with other pedal cycle, unspecified pedal cyclist, nontraffic accident, while resting, sleeping, eating or engaging in other vital activities V13.90 Pedal cyclist injured in collision with car, pick-up truck or van, unspecified pedal cyclist, traffic accident, while engaged in sports activity
V11.28 Pedal cyclist injured in collision with other pedal cycle, unspecified pedal cyclist, nontraffic accident, while engaged in other specified activities V13.91 Pedal cyclist injured in collision with car, pick-up truck or van, unspecified pedal cyclist, traffic accident, while engaged in leisure activity
V11.29 Pedal cyclist injured in collision with other pedal cycle, unspecified pedal cyclist, nontraffic accident, during unspecified activity
V13.92 Pedal cyclist injured in collision with car, pick-up truck or van, unspecified pedal cyclist, traffic accident, while working for an income
V11.3 Pedal cyclist injured in collision with other pedal cycle, while boarding or alighting
V11.30 Pedal cyclist injured in collision with other pedal cycle, while boarding or alighting, while engaged in sports activity V13.93 Pedal cyclist injured in collision with car, pick-up truck or van, unspecified pedal cyclist, traffic accident, while engaged in other types of work
V11.31 Pedal cyclist injured in collision with other pedal cycle, while boarding or alighting, while engaged in leisure activity V13.94 Pedal cyclist injured in collision with car, pick-up truck or van, unspecified pedal cyclist, traffic accident, while resting, sleeping, eating or engaging in other vital activities
V11.32 Pedal cyclist injured in collision with other pedal cycle, while boarding or alighting, while working for an income V13.98 Pedal cyclist injured in collision with car, pick-up truck or van, unspecified pedal cyclist, traffic accident, while engaged in other specified activities
V11.33 Pedal cyclist injured in collision with other pedal cycle, while boarding or alighting, while engaged in other types of work
V13.99 Pedal cyclist injured in collision with car, pick-up truck or van, unspecified pedal cyclist, traffic accident, during unspecified activity
V11.34 Pedal cyclist injured in collision with other pedal cycle, while boarding or alighting, while resting, sleeping, eating or engaging in other vital activities
V11.38 Pedal cyclist injured in collision with other pedal cycle, while boarding or alighting, while engaged in other specified activities V14 Pedal cyclist injured in collision with heavy transport vehicle or bus
V11.39 Pedal cyclist injured in collision with other pedal cycle, while boarding or alighting, during unspecified activity V14.0 Pedal cyclist injured in collision with heavy transport vehicle or bus, driver, nontraffic accident
V11.4 Pedal cyclist injured in collision with other pedal cycle, driver, traffic accident
V14.00 Pedal cyclist injured in collision with heavy transport vehicle or bus, driver, nontraffic accident, while engaged in sports activity
V11.40 Pedal cyclist injured in collision with other pedal cycle, driver, traffic accident, while engaged in sports activity
V11.41 Pedal cyclist injured in collision with other pedal cycle, driver, traffic accident, while engaged in leisure activity V14.01 Pedal cyclist injured in collision with heavy transport vehicle or bus, driver, nontraffic accident, while engaged in leisure activity
V11.42 Pedal cyclist injured in collision with other pedal cycle, driver, traffic accident, while working for an income V14.02 Pedal cyclist injured in collision with heavy transport vehicle or bus, driver, nontraffic accident, while working for an income
V11.43 Pedal cyclist injured in collision with other pedal cycle, driver, traffic accident, while engaged in other types of work V14.03 Pedal cyclist injured in collision with heavy transport vehicle or bus, driver, nontraffic accident, while engaged in other types of work
V11.44 Pedal cyclist injured in collision with other pedal cycle, driver, traffic accident, while resting, sleeping, eating or engaging in other vital activities
V14.04 Pedal cyclist injured in collision with heavy transport vehicle or bus, driver, nontraffic accident, while resting, sleeping, eating or engaging in other vital activities
V11.48 Pedal cyclist injured in collision with other pedal cycle, driver, traffic accident, while engaged in other specified activities
V11.49 Pedal cyclist injured in collision with other pedal cycle, driver, traffic accident, during unspecified activity V14.08 Pedal cyclist injured in collision with heavy transport vehicle or bus, driver, nontraffic accident, while engaged in other specified activities
V11.5 Pedal cyclist injured in collision with other pedal cycle, passenger, traffic accident V14.09 Pedal cyclist injured in collision with heavy transport vehicle or bus, driver, nontraffic accident, during unspecified activity
V11.50 Pedal cyclist injured in collision with other pedal cycle, passenger, traffic accident, while engaged in sports activity
V14.1 Pedal cyclist injured in collision with heavy transport vehicle or bus, passenger, nontraffic accident
V11.51 Pedal cyclist injured in collision with other pedal cycle, passenger, traffic accident, while engaged in leisure activity
V11.52 Pedal cyclist injured in collision with other pedal cycle, passenger, traffic accident, while working for an income V14.10 Pedal cyclist injured in collision with heavy transport vehicle or bus, passenger, nontraffic accident, while engaged in sports activity
V11.53 Pedal cyclist injured in collision with other pedal cycle, passenger, traffic accident, while engaged in other types of work V14.11 Pedal cyclist injured in collision with heavy transport vehicle or bus, passenger, nontraffic accident, while engaged in leisure activity
V11.54 Pedal cyclist injured in collision with other pedal cycle, passenger, traffic accident, while resting, sleeping, eating or engaging in other vital activities V14.12 Pedal cyclist injured in collision with heavy transport vehicle or bus, passenger, nontraffic accident, while working for an income
V11.58 Pedal cyclist injured in collision with other pedal cycle, passenger, traffic accident, while engaged in other specified activities
V14.13 Pedal cyclist injured in collision with heavy transport vehicle or bus, passenger, nontraffic accident, while engaged in other types of work
V11.59 Pedal cyclist injured in collision with other pedal cycle, passenger, traffic accident, during unspecified activity
V11.9 Pedal cyclist injured in collision with other pedal cycle, unspecified pedal cyclist, traffic accident V14.14 Pedal cyclist injured in collision with heavy transport vehicle or bus, passenger, nontraffic accident, while resting, sleeping, eating or engaging in other vital activities
V11.90 Pedal cyclist injured in collision with other pedal cycle, unspecified pedal cyclist, traffic accident, while engaged in sports activity V14.18 Pedal cyclist injured in collision with heavy transport vehicle or bus, passenger, nontraffic, while engaged in other specified activities accident
V11.91 Pedal cyclist injured in collision with other pedal cycle, unspecified pedal cyclist, traffic accident, while engaged in leisure activity
V14.19 Pedal cyclist injured in collision with heavy transport vehicle or bus, passenger, nontraffic, during unspecified activity accident
V11.92 Pedal cyclist injured in collision with other pedal cycle, unspecified pedal cyclist, traffic accident, while working for an income
V11.93 Pedal cyclist injured in collision with other pedal cycle, unspecified pedal cyclist, traffic accident, while engaged in other types of work V14.2 Pedal cyclist injured in collision with heavy transport vehicle or bus, unspecified pedal cyclist, nontraffic accident
V11.94 Pedal cyclist injured in collision with other pedal cycle, unspecified pedal cyclist, traffic accident, while resting, sleeping, eating or engaging in other vital activities V14.20 Pedal cyclist injured in collision with heavy transport vehicle or bus, unspecified pedal cyclist, nontraffic accident, while engaged in sports activity
V11.98 Pedal cyclist injured in collision with other pedal cycle, unspecified pedal cyclist, traffic accident, while engaged in other specified activities V14.21 Pedal cyclist injured in collision with heavy transport vehicle or bus, unspecified pedal cyclist, nontraffic accident, while engaged in leisure activity
V11.99 Pedal cyclist injured in collision with other pedal cycle, unspecified pedal cyclist, traffic accident, during unspecified activity
V14.22 Pedal cyclist injured in collision with heavy transport vehicle or bus, unspecified pedal cyclist, nontraffic accident, while working for an income
V12 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle
V12.0 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, driver, nontraffic accident V14.23 Pedal cyclist injured in collision with heavy transport vehicle or bus, unspecified pedal cyclist, nontraffic accident, while engaged in other types of work
V12.00 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, driver, nontraffic accident, while engaged in sports activity V14.24 Pedal cyclist injured in collision with heavy transport vehicle or bus, unspecified pedal cyclist, nontraffic accident, while resting, sleeping, eating or engaging in other vital activities
V12.01 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, driver, nontraffic accident, while engaged in leisure activity
V14.28 Pedal cyclist injured in collision with heavy transport vehicle or bus, unspecified pedal cyclist, nontraffic accident, while engaged in other specified activities
V12.02 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, driver, nontraffic accident, while working for an income
V12.03 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, driver, nontraffic accident, while engaged in other types of work V14.29 Pedal cyclist injured in collision with heavy transport vehicle or bus, unspecified pedal cyclist, nontraffic accident, during unspecified activity
V12.04 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, driver, nontraffic accident, while resting, sleeping, eating or engaging in other vital activities V14.3 Pedal cyclist injured in collision with heavy transport vehicle or bus, while boarding or alighting
V12.08 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, driver, nontraffic accident, while engaged in other specified activities V14.30 Pedal cyclist injured in collision with heavy transport vehicle or bus, while boarding or alighting, while engaged in sports activity
V12.09 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, driver, nontraffic accident, during unspecified activity
V14.31 Pedal cyclist injured in collision with heavy transport vehicle or bus, while boarding or alighting, while engaged in leisure activity
V12.1 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, passenger, nontraffic accident
V12.10 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, passenger, nontraffic accident, while engaged in sports activity V14.32 Pedal cyclist injured in collision with heavy transport vehicle or bus, while boarding or alighting, while working for an income
V12.11 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, passenger, nontraffic accident, while engaged in leisure activity V14.33 Pedal cyclist injured in collision with heavy transport vehicle or bus, while boarding or alighting, while engaged in other types of work
V12.12 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, passenger, nontraffic accident, while working for an income
V14.34 Pedal cyclist injured in collision with heavy transport vehicle or bus, while boarding or alighting, while resting, sleeping, eating or engaging in other vital activities
V12.13 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, passenger, nontraffic accident, while engaged in other types of work
