IntroductionOWLv2

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BioHealth

Informatics

Group

A Practical
Introduction to
Ontologies & OWL


Sean Bechhofer and Georgina Moulton

Copyright © 2006, The University of

Manchester

Ontogenesis Network Tutorial


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


Hands On: Protégé
-
OWL 2


Using a reasoner for computing a classification


Formal Modelling Issues


Why classify?


Untangling


Q&A, Open Discussion


Feedback


Overview

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Ontogenesis Network Tutorial

The Car

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Manchester

Ontogenesis Network Tutorial

Coche

Automobile

Voiture

Araba

The Car

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Ontogenesis Network Tutorial

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

Hard Work using the
Syntactic Web…

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Manchester

Ontogenesis Network Tutorial


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

Impossible (?) using the
Syntactic Web…

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Ontogenesis Network Tutorial

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 is the Problem?

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Manchester

Ontogenesis Network Tutorial

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 7
th

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 …



What information can we
see…

Copyright © 2006, The University of

Manchester

Ontogenesis Network Tutorial

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 7
th

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 



What information can a
machine see…

Copyright © 2006, The University of

Manchester

Ontogenesis Network Tutorial

<
name
>
WWW2002The eleventh international world wide
webcon
</name
>

<
location
>
Sheraton waikiki hotel Honolulu, hawaii,
USA
</location
>

<
date
>
7
-
11 may 2002
</date>

<
slogan
>
1 location 5 days learn interact
</slogan
>

<
participants
>
Registered participants coming
fromaustralia, 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
</participants
>

<
introduction
>
Register nowOn the 7
th

May Honolulu will
provide the backdrop of the eleventh
international world wide web conference This
prestigious event Speakers confirmed
</introduction
>

U
speaker>
Tim berners
-
lee
U⽳灥/步k
>

U
bio
>
Tim is the well known inventor of theWeb,

bio
>




Solution: XML markup with
“meaningful” tags?

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Manchester

Ontogenesis Network Tutorial

But What About…

<conf>
WWW2002The eleventh international world wide
webcon
</conf>

<place>
Sheraton waikiki hotelHonolulu, hawaii,
USA
U⽰污捥W

<date>
7
-
11 may 2002
U⽤慴放

<slogan>
1 location 5 days learn interact
㰯獬潧慮o

<participants>
Registered participants coming
fromaustralia, 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
㰯灡U瑩t楰慮瑳z

<introduction>
Register nowOn the 7
th

May Honolulu will
provide the backdrop of the eleventh international world
wide web conference This prestigious event 

Speakers confirmed
U⽩湴牯摵捴楯渾

㱳灥U步kW
Tim berners
-
lee
㰯獰敡步kW

㱢U漾
Tim is the well known inventor of the Web,




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Manchester

Ontogenesis Network Tutorial


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

Need to Add “Semantics”

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Ontogenesis Network Tutorial



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?

Ontology in Philosophy

Ontology: Origins and
History

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Manchester

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“Tank“

Referent

Form

Stands for

Relates to

activates

Concept

[Ogden, Richards, 1923]

?

Ontology in Linguistics

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Manchester

Ontogenesis Network Tutorial


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]

Ontology in Computer
Science

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Manchester

Ontogenesis Network Tutorial


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_Elephant
s