V12.14 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, passenger, nontraffic accident, while resting, sleeping, eating or engaging in other vital activities V14.38 Pedal cyclist injured in collision with heavy transport vehicle or bus, while boarding or alighting, while engaged in other specified activities
V12.18 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, passenger, nontraffic accident, while engaged in other specified activities V14.39 Pedal cyclist injured in collision with heavy transport vehicle or bus, while boarding or alighting, during unspecified activity
V12.19 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, passenger, nontraffic accident, during unspecified activity V14.4 Pedal cyclist injured in collision with heavy transport vehicle or bus, driver, traffic accident
V12.2 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, unspecified pedal cyclist, nontraffic accident
V14.40 Pedal cyclist injured in collision with heavy transport vehicle or bus, driver, traffic accident, while engaged in sports activity
V12.20 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, unspecified pedal cyclist, nontraffic accident, while engaged in sports activity
V12.21 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, unspecified pedal cyclist, nontraffic accident, while engaged in leisure activity V14.41 Pedal cyclist injured in collision with heavy transport vehicle or bus, driver, traffic accident, while engaged in leisure activity
V12.22 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, unspecified pedal cyclist, nontraffic accident, while working for an income V14.42 Pedal cyclist injured in collision with heavy transport vehicle or bus, driver, traffic accident, while working for an income
V12.23 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, unspecified pedal cyclist, nontraffic accident, while engaged in other types of work
V14.43 Pedal cyclist injured in collision with heavy transport vehicle or bus, driver, traffic accident, while engaged in other types of work
V12.24 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, unspecified pedal cyclist, nontraffic accident, while resting, sleeping, eating or engaging in other vital activities
V12.28 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, unspecified pedal cyclist, nontraffic accident, while engaged in other specified activities V14.44 Pedal cyclist injured in collision with heavy transport vehicle or bus, driver, traffic accident, while resting, sleeping, eating or engaging in other vital activities
V12.29 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, unspecified pedal cyclist, nontraffic accident, during unspecified activity V14.48 Pedal cyclist injured in collision with heavy transport vehicle or bus, driver, traffic accident, while engaged in other specified activities
V12.3 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, while boarding or alighting V14.49 Pedal cyclist injured in collision with heavy transport vehicle or bus, driver, traffic accident, during unspecified activity
V12.30 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, while boarding or alighting, while engaged in sports activity V14.5 Pedal cyclist injured in collision with heavy transport vehicle or bus, passenger, traffic accident
V12.31 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, while boarding or alighting, while engaged in leisure activity V14.50 Pedal cyclist injured in collision with heavy transport vehicle or bus, passenger, traffic accident, while engaged in sports activity
V12.32 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, while boarding or alighting, while working for an income V14.51 Pedal cyclist injured in collision with heavy transport vehicle or bus, passenger, traffic accident, while engaged in leisure activity
V12.33 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, while boarding or alighting, while engaged in other types of work V14.52 Pedal cyclist injured in collision with heavy transport vehicle or bus, passenger, traffic accident, while working for an income
V12.34 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, while boarding or alighting, while resting, sleeping, eating or engaging in other vital activities V14.53 Pedal cyclist injured in collision with heavy transport vehicle or bus, passenger, traffic accident, while engaged in other types of work
V12.38 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, while boarding or alighting, while engaged in other specified activities V14.54 Pedal cyclist injured in collision with heavy transport vehicle or bus, passenger, traffic accident, while resting, sleeping, eating or engaging in other vital activities
V12.39 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, while boarding or alighting, during unspecified activity V14.58 Pedal cyclist injured in collision with heavy transport vehicle or bus, passenger, traffic accident, while engaged in other specified activities
V12.4 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, driver, traffic accident V14.59 Pedal cyclist injured in collision with heavy transport vehicle or bus, passenger, traffic accident, during unspecified activity
V12.40 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, driver, traffic accident, while engaged in sports activity V14.9 Pedal cyclist injured in collision with heavy transport vehicle or bus, unspecified pedal cyclist, traffic accident
V12.41 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, driver, traffic accident, while engaged in leisure activity V14.90 Pedal cyclist injured in collision with heavy transport vehicle or bus, unspecified pedal cyclist, traffic accident, while engaged in sports activity
V12.42 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, driver, traffic accident, while working for an income V14.91 Pedal cyclist injured in collision with heavy transport vehicle or bus, unspecified pedal cyclist, traffic accident, while engaged in leisure activity
V12.43 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, driver, traffic accident, while engaged in other types of work V14.92 Pedal cyclist injured in collision with heavy transport vehicle or bus, unspecified pedal cyclist, traffic accident, while working for an income
V12.44 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, driver, traffic accident, while resting, sleeping, eating or engaging in other vital activities V14.93 Pedal cyclist injured in collision with heavy transport vehicle or bus, unspecified pedal cyclist, traffic accident, while engaged in other types of work
V12.48 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, driver, traffic accident, while engaged in other specified activities V14.94 Pedal cyclist injured in collision with heavy transport vehicle or bus, unspecified pedal cyclist, traffic accident, while resting, sleeping, eating or engaging in other vital activities
V12.49 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, driver, traffic accident, during unspecified activity V14.98 Pedal cyclist injured in collision with heavy transport vehicle or bus, unspecified pedal cyclist, traffic accident, while engaged in other specified activities
V12.5 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, passenger, traffic accident V14.99 Pedal cyclist injured in collision with heavy transport vehicle or bus, unspecified pedal cyclist, traffic accident, during unspecified activity
V12.50 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, passenger, traffic accident, while engaged in sports activity V15 Pedal cyclist injured in collision with railway train or railway vehicle
V12.51 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, passenger, traffic accident, while engaged in leisure activity V15.0 Pedal cyclist injured in collision with railway train or railway vehicle, driver, nontraffic accident
V12.52 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, passenger, traffic accident, while working for an income V15.00 Pedal cyclist injured in collision with railway train or railway vehicle, driver, nontraffic accident, while engaged in sports activity
V12.53 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, passenger, traffic accident, while engaged in other types of work V15.01 Pedal cyclist injured in collision with railway train or railway vehicle, driver, nontraffic accident, while engaged in leisure activity
V12.54 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, passenger, traffic accident, while resting, sleeping, eating or engaging in other vital activities V15.02 Pedal cyclist injured in collision with railway train or railway vehicle, driver, nontraffic accident, while working for an income
V12.58 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, passenger, traffic accident, while engaged in other specified activities V15.03 Pedal cyclist injured in collision with railway train or railway vehicle, driver, nontraffic accident, while engaged in other types of work
V12.59 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, passenger, traffic accident, during unspecified activity V15.04 Pedal cyclist injured in collision with railway train or railway vehicle, driver, nontraffic accident, while resting, sleeping, eating or engaging in other vital activities
V12.9 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, unspecified pedal cyclist, traffic accident V15.08 Pedal cyclist injured in collision with railway train or railway vehicle, driver, nontraffic accident, while engaged in other specified activities
V12.90 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, unspecified pedal cyclist, traffic accident, while engaged in sports activity V15.09 Pedal cyclist injured in collision with railway train or railway vehicle, driver, nontraffic accident, during unspecified activity
V12.91 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, unspecified pedal cyclist, traffic accident, while engaged in leisure activity V15.1 Pedal cyclist injured in collision with railway train or railway vehicle, passenger, nontraffic accident
V12.92 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, unspecified pedal cyclist, traffic accident, while working for an income V15.10 Pedal cyclist injured in collision with railway train or railway vehicle, passenger, nontraffic accident, while engaged in sports activity
V12.93 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, unspecified pedal cyclist, traffic accident, while engaged in other types of work V15.11 Pedal cyclist injured in collision with railway train or railway vehicle, passenger, nontraffic accident, while engaged in leisure activity
V12.94 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, unspecified pedal cyclist, traffic accident, while resting, sleeping, eating or engaging in other vital activities V15.12 Pedal cyclist injured in collision with railway train or railway vehicle, passenger, nontraffic accident, while working for an income
V12.98 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, unspecified pedal cyclist, traffic accident, while engaged in other specified activities V15.13 Pedal cyclist injured in collision with railway train or railway vehicle, passenger, nontraffic accident, while engaged in other types of work
V12.99 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, unspecified pedal cyclist, traffic accident, during unspecified activity V15.14 Pedal cyclist injured in collision with railway train or railway vehicle, passenger, nontraffic accident, while resting, sleeping, eating or engaging in other vital activities
V15.18 Pedal cyclist injured in collision with railway train or railway vehicle, passenger, nontraffic accident, while engaged in other specified activities
V15.19 Pedal cyclist injured in collision with railway train or railway vehicle, passenger, nontraffic accident, during unspecified activity
Ontologies:
Goodbye to picking lists…
S uc u ed Da a En y
F E H
Cyc ng Acc den
What you hit
Your Role
Activity
Location
On o ogy Tu o a © 2005 Un v o Manches e
92
Reasoning and GIGO
► How do you classify things…

► If the ontology isn’t complete?
► How do you tell if the ontology isn’t complete?

► No gold standard
► Quality Assurance of ontologies?
►Philosophical purity
►Schema consistency
►Knowledge accuracy/completeness
►Operational utility
► Right answers for wrong reason?
Outline

►Mission creep
►Reasoning
93
Engineering ontologies:
A process not a product
Record Record
Problems Monitoring Changes
ASSESS
Identify
Conformance Use/Test cases
problems
Testing & exemplars
Provenance
Metadata
REVIEW PLAN
Documentation
Explore Decide
consequences amongst
alternatives
Specify Machine
Reference Solutions Readable
Implementations IMPLEMENT
solutions Human
Readable
Outline

►Mission creep
►Reasoning
94
Complexity Monsters
►Domain Complexity
►Artefactual Complexity
►Cognitive Complexity
Domain Complexity
►E.g. the biomedical domain

► Very large and inherently complex
► Many different views & perspectives: Pain
► Subspecialties have no clear boundaries: Anatomy
►External or legacy KBs

► require obscure categories and properties
►Large ontologies with many axes of classification

► Inherently confusing to navigate
95
Artefactual Complexity
►Unreadable notations
(ClinicalSituation which <isCharacterisedBy (presence which isExistenceOf (ContractionProcess which
<isSpecificFunctionOf SphincterAniMuscle hasImmediateConsequence Pain hasIntentionality
(Intentionality which hasAbsoluteState involuntary) hasDuration (Duration which hasAbsoluteState
longTerm) hasTemporalPattern (TemporalPattern which hasAbsoluteState ongoing) >))
isCharacterisedBy (presence which isExistenceOf (UrgeToVoidUrineOrFaeces which hasProcessActivity
(ProcessActivity which hasQuantity (Level which hasMagnitude highLevel)))) isCharacterisedBy
(presence which isExistenceOf AbdominalStraining) >)
►Limitations in formalism Æ Workarounds
Cognitive Complexity
►Natural Language can misdirect

►Formal ontologies require great precision
► Poor debugging tools
►Scale of task
96
#1 Challenge for Ontology Engineering:
Hide the complexity

► Intermediate representations
► OWL is the “Assembly language” for ontology building
►The goal is to make it disappear in tools and environments
► Loosened constraints plus post-hoc normalisation

► Tools
From this to this…
(SurgicalDeed which MAIN replacing

isCharacterisedBy (performance whichG ACTS_ON heart valve
isEnactmentOf (Dividing whichG <
HAS_ FEATURE induced arrest of heart
playsClinicalRole SurgicalRole
actsSpecificallyOn HeartValve
hasSubprocess (TemporalFeature which <
isSpecificImmediateConsequenceOf VolitionalAct
involves Heart
hasSpecificConsequence (BodyProcess which < (And back again)
isSpecificFunctionOf Heart
hasProcessActivity (ProcessActivity which
hasQuantity (Level which
hasMagnitude undetectedLevel)) >)
hasPathologicalStatus pathological >)>)))
97
Outline

►Mission creep
►Reasoning
►The User
Inter-rater variability 1 X X
Headcloth
Cloth X X X
Scarf X
Model Person X X X
Woman X X X X X
Adults X
Standing X X X X X
Background X X
Brown X X X X X
Blue X X X
Chemise X
Dress X X X X
Tunics X
Clothes X
Suitcase X X X X
Luggage X
Attache case X
Brass Instrument X X X
French Horn X
Horn X
Tuba X X
98
Inter-rater variability 2
New codes added per Dr per year
READ CODE Practice A Practice B

Sore Throat Symptom 0.6 117
Visual Acuity 0.4 644
ECG General 2.2 300
Ovary/Broad Ligament Op 7.8 809
Specific Viral Infections 1.4 556
Alcohol Consumption 0 106
H/O Resp Disease 0 26
Full Blood Count 0 838
Conclusion
► Ontologies are conceptualisation of domains for use on

computers TO DO SOME TASK(S)
► Always ask “What’s it for?”
► Perfection and completeness will seduce you

► Only build what’s useful
► Iterative process more important than static product

► In theory, classifiers make large ontologies possible
► In practice, field is full of confusions in language, notation,
assumptions & goals
► And your users won’t want to know about any of these
99
Protégé-OWL part 2
Nick Drummond
Matthew Horridge
100
Ontologies & OWL
Session 2: Defined Classes and Additional
Modelling Constructs in OWL
O p enG A LEN
BioHealth
Informatics
Group
Overview
► Defined Classes
► Untangling
► Defining Vegetarian Pizzas
► Union Classes
► Universal Restrictions
► The Open World Assumption
► Closure
101
CheeseyPizza
► A CheeseyPizza is any pizza that has some cheese
on it
► We would expect then, that some pizzas might be

named pizzas and cheesey pizzas (among other
things later on)
► We can use the reasoner to help us produce this

polyhierarchy without having to assert multiple
parents
Creating a CheeseyPizza
► We normally create primitive classes and then migrate them to defined
classes
► All of our defined pizzas will be direct subclasses of Pizza
► So, we create a CheesyPizza Class (do not make it disjoint) and add a
restriction:
“Every CheeseyPizza must have at least one CheeseTopping”
► Classifying shows that we currently don’t have enough information to
do any classification
► We then move the conditions

from the Necessary block to
the Necessary & Sufficient
block which changes the
meaning
► And classify again…
102
Reasoner Classification
► The reasoner has been able to infer that anything that is a Pizza
that has at least one topping from CheeseTopping is a
CheeseyPizza
► The inferred hierarchy is

updated to reflect this and
moved classes are highlighted
in blue
Why?
Necessary & Sufficient Conditions
► Each set of necessary & sufficient conditions is an Equivalent
Class
∃ hasTopping
Pizza CheeseTopping
CheeseyPizza
► CheeseyPizza is equivalent to the intersection of Pizza and ∃ hasTopping

CheeseTopping
► Classes, all of whose individuals fit this definition are found to be subclasses of
CheeseyPizza, or are subsumed by CheeseyPizza
103
Untangling
► We can see that certain Pizzas are

now classified under multiple parents
► MargheritaPizza can be found under

both NamedPizza and CheeseyPizza
in the inferred hierarchy
Mission Successful!
Untangling
► However, our unclassified version of the ontology is a
simple tree, which is much easier to maintain
► We’ve now got a polyhierarchy without asserting

multiple superclass relationships
► Plus, we also know why certain pizzas have been
classified as CheeseyPizzas
104
Untangling
► We don’t currently have many kinds of primitive pizza
but its easy to see that if we had, it would have been a
substantial task to assert CheeseyPizza as a parent
of lots, if not all, of them
► And then do it all over again for other defined classes

like MeatyPizza or whatever
Viewing polyhierarchies
► As we now have
multiple inheritance, the
tree view is less than
helpful in viewing our
“hierarchy”
105
Viewing our Hierarchy

Graphically
OWLViz Tab
Show All Classes
View Asserted Model View Inferred Model
Polyhierarchy
tangle
106
Using OWLViz to untangle

► The asserted hierarchy should, ideally, be a tidy tree
of disjoint primitives
► The inferred hierarchy will be tangled
► By switching from the asserted to the inferred
hierarchy, it is easy to see the changes made by the
reasoner
► OWLViz can be used to spot tangles in the primitive
tree and also disjoints (including inherited ones) are
marked (with a ¬)
Defined Classes
► We’ve created a Defined Class, CheeseyPizza
► It has a definition. That is at least one Necessary and Sufficient condition

► Classes, all of whose individuals satisfy this definition, can be inferred to be
subclasses
► Therefore, we can use it like a query to “collect” subclasses that satisfy its
conditions
► Reasoners can be used to organise the complexity of our hierarchy
► It’s marked with an equivalence symbol in the interface

► Defined classes are rarely disjoint
107
Exercise 5: Define a MeatyPizza
► Add a CheeseyPizza to your ontology as well
Define a Vegetarian Pizza

► Not as easy as it looks…
► Define in words?
► “a pizza with only vegetarian toppings”?
► “a pizza with no meat (or fish) toppings”?
► “a pizza that is not a MeatyPizza”?
► More than one way to model this
We’ll start with the first example
108
Define a Vegetarian Pizza

To be able to define a vegetarian pizza as
a Pizza with only Vegetarian Toppings
we need:
1. To be able to create a vegetarian topping

This requires a Union Class
2. To be able to say “only”

This requires a Universal Restriction
Union Classes
► aka “disjunction”
► This OR That OR TheOther
► This That TheOther
B
A B includes all A
individuals of class A and
all individuals from class B
and all individuals in the
overlap (if A and B are not
disjoint)
► Commonly used for:

► Covering axioms
► Closure
109
Covering Axioms
► Covering axiom – a union expression containing several

covering classes
► A covering axiom in the Necessary & Sufficient Conditions of

a class means:
the class cannot contain any instances other than those from
the covering classes
► NB. If the covering classes are subclasses of the covered

class, the covering axiom only needs to be a Necessary
condition – it doesn’t harm to make it Necessary & Sufficient
though – its just redundant
Covering PizzaBase
PizzaBase ≡ ThinAndCrispy DeepPan
PizzaBase
► In this example, the class
PizzaBase is covered by
ThinAndCrispy or DeepPan
DeepPan ► “All PizzaBases must be

ThinAndCrispy ThinAndCrispy or DeepPan”
► “There are no other types of

PizzaBase”
110
Exercise 6: Define a
VegetarianTopping
► We need to say our VegetarianPizza can only have

toppings that are vegetarian toppings
► We can do this by creating a Universal or

AllValuesFrom restriction
► We’ll first look at an example…
111
Real Italian Pizzas

► “RealItalianPizzas only have bases that are
ThinAndCrispy”
► A Universal Restriction is
added just like an
Existential one, but the
restriction type is different
► For now, this can be primitive – you can make it

defined if you like
► We have created a restriction: ∀ hasBase ThinAndCrispy on

Class RealItalianPizza as a necessary condition
ase
RealItalianPizza hasB ThinAndCrispy
ase
hasB
ase
hasB
hasB
ase

must only have a hasBase relationship with an individual from
the class ThinAndCrispy”
112
► We have created a restriction: ∀ hasBase ThinAndCrispy on

Class RealItalianPizza as a necessary condition
ase
DeepPan RealItalianPizza hasB ThinAndCrispy
hasBase
ase
hasB
ase
hasB
hasB
ase
► “No individual of the RealItalianPizza class can have a base

from a class other than ThinAndCrispy”
► NB. DeepPan and ThinAndCrispy are disjoint
Warning: Trivial Satisfaction
► If we had not already inherited: ∃ hasBase PizzaBase

from Class Pizza the following could hold
ase
RealItalianPizza hasB ThinAndCrispy
Trivially ase
satisfied hasB
by this ase
hasB
individual
hasB
ase

must only have a hasBase relationship with an individual from
the class ThinAndCrispy, or no hasBase relationship at all”
► Universal Restrictions by themselves do not state “at least one”
113
Exercise 7: Create VegetarianPizza
VegetarianPizza Classification
► Nothing classifies under VegetarianPizza
► Actually, there is nothing wrong with our definition of

VegetarianPizza
► It is actually the descriptions of our Pizzas that are incomplete
► The reasoner has not got enough information to infer that any
Pizza is subsumed by VegetarianPizza
► This is because OWL makes the Open World Assumption
114
Open World Assumption

► In a closed world (like DBs), the information we have is
everything
► In an open world, we assume there is always more information
than is stated
► Where a database, for example, returns a negative if it cannot

find some data, the reasoner makes no assumption about the
completeness of the information it is given
► The reasoner cannot determine something does not hold unless it
is explicitly stated in the model
Open World Assumption

► Typically we have a pattern of several Existential
restrictions on a single property with different fillers –
like primitive pizzas on hasTopping
► Existential restrictions should be paraphrased by

“amongst other things…”
► Must state that a description is complete

► We need closure for the given property
115
Exercise 8: Closing Pizzas
Exercise 9: Your PizzaFinder
► You can now plug your pizza ontology into the

PizzaFinder application
116
Closure
► This is in the form of a Universal Restriction with a
filler that is the Union of the other fillers for that
property
► Closure works along a single property
Closure example: MargheritaPizza
All MargheritaPizzas must have:

at least 1 topping from MozzarellaTopping and
at least 1 topping from TomatoTopping and
only toppings from MozzarellaTopping or TomatoTopping
► The last part is paraphrased into “no other toppings”

► The union closes the hasTopping property on MargheritaPizza
117
Summary
► Create Defined Classes and classify using a Reasoner
to check expected results
► Create Covering Axioms
► Close Class Descriptions and understand the Open
World Assumption
118
Formal Modelling
Issues
Alan Rector
119
Formal Modelling
Alan Rector
O p enG A LEN
BioHealth
Informatics
Group 1 Ontology tutorial, © 2005 Univ. of Manchester
The problem
Knowledge is Big, Fractal & Changeable!

But we want to
► Build ontologies cooperatively with different groups
► Extend ontologies smoothly
► Re-use pieces of ontologies
► Build new ontologies on top of old
► Quit starting from scratch
O p enG A LEN
BioHealth
Informatics
120
Assertion:
The arrival of logic-based
ontologies/OWL gives new opportunities
to make ontologies more manable and
modular
► Let the ontology authors

► create discrete modules
► describe the links between modules
► Let the logic reasoner

► Organise the result
O p enG A LEN
BioHealth
Informatics
When to use a classifier

1. At author time: As a compiler – Pre-coordination
► Ontologies will be delivered as “pre-coordinated” ontologies to be
used without a reasoner
► To make extensions and additions quick, easy, and responsive,
distri but developments, empower users to make changes
► Part of an ontology life cycle
2. At delivery time: As a service: - Post-coordination
► Many fixed ontologies are too big and too small
► Too big to find things; too small to contain what you need
► Create them on the fly
► Part of an ontology service
3. At application time: as a reasoner - Post-
coordination & inference
O p enG A LEN ► Decision support, query optimisation, schema integration, …, …, …
► Part of a reasoning service
BioHealth
Informatics
121
When to use a classifier 1:

Pre-coordinated delivery
classifier as compiler
► The life cycle
► Gather requirements, sketch, experiment
► Establish patterns – design a “language”
► Criteria for success: What a subject domain expert can learn in a few days
► Bulk authoring
► Classification
Development & evolution
► Quality assurance
► Commit classifier results to a pre-coordinated ontology & deliver

► Polyhierarchies (Protégé, DAG-Edit, OWL-Lite, RDF(S), Topic Maps, …
► Query and use with you favourite tool
O p enG A LEN
BioHealth
Informatics
Commit Results to a Pre-

Coordinated Ontology
Assert
(“Commit”)
changes
inferred by
classifier
O p enG A LEN
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Informatics
122
Precoordinated Ontologies
► Author
► Classify
► Export to OWL-Lite or RDF
► Query with RDQL, SparQL, or your favourite
RDF/RDF(S) query tool
► Use as a vocabulary in your database
O p enG A LEN
BioHealth
Informatics
Content
Surgical
Procedure
Disease
has diagnosis has treatment Surgical

Patient Disease Procedure
tion
complica
has
O p enG A LEN Disease
BioHealth
Informatics
123
Content
Surgical
Procedure
Disease
Excision
Melanoma Infection
has diagnosis has treatment

Mrs Smith aMelanoma anExcision
tion
complica
has
O p enG A LEN anInfection
BioHealth
Informatics
When to use a classifier 2:

Post Coordination
► When the ontology too big – “Lazy classification” on
demand
API
kernel
model
Externally available
resource
O p enG A LEN
Big on the outside: small kernel on the inside
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Informatics
124
Often combined with other

services:
Example - the GALEN Server
Client Ontology Services

Multilingual
Module
Multilingual Lexicons
Client
Service API
Ontology
Applications Module
Users Ontologies & Classifier
External Resources &

“Coding” Module
Resource References
Run time classifier

O p enG A LEN
BioHealth
Informatics
Logic-based Ontologies:
Conceptual Lego
gene
hand
protein
extremity
body cell
expression
chronic Lung
acute inflammation
infection
abnormal
normal bacterial
deletion polymorphism
ischaemic
O p enG A LEN
BioHealth
Informatics
125
Logic-based Ontologies:
Conceptual Lego
“SNPolymorphism of CFTRGene causing Defect in MembraneTransport of
Chloride Ion causing Increase in Viscosity of Mucus in CysticFibrosis…”
“Hand which is
anatomically
normal”
O p enG A LEN
BioHealth
Informatics
Species
Genes
Protein
Function
Gene in humans
Disease
Protein coded by
gene in humans
Logical Constructs Function of

build complex Protein coded by
gene in humans
concepts from Disease caused by abnormality in
modularised Function of
O p enG A LEN Protein coded by
primitives gene in humans
BioHealth
Informatics
126
Normalising (untangling)
Ontologies
Structure
Structure Part-whole Function
Function
Part-whole
O p enG A LEN
BioHealth
Informatics
Rationale for Normalisation
► Explicit distinctions between modules

► Primitives are opaque to the reasoner
►Information implicit in primitive names cannot contribute to modularisation
► Primitives are indivisible to both human and reasoner
►Each primitive should represent a single notion
► Therefore, each primitive must belong to exactly one module
►If a primitive belongs to two modules, they are not modular.
►If a primitive belongs to two modules, it probably conflates two notions
► Therefore concentrate on the “primitive skeleton” of the domain
ontology
O p enG A LEN
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Informatics
127
Normalisation and
Untangling
Let the reasoner do multiple classification
► Tree
► Everything has just one parent
►A ‘strict hierarchy’
► Directed Acyclic Graph (DAG)

► Things can have multiple parents
►A ‘Polyhierarchy’
► Normalisation
► Separate primitives into disjoint trees
► Link the trees with restrictions
O p enG A LEN
►Fill in the values
BioHealth
Informatics
Tables are easier to manage

than DAGs /
Polyhierarchies
…and get the benefit of inference:

Grass and Leafy_plants are both kinds of
Plant
O p enG A LEN
BioHealth
Informatics
128
Remember to add any

closure axioms
Closure
Axiom
Then let the reasoner do the work

O p enG A LEN
BioHealth
Informatics
Normalisation:
From Trees to DAGs
Before classification After classification

A tree A DAG
Directed Acyclic Graph
O p enG A LEN
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Informatics
129
Normalisation: Criterion 1
The skeleton should consist
of disjoint trees
► Every primitive concept should have exactly one

primitive parent
► All multiple hierarchies the result of inference by reasoner
O p enG A LEN
BioHealth
Informatics
Normalisation Criterion 2:
No hidden changes of meaning
►Each branch should be homogeneous and

logical
(“Aristotelian”)
► Hierarchical principle should be subsumption
►Otherwise we are “lying to the logic”
► The criteria for differentiation should follow consistent principles in
each branch
eg. structure XOR function XOR cause
O p enG A LEN
BioHealth
Informatics
130
A Non-homogeneous
taxonomy
“On those remote pages it is written that animals are divided into:
a. those that belong to the Emperor

b. embalmed ones
c. those that are trained
d. suckling pigs
e. mermaids
f. fabulous ones
g. stray dogs
h. those that are included in this classification
i. those that tremble as if they were mad
j. innumerable ones
k. those drawn with a very fine camel's hair brush
l. others
m. those that have just broken a flower vase
O p enG A LEN n. those that resemble flies from a distance"
From The Celestial Emporium of Benevolent Knowledge, Borges
BioHealth
Informatics
Normalisation Criterion 3
Distinguish “Self-standing” and
“Refining” Concepts
►Self-standing concepts
► Roughly Welty & Guarino’s “sortals”
►person, idea, plant, committee, belief,…
► Refining concepts – depend on self-standing

concepts
►mild|moderate|severe, hot|cold, left|right,…
► Roughly Welty & Guarino’s non-sortals
► Closely related to Smith’s “fiat partitions”
► Usefully thought of as Value Types by engineers
O p enG A LEN ► For us an engineering distinction…
BioHealth
Informatics
131
Normalisation Criterion 3a
Self-standing primitives should be
globally disjoint & open
► Primitives are atomic
► If primitives overlap, the overlap conceals implicit information
► A list of self-standing primitives can never be

guaranteed complete
► How many kinds of person? of plant? of committee? of belief?
► Can’t infer: Parent & ¬sub1 &…& ¬subn-1 Æ subn
► Heuristic:
► Diagnosis by exclusion about self-standing concepts should NOT
O p enG A LEN be part of ‘standard’ ontological reasoning
BioHealth
Informatics
Normalisation Criterion 3b
Refining primitives should be locally
disjoint & closed
► Individual values must be disjoint
► but can be hierarchical
►e.g. “very hot”, “moderately severe”
► Each list can be guaranteed to be complete

► Can infer Parent & ¬sub1 &…& ¬subn-1 Æ subn
► Value types themselves need not be disjoint

► “being hot” is not disjoint from “being severe”
►Allowing Valuetypes to overlap is a useful trick, e.g.
►restriction has_state someValuesFrom (severe and hot)
O p enG A LEN
BioHealth
Informatics
132
Normalisation Criterion 4
Axioms
► No axiom should denormalise the ontology

No axiom should imply that a primitive is part of
more than one branch of primitive skeleton
► If all primitives are disjoint, any such axioms will make that
primitive unsatisfiable
►A partial test for normalisation:
►Create random conjunctions of primitives which do not subsume
each other.
►If any are satisfiable, the ontology is not normalised
O p enG A LEN
BioHealth
Informatics
Consequences 1
► All self-standing primitives are disjoint

► All multiple classification is inferred
► For any two primitive self-standing classes, either
one subsumes the other or they are disjoint
► Every self standing concept is part of exactly one
primitive branch of the skeleton
► Every self-standing concept has exactly one most
specific primitive ancestor
O p enG A LEN
BioHealth
Informatics
133
Consequences 2
► Primitives introduced by a conjunction of one class and

a boolean combination of zero or more restrictions
► Tree subclass-of Plant and
restriction isMadeOf someValuesFrom Wood
► Resort subclass-of Accommodation
restriction isIntendedFor someValueFrom Holidays
O p enG A LEN
BioHealth
Informatics
Consequences 3
►Use of axioms limited (outside of skeleton

construction)
The following are a safe but not exhaustive
guide:
►The right side of subclass axioms limited to
restrictions
►Both sides of disjointness axioms limited to
restrictions
►No equivalence axioms with primitives on either
side
O p enG A LEN
BioHealth
Informatics
134
A real example:
Build a simple treee
easy to maintain
O p enG A LEN
BioHealth
Informatics
Let the classifier organise it
O p enG A LEN
BioHealth
Informatics
135
If you want more

abstractions,
just add new definitions
(re-use existing data)
O p enG A LEN
“Diseases linked to abnormal
proteins”
BioHealth
Informatics
And let the classifier work

again
O p enG A LEN
BioHealth
Informatics
136
And again – even for a quite

different category
O p enG A LEN
“Diseases linked genes
described in the mouse”
BioHealth
Informatics
And let classifier check

consistency
(My first try wasn’t)
O p enG A LEN
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Informatics
137
Summary
Why use a Classifier?
► To compose concepts
► Allow conceptual lego
► To manage polyhierarchies
► Adding abstractions (“axes”) as needed
► Normalisation
► Untangling
► labelling of “kinds of is-a”
► To avoid combinatorial explosions

► Keep bicycles from exploding
► To manage context
► Cross species, Cross disciplines, Cross studies
► To check consistency and help users find errors
O p enG A LEN
BioHealth
Informatics
Limitations on OWL (1)

► Ontologies are not databases
► About classes / schemas
►Individuals only to define classes
►And that poorly supported by classifiers
► Open World
►Negation as impossibility
► Databases are not ontologies

► About individuals
►Classes only as part of schemas
► Closed world
►Negation as failure
► Variants
►Instance store
►RDF Triple Store
O p enG A LEN
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Informatics
138
Limitations on OWL
► Expressivity
► Binary relational
►only two variables
►no way of saying equal
►No way to express “A person who teaches themselves”
“A play directed by its producer”
► Basic patterns
►Supported
►All – Some, All – Only
►Some support
►at least n ; at most n
►Qualified cardinality restrictions
►No support
►Some-All, Some-Some
►All-All*
O p enG A LEN
►“Generally, but subject to exceptions”
BioHealth
Informatics
Limitations on OWL
► Metadata and Annotations

► OWL statements are always about “all members of class C…”
►Statements about Class C itself or the implementation of Class C are
metadata or higher order data
► Confused and not well standardised
►Annotation properties in OWL DL are arbitrarily restricted
►Choice between annotations and OWL-Full around an OWL DL core
is unclear
►Experience and use cases needed
►Need experience leading to standards – at least for UK community
►One function potentially growing out of this group
O p enG A LEN
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Informatics
139
Ontology
Applications
Sean Bechhofer
Daniele Turi
Matthew Horridge
140
Application/Service
Issues
Sean Bechhofer
O p enG A LEN
BioHealth
Informatics
Group
Ontologies in Applications
► If we want to make use of ontologies within

applications, there are a number of things that we
need to consider.
► How are we to make the information in the ontology
available to the application?
► There are no “right” answers to these questions.
141
Classifier limitations
► Numbers and strings

► Simple concrete data types in spec
► User defined XML data types enmeshed in standards disputes
► No standard classifier deals with numeric ranges
►Although several experimental ones do
► is-part-of and has-part

► Totally doubly-linked structures scale horridly
► Handling of individuals
► Variable with different classifiers
O p enG A LEN
► oneOF works badly with all classifiers at the moment
BioHealth
Informatics
Axiom Schemas and Tools
► Many things that would need extra variables can be

expressed as axiom schemas
► All right body parts can only be part of right or midline body parts
► All left body parts can only be part of left or midline body parts
► All X-sided body parts can only be part of X-sided or midline body
parts.
►For small numbers can do by hand
►For large numbers need tool support
O p enG A LEN
BioHealth
Informatics
142
Ontologies in Applications
► In the past, ontologies have been embedded in the

application
► This introduces problems with:
► Maintenance
► Implementation
► Exchange of terms
► Considering the ontology as a separate resource

provides greater flexibility
What is an Ontology?
► It’s a collection of statements about concepts

► Definitions, relationships etc.
► In the Semantic Web, ontologies are considered as

resources in their own right
► However, they are often implicitly thought of as some
kind of static resource.
► “Ontologies are OWL/RDF files.”
143
What is an Ontology?
► Recall that one of the key aspects of OWL is the

provision of semantics that ensure that everyone
interprets descriptions in a consistent manner.
► Considering ontologies as static resources requires
applications to be able to provide implementations of
the language semantics (potentially non-trivial in the
case of OWL).
► Instead we can think of them as dynamic objects
providing services.
► Pushes the onus for implementation on to the service provider.
Grid Aside: Ontologies as

Service
Resources Services
Data Access Dataset Data Service

query/update etc
Ontologies Ontology source Ontology Service

(e.g. RDF file) query/inference etc.
144
Ontology Services
► Terminological
► Classification
► Validity and consistency checking
► Intentional Concept Descriptions
► Query
► Linguistic
► Mappings to/from terms
► Extrinsic/Annotation
► Application specific information
► Annotations that are not intensional or part of the intrinsic definition
of the concepts.
Implementations of OWL
► What does it mean to provide implementations of

ontologies?
► What do you want to do with the ontology?
► Read it
► Manipulate it
► Reason about it
► Where does the reasoner go?
►Inside or outside?
145
Ontology interactions
► Modelling
► Provide data structures that represent OWL ontologies/documents
► Parsing
► Taking some syntactic presentation, e.g. OWL-RDF and converting it to some [useful]
internal data structure
► Serialization
► Producing a syntactic presentation, e.g. OWL-XML from a local data structure
► Manipulation
► Being able to manipulate the underlying objects
► Inference
► Providing a representation that implements/understands the formal semantics of the
language
Implementation Aspects
Format Translation
Simple Editing
Consistency Checking
Parsing Manipulation
Modelling
Serializing Inference
146
Files/Libraries/Services
► Access to Ontologies via URIs

► Basic representations e.g. RDF/XML
► Code Libraries/APIs
► Code libraries that expose the ontology and associated functionality
via some API.
► Services (Web or otherwise).

► Shared resources.
Layering
► OWL can be layered on RDF.

► This layering provides us with a number of different
options in terms of accessing the ontology.
► Direct access to the RDF triple structures
► E.g. Jena, Sesame, 3store
► May require client applications to “understand” or implement aspects
of the language, e.g. inference.
► Access at a “higher level” using some API.

► OWL-API, Protégé API, Jena Ontology API
147
Modularisation
► Ontologies are likely to be distributed and modular

► Modularisation is poorly supported in the OWL
specification
► owl:imports
► Simply grabs the RDF graph and includes it.
► Ontology naming is problematic

► There’s no consistent mechanism for referring to context or
collections of axioms.
Inside or Outside?
Application Reasoner
Reasoner sits outside

the Ontology Service.
Service API Requests are answered
w.r.t. the basic facts
Ontology Service asserted in the
ontology.
Ontology Ontology Ontology
148
Inside or Outside?
Application
Reasoner sits inside the
Ontology Service.
Requests are answered
w.r.t. the semantics.
Service API
Ontology Service Reasoner
Ontology Ontology Ontology
Do You Really Need

Reasoning?
Ontology Service answers
Application requests w.r.t. the basic
facts asserted in the
ontology.
Reasoner used during

Service API design of the ontology,
to ensure a consistent
Ontology Service and coherent hierarchy.
Ontology
Ontology Ontology Taxonomy Reasoner
149
COHSE
► We saw COHSE demonstrated yesterday.

► It’s a system that uses an ontology to drive dynamic
linking of documents
► An Ontology Service provides access to the
ontologies.
► Ontologies are represented in OWL
► Third party ontologies (and documents) can be used
COHSE
Ontologies &
Lexicons
Semantics and
world knowledge
Unlinked
Document in Ontology
Service
Reasoner
COHSE
Agent
Annotation
Linked Resource Descriptions
Document out Service
Resource Discovery &

Metadata Management Search Engines
150
COHSE
► Ontologies accessed via URLs

► Third party ontologies
► Loaded into an Ontology Service
► Handled using OWL-API library code.
► This then exposes the ontology through a number of API calls

► “Web Service” like.
► May involve the use of a reasoner to, e.g. calculate the taxonomy.
► COHSE doesn’t currently use much reasoning at deployment time, other
than traversing the hierarchy.
► Ontology service reused in other applications
151
OWL Instance Store

reasoning over large volumes of
individuals
Daniele Turi
S Bechhofer, I Horrocks, L Li, P Lord, U Sattler
Protégé Tutorial, 30th June 2005
Copyright © 2005, The University of Manchester 1
Scalable Ontological Reasoning
• Semantic web and bioinformatics applications:
• millions of individuals
• Existing reasoners cannot cope
Î instance Store
152
Example: Gene Ontology
• 10,000s classes (gene terms)
• 1,000,000s individuals (gene products)
• Example individual: 1433_CANAL

corresponding description:
takesPartIn IntracellularSignallingCascade
and isPartOf Chloroplast
and hasFunction
ProteinDomainSpecificBindingActivity
Schema v Instance Data

in ontologies
• Classes and properties Schema

• more or less static
• Individuals: dynamic Instance Data

• Frequent updates
• Concurrency
• Persistency
• Security
153
Instance Store
z Main observation:
z Reasoning over individuals can often be
reduced to reasoning over their descriptions
(i.e. the classes they belong to)
Îclass-level reasoner + relational database

Schema Instance Data
z Use reasoner only when strictly necessary
z Cache inferred schema information in database
Instance Store
basic functionality
• Stores assertions
assert(Individual I, Description D)
• Answers retrieval questions

retrieve(Description Q): Set of Individuals
154
OWL
Ontology
(individual, description) Java retrieve(description)

assert
individual 1
individual 2
individual 3
…
instance
data Database schema
(MySQL,
+
Oracle,
inferred PostgreSQL,
Hypersonic, etc) Class-level Reasoner
schema (FaCT, FaCT++, Racer, etc)
Relational Database
Cache descriptions used in assertions and queries
z Descriptions table
Oracle
z Assertions table MySQL
z individual Hypersonic
z description id
z Types, Equivalents, Children, Parents tables

z concept
z description id
155
z Relational databases
Æ persistency & scalability
z Java + relational databases

Æ enterprise technology (J2EE)
Æ concurrency & security
Æ robust
156
Class-level Reasoner
z Reasoners do not speak OWL, but DIG
z DIG is the de-facto standard XML language for

communicating with Description Logic reasoners
z DIG Interface
z RACER
z FaCT
z FaCT++
z …
OWL
z OWL Wrapper
z OWL to DIG (and back)
z OWL Abstract Syntax
DIG API
OWL API
157
Assertion (example)
jo: Kid and some hasPet Cat
Types Parents
1. Animal 1. CatOwner
2. CatOwner 2. Kid
3. Kid
4. Person Children and Equivalents:
5. PetOwner no new entry
6. Young
158
Retrieval
z Delegate most of work to database
z Worst case: query not equivalent to
z either a class in ontology
z or the conjunction of its parents
Îa subsumption test for each concept in the

following result set (parametric in parents
of query):
SELECT DISTINCT description FROM Descriptions

WHERE Descriptions.id IN (
SELECT descriptionId FROM Types
WHERE concept = parent-1
INTERSECT
...
INTERSECT
SELECT descriptionId FROM Types
WHERE concept = parent-n
MINUS
SELECT Types.descriptionId FROM Types, Children
WHERE Children.concept = Types.concept
AND Children.descriptionId = id )
159
Work in Progress
• No relation between individual:

usedBy
1433_CANAL daniele_turi
• Solution: precompletion
reduces most inferences to inferences about
classes
• Core precompletion component ready and
under testing
160
Conclusions
Appropriate technologies for appropriate tasks

• Reasoner only when strictly necessary
• Database
• scalability, performance (set operations)
• Java + database
• EJB
• concurrency
• security
Related Work
• “Loading data into description reasoners”

(Borgida and Brachman ’93)
• Parka system (University of Maryland ’95)
• “Semantic indexing” (Schmiedel ’94)
161
System details
http://instancestore.man.ac.uk
Code available from SourceForge
Demo
• Enriched Gene Ontology (GO)

• 25,180 classes
• 4 properties
• Instance data mined from GO SWISS-PROT

database (in June 03)
• 653,762 individuals
• involving 48,584 distinct descriptions
162
Intelligent Curation
Using Ontologies
K.Wolstencroft
O p enG A LEN
BioHealth
Informatics
Group
Introduction
► Developing an automated system for extracting and

classifying proteins from newly sequenced genomes
1. Background
2. Architecture
3. Advantages
163
Motivation
► Genome sequencing techniques greatly improved

► More whole genomes are being sequenced quickly -
lots of data being generated
► Without analysis and classification – sequences are
simply a series of letters
► Therefore, data analysis is now the rate-limiting step
Why Classify?
► Classification and curation of a genome is the first step

in understanding the processes and functions
happening in an organism
► Classification enables comparative genomic studies -
what is already known in other organisms
► The similarities and differences between processes
and functions in related organisms often provide the
greatest insight into the biology
164
Background
DNA to Proteins
Genome sequencing – produces DNA sequences
► DNA – blueprint of an organism

► DNA encodes complex molecules – mostly proteins
► Proteins are the functional molecules of a cell
Proteins
► Complex molecules constructed from sequences of

amino acids
► 20 different amino acids with different chemical
properties
165
Proteins
Primary Structure
► Amino acid sequences can be represented as a series

of single letters
>1A5Y:_ PROTEIN TYROSINE PHOSPHATASE 1B

MEMEKEFEQIDKSGSWAAIYQDIRHEASDFPCRVAKLPKNKNR
NRYRDVSPFDHSRIKLHQEDNDYINASLIKMEEAQRSYILTQGP
LPNTCGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQ
KEEKEMIFEDTNLKLTLISEDIKSYYTVRQLELENLTTQETREILH
FHYTTWPDFGVPESPASFLNFLFKVRESGSLSPEHGPVVVHXS
AGIGRSGTFCLADTCLLLMDKRKDPSSVDIKKVLLDMRKFRMG
LIATAEQLRFSYLAVIEGAKFIMGDSSVQDQWKELSHEDLEPPP
EHIPPPPRPPKRILEPHNGKCREFFPN
Proteins
Tertiary Structure
► Sequence determines structure
166
Searching for Features
► The relationship between amino acid sequence and

eventual protein structure means that we can search
for distinct structural (and functional) domains within
the sequence
► Domains could be several amino acids long – or could
span most of the protein
Example
A search of the linear sequence of protein tyrosine phosphatase type

K – identified 9 functional domains
>uniprot|Q15262|PTPK_HUMAN Receptor-type protein-tyrosine phosphatase kappa precursor (EC 3.1.3.48) (R-

PTP-kappa).
MDTTAAAALPAFVALLLLSPWPLLGSAQGQFSAGGCTFDDGPGACDYHQDLYDDFEWVHV
SAQEPHYLPPEMPQGSYMIVDSSDHDPGEKARLQLPTMKENDTHCIDFSYLLYSQKGLNP
GTLNILVRVNKGPLANPIWNVTGFTGRDWLRAELAVSSFWPNEYQVIFEAEVSGGRSGYI
AIDDIQVLSYPCDKSPHFLRLGDVEVNAGQNATFQCIATGRDAVHNKLWLQRRNGEDIPV………..
167
Human Expert Annotation
► Bioinformaticians use a series of tools to identify functional

domains
Similarity searching, domain/motif identification
Tools include – BLAST / INTERPRO
► Tools simply show presence of domains
► Use expert knowledge to classify proteins according to domain
arrangements
Presence / order / number of each important
► Can an ontology be used to capture this knowledge to the

standard of a human annotator?
Protein Family
Classification
► Proteins divided into broad functional classes “Protein

Families”
► Often diagnostic domains/motif signify family
membership
► Initial Study focuses on the protein phosphatase family
168
The Protein Phosphatases
► large superfamily of proteins – involved in the removal

of phosphate groups from molecules
► Important proteins in almost all cellular processes
► Involved in diseases – diabetes and cancer
► human phosphatases well characterised
Characterisation allows
classification
► Diagnostic phosphatase domains/motifs – sufficient for

membership of the protein phosphatase superfamily
► Other motifs determine a protein’s place within the
family
► This human expert knowledge can be captured and
incorporated into the model if the domain
organisations are represented in a formal DL OWL
ontology
169
Protein Functional Domains
Andersen et al (2001) Mol. Cell. Biol. 21 7117-36
Determining Class
Definitions
R2A
- Contains 2 protein tyrosine phosphatase domains
- Contains 1 transmembrane domain
- Contains 4 fibronectin domains
- Contains 1 immunoglobulin domain
- Contains 1 MAM domain
- Contains 1 cadherin-like domain
170
Protégé OWL Modelling
Requirements
► Extract phosphatase sequences from rest of protein

sequences from a whole genome
► Identify the domains present in each
► Compare these sequences to the formal ontology
descriptions
► Classify each protein instance to a place in the
hierarchy
171
Technology
OWL DL
ontology
Raw protein myGrid Instance Classified Protein

sequences Workflow Store Phosphatases
Reasoner
(racer)
myGrid Workflow
► extract sequences from whole genome

► perform simple filtering – patmatdb
► performs InterproScan to determine domain
architecture
► transform the InterproScan results into abstract OWL
instance descriptions
172
myGrid Workflow
InterproScan Results
173
Conversion to abstract
OWL format
restriction(<http://www.owl-
ontologies.com/unnamed.owl#containsDomainIPR000
340> cardinality(1))
Instance Store
► Instance Store enables reasoning over individuals

► Can support much higher numbers of individuals
► OWL ontology is loaded into the instance store

► A DL reasoner (racer) is used to compare individuals
to the OWL ontology definitions
174
Instance Store
Example Instances
► Protein Individual ► Ontology Definition of Dual

Dual Specificity Specificity Phosphatase
Phosphatase DUSE containsDomain IPR000340
restriction(<http://www.owl- Necessary and Sufficient for
ontologies.com/unnamed.owl# class membership
containsDomainIPR000340> Also inherits
cardinality(1))
containsDomain IPR000387 from
restriction(<http://www.owl- Parent Class PTP
ontologies.com/unnamed.owl#
containsDomainIPR000387>
cardinality(1))
175
So Far…..
► Human phosphatases have been classified using the

system
► The ontology classification performed equally well as
expert classification
► The ontology system refined classification
- DUSC contains zinc finger domain
Characterised and conserved – but not in classification
- DUSA contains a disintegrin domain
previously uncharacterised – evolutionarily conserved
Aspergillus fumigatus
► Phosphatase compliment very different from human

>100 human <50 A.fumigatus
► Whole subfamilies ‘missing’
Different fungi-specific phosphorylation pathways?
No requirement for tissue-specific variations?
► Novel serine/threonine phosphatase with homeobox
conserved in aspergillus and closely related species, but not in
any other
176
Conclusions
► Using ontology allows automated classification to

reach the standard of human expert annotation
► Reasoning capabilities allow interpretation of domain
organisation
► Produces interesting biological questions
► Allows fast, efficient comparative genomics studies
► System currently describes protein phosphatases -
but possible to expand to other protein families
Acknowledgements
Group : myGrid
PhD Supervisors: Andy Brass, Robert Stevens
Phosphatase Biologist: Lydia Tabernero
Ontogrid and NIBHI
177
Open Discussion
Q&A
Panel
Questions:
Possible Topics:
- Current (known) limitations of OWL
- Modularisation of ontologies
- Ontological Patterns
- Protégé-OWL UI questions & feedback
(shortcuts, debugging, future development)
178
Appendices
Terminology
Syntax
Resources
Application Overviews
179
Appendix A: Terminology
“Class” ≈ “Concept” ≈ “Category” ≈ “Type”
“Individual” ≈ “Instance”
“Property” ≈ “Slot” ≈ “Relation” ≈ “Relationtype” ≈ “Attribute” ≈ Semantic link type” ≈ “Role”
NB be careful about “role”

• Means “property” in DL-speak
• Means “role played” in most ontologies
– E.g. “doctor_role”, “student role” …
“Entity” ≈ “Object” ≈ “Resource”, Class or Individual
180
Appendix B: Syntax
Three official syntaxes + Protégé-OWL syntax:
Abstract syntax-- - Specific to OWL
N3 ---------------- - OWL & RDF

- used in all SWBP documents
XML/RDF ------- - very verbose, not for human consumption
Protégé-OWL---- - Compact, derived from DL syntax
Alternatives:
“German DL”---- - very concise, symbolic
First order logic - - complete but more powerful than DL
Paraphrase-------- - Verbose but precise
Protégé/OWL can generate all syntaxes except German
Simplified abstract syntax

someValuesFrom some ∃
allValuesFrom only ∀
intersectionOf AND П
unionOf OR
complementOf NOT ¬
complete definition necessary & sufficient
partial description necessary
181
Symbol Meaning OWL
∃ “some” someValuesFrom
∃ hasCause X “hasCause SOME X” hasCause someValuesFrom(X)
∀ “only” allValuesFrom
∀ hasCause X “hasCause ONLY X” hasCause allValuesFrom(X)
П “and” intersectionOf
“or” unionOf
≡ “are necessary & sufficient equivalentClass
conditions for”
“necessarily implies” subclassOf
182
Appendix C: Resources
W3C OWL Pages – http://www.w3.org/2004/OWL/
Including specs, pointers to other material, including applications and related projects
Protégé – http://protege.stanford.edu
See also the WIKI available at http://protege.cim3.net/cgi-bin/wiki.pl
Especially useful for the mailing list – subscribe to Protégé-OWL for support and
discussion
Protégé-OWL homepage - http://protege.stanford.edu/plugins/owl/ includes most

recent versions of the rapidly changing software, documentation, papers and details of
the Java API as well as examples of producing plugins
CO-ODE – http://www.co-ode.org
Plugins and other resources/materials available, including:
• OWLViz - graph view of the ontology
• Protégé Wizards- several basic wizards to automate some of the class creation process
• Class Description Display - A floating dialog that can be invoked to display various renderings the
selected OWL Class
• OWLDoc - Generates JavaDoc style HTML docs for your OWL ontology
• Abstract Syntax Package - Viewing and Exporting OWL Ontologies in the OWL Abstract Syntax.
• RDFS Class Hierarchy Exporter - Export a 'bare bones' RDFS Class Hierarchy with optional
annotations.
Semantic Web Best Practices Working Group

Producing documentation on ontology quality and other aspects such as identifying
Design Patterns
W3C Documentation - http://www.w3.org/2001/sw/BestPractices/
WIKI - http://esw.w3.org/topic/FrontPage
AKT applications
A good source of example applications, including ArtEquAkt, Magpie and CS AKTiveSpace
and technologies like the 3store
http://www.aktors.org/technologies/
183
Appendix D: Application Overviews

Manchester Pizza Finder
The Pizza Finder uses a remote Pizza Ontology, and a remote Description Logic (DL) reasoner to
dynamically generate pizza toppings and pizza topping categories. The user can include toppings that they
would like on their pizza and exclude any toppings that they do not want on their pizza. The description
logic reasoner is used to determine if the choices that have been made contradict each other - for
example, choosing to include Jalapeno Pepper topping, but choosing to exclude all hot toppings - the
choices are automatically adjusted to modify any decisions that could potentially lead to contradictions
and inconsistent results.
For more information please visit: http://www.co-ode.org/downloads/pizzafinder/
184
COHSE
The aim of this project was to research into methods to improve significantly the quality,
consistency and breadth of linking of WWW documents at retrieval time (as readers
browse the documents) and authoring time (as authors create the documents). It has
produced a COHSE (Conceptual Open Hypermedia Services Environment) using three
leading-edge technologies:
• an ontological reasoning service which is used to represent a sophisticated conceptual model of

document terms and their relationships;
• a Web-based open hypermedia link service that can offer a range of different link-providing
facilities in a scalable and non-intrusive fashion;
• the integration of the ontology service and the open hypermedia link service to form a conceptual
hypermedia system to enable documents to be linked via metadata describing their contents;
Figure 1 illustrates how all the COHSE software fits together. Ontologies can be created in any DAML
enabled ontology constructor, although we used the OILEd ontology editor throughout this project. The
constructed ontologies (1) are loaded by the Ontology Service (2) which can answer queries about it (e.g.
What concept is described by the term 'block'? What are the super-concepts of 'data type'?). Annotations
are stored in a database and the Annotation Service adds and retrieves annotations from it (3).
Annotations are constructed using the Mozilla Annotator tool which communicates with the Ontology
Service (4) and Annotation Service (5). To assist in annotating complex concepts, a concept browser (a cut
down version of OILed) can be used which loads an ontology (10) and then communicates with the
annotator (9).
COHSE linking can be applied through the Mozilla DLRS tool or the browser independent proxy solution.
Both tools communicate with the Ontology Service (4 & 6) and the Annotation Service (5 & 7). The Mozilla
DLRS tool dynamically updates the Web page it has loaded from the Web (8.1). The proxy downloads the
Web page (8.2), decorates it with COHSE linking, and then returns it to the browser (11).
• For more information please visit: http://cohse.semanticweb.org/
185
Instance Store
The instance Store (iS) is a Java application for performing efficient and scalable
Description Logic (DL) reasoning over individuals.
DL reasoning over individuals is an important aspect of the vision behind the Semantic
Web and it is crucial in applications of ontologies in areas such as bioinformatics (gene
description) and web service discovery. This also poses new challenges for ontological
reasoning. Firstly, applications might now require vast volumes of individuals exceeding
the capabilities of existing reasoners. Secondly, while one can assume that changes in
the terminological part of an ontology are relatively infrequent, various scenarios, such
as web service discovery, postulate dynamic, frequent and, possibly, concurrent
modification of the information related to the individuals in ontologies.
The iS system tackles this problem by applying a well-known idea in knowledge

representation, namely supporting reasoning by means of databases. Assertions over
individuals are stored in a database, together with information inferred using a DL
reasoner over the position in the ontological taxonomy of their corresponding
descriptions. This allows to reduce the amount of reasoning to pure terminological
reasoning, while maintaining soundness and completeness (provided that no relation
between individuals occurs). Moreover, it allows to deploy iS using enterprise
technologies such as Enterprise Java Beans, thus handling the delicate concurrency,
security, and transaction management issues using robust technologies.
More information is available at: http://instancestore.man.ac.uk/
186
Intelligent Curation Through Ontology
Classification of proteins is a central step in understanding the molecular biology of an

organism. Sequencing is simply a first step in revealing the molecular machinery of a cell.
Techniques involved in sequencing, especially the high throughput sequencing of whole
genomes, have improved dramatically in recent years. Consequently, analysis and
annotation of the data is now the rate-limiting step.
Approaches to analysing the large data sets produced in genome sequencing projects
have ranged from the ‘gold-standard’ of human expert annotation to the simple
automation of bioinformatics tools. Expert annotation enables protein classification to be
driven by community knowledge and can add rich, accurate information to data, but it is
a slow process. Automated annotation methods are often much faster, but generate a
much higher degree of errors.
To bring automated classification up to the standard of expert annotation, we use a

description logic ontology. The use of an ontology incorporates community knowledge
into the automatic curation process.
The automated classification tool uses myGrid workflows to extract and describe the
properties of individual proteins. By comparing these individual descriptions to DL
ontology class definitions, DL reasoners are able to classify each protein using the
knowledge from human experts.
187
Appendix E: Hands-On – Protégé-OWL part 3
The following slides are used to demonstrate several issues around modelling in OWL and
are provided as additional material to support the further exercises in the handouts. It is
unlikely that this material will be presented, unless time permits.
188
Ontologies & OWL
Additional Exercises: Common
Errors and how to correct them
O p enG A LEN
BioHealth
Informatics
Group 1 Copyright © 2005, The University of Manchester
Overview
► Elephant Traps
► Property Domain & Range
► Property Characteristics – functional properties
► Intersection
► Negation in OWL – ComplementOf

► Class expressions test
► Q&A – 20 mins
2 Copyright © 2005, The University of Manchester
189
Elephant Traps
Common Errors in OWL generally include:

► Disjoint misuse – often used on defined classes by
mistake
► Confusing AllValueFrom and SomeValuesFrom –
some doesn’t imply only, and only doesn’t imply some
► Forgetting to close class descriptions
► Incorrect expectations of Domain and Range defined
for properties
► Incorrect use of Functional Properties
► Using intersection (AND) instead of union (OR), where
the members of the intersection are disjoint
Property Domain & Range

► If a relation is:
subject_individual Æ hasProperty Æ object_individual
► The domain is the class of the subject individual
► The range is the class of the object individual (or a datatype if
hasProperty is a Datatype Property)
rty
rope
hasP
DomainClass rty RangeClass
rope
hasP
rty
rope
hasP
190
Setting a Domain & Range

► Setting a domain & range on a property has global implications
► Be careful not to over-constrain your ontology
► The domain & range can be set in the Properties Tab – just click
Add named class(es)
eg. Setting a domain of Pizza on hasBase
► Using a Universal Restriction on a Class is like setting a local

range
Semantics of Domain & Range
► Domain and Range are not used to restrict the interface

► They are used by the reasoner to infer additional information
about individuals
► Any individual that uses a property with a domain set can be
inferred to be a member of the domain class
► the same holds for range
191
Exercise 10: IceCream and Domain
Trap: Property Domain reclassification
► Any Class that uses a property with a domain set in an

existential restriction will be inferred to be a subclass
of the domain class
► This is because all individuals in this class must have
at least one relationship using this property –
therefore, all members of this class must be members
of the domain class
► If these classes are disjoint with the domain then they
will come out inconsistent – another reason to check
all your disjoints are set
► The same does not apply to range

192
Property Characteristics
► Inverses – if property p has inverse property q, and p relates A-B,
then it can be inferred q relates B-A
► Functional – if property p relates A-B then all relations along p relate
A-B (m..1 relation)
(B could also be a datatype value)
► Inverse Functional – the inverse of the property is functional
► Symmetric – if a property relates A-B then it also relates B-A
► Transitive – if a property relates A-B and B-C then it relates A-C
Functional Properties
► An individual can only have relationships with at most one other
individual along a functional property
eg Setting hasBase to Functional means:
“Every Pizza can have at most one PizzaBase”
Description of DoubleBasePizza:
► The reasoner finds this inconsistent

► It looks like the interface is warning us that we can’t use the property
more than once, but actually…
193
Exercise 11: Functional Properties
Trap: Functional Property Misuse
► If a property is functional and is used in several

Existential restrictions on a class, the reasoner will
infer that the filler classes must overlap
► If any of the fillers are disjoint from each other then

this cannot be the case and therefore causes an
inconsistency
► If they are not, no inconsistency is found
194
Intersection Classes
► aka “conjunction”
► This AND That AND TheOther
► This That TheOther
► Each class description or definition is an intersection of the conditions in
it
► CheeseyPizza ≡ Pizza and ∃ hasTopping CheeseTopping
∃ hasTopping
Pizza CheeseTopping
CheeseyPizza
Intersection
=
► People often ask what the difference is between using

2 existential restrictions (which are, by default, in an
intersection in the interface) and using a single
restriction with a filler containing both the classes
195
Trap: Intersection
≠
There are 2 problems:

1. Often we paraphrase “AND” when we logically mean “OR”
The filler “CheeseTopping AND MeatTopping” cannot contain any
individuals as they are disjoint, and is therefore inconsistent
2. If we correct this to OR, it is still wrong as we’ve got a class description
that can be fulfilled by a Pizza with a single topping – either Cheese or
Meat. If we had 2 existential restrictions, there would have to be at least
2 (disjoint) toppings
ComplementOf Classes
► aka “Negation” “Not”
► Not Something
► ¬ Something
owl:Thing
A
All individuals in
here are members
of ¬A
196
ComplementOf Classes
► Commonly used to model 3 things:
► A is any C that is not B
► A does not have some relation with B
► A only has relations with things that are not B
Exercise 12: Variations of VeggiePizza
► The ontology used in this example will be available at:

www.co-ode.org/ontologies/brokenPizza/
197
Summary
► Avoid some of the more common modelling errors in
OWL
► Appreciate that all OWL statements are reasoned with
and many mistakes are only caught because of
disjoints
► Understand different characteristics of properties
► Spot various similar looking statements in OWL are
very different
198
Acknowledgements & Contacts:

Thanks to the following people for putting this tutorial together, either physically or
mentally.
Speakers:
Robert Stevens – BioInformatics – robert.stevens@cs.man.ac.uk
Alan Rector – Medical Informatics
Sean Bechhofer – OntoGrid, COHSE
Matthew Horridge – CO-ODE – matthew.horridge@cs.man.ac.uk
Nick Drummond – CO-ODE – nick.drummond@cs.man.ac.uk
Jeremy Rogers – OpenGALEN – Jeremy.e.rogers@manchester.ac.uk
Daniele Turi – IMG, Instance Store
Katy Wolstencroft – Phosphabase, mygrid
Other Contributors:
Holger Knublauch & the Protégé team – Protégé-OWL
Harith Alani, Nick Gibbins and Nigel Shadbolt – AKT
Hai Wang and Julian Seidenberg - HyOntUse
Also:
Georgina Moulton – NIBHI - georgina.moulton@manchester.ac.uk
Sam Creighton and Karon Mee – Computer Science
Tracy Harrison and Kath Melville – MBS
Susan House & Lynn Howarth – Computer Science
199

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A Practical

The CO-ODE and HyOntUse projects

Advanced Knowledge Technologies

NorthWest Institute for Bio-Health Informatics

The Joint Information Systems Council

The Engineering and Physical Sciences Research Council

Document date 5th July 2005

All materials (this document, slides,

Tutorial details available at www.co-ode.org/events/tutorials/escience02/

All Material © 2005, The University of Manchester

10:30 Participants Introductions

10:45 Introduction to Ontologies

11:45 OWL overview

13:30 Hands On: Protégé-OWL tutorial part 1

Nick Drummond, Matthew Horridge

16:00 Ontology Engineering

16:30 Discussion and Q&A

09:30 Knowledge Acquisition

10:00 Hands On: Protégé-OWL tutorial part 2

Nick Drummond, Matthew Horridge

10:45 • Defined Classes

12:00 Formal Modelling Practice

13:45 Ontology Applications

Sean Bechhofer, Daniele Turi, Matthew Horridge

• General themes / Architectures

15:00 Discussion and Q&A

2 Copyright © 2005 Univ. of Manchester

►Introduction and Motivation

►OWL Language Overview

►Hands On: Protégé-OWL 1

3 Copyright © 2005 Univ. of Manchester

►Formal Modelling Issues

►Q&A, Open Discussion

4 Copyright © 2005 Univ. of Manchester

5 Copyright © 2005 Univ. of Manchester

6 Copyright © 2005 Univ. of Manchester

Hard Work using the

7 Copyright © 2005 Univ. of Manchester

Impossible (?) using the

► Locating information in data repositories

► Finding and using “web services”

► Delegating complex tasks to web “agents”

8 Copyright © 2005 Univ. of Manchester

What is the Problem?

Consider a typical web page:

9 Copyright © 2005 Univ. of Manchester

What information can we

10 Copyright © 2005 Univ. of Manchester

What information can a

11 Copyright © 2005 Univ. of Manchester

Solution: XML markup with

But What About…

13 Copyright © 2005 Univ. of Manchester

14 Copyright © 2005 Univ. of Manchester

Need to Add “Semantics”

► External agreement on meaning of annotations

► Use Ontologies to specify meaning of annotations

15 Copyright © 2005 Univ. of Manchester

Ontology: Origins and

► Science of Being (Aristotle, Metaphysics, IV, 1)

► Tries to answer the questions:

What characterizes being?

Eventually, what is being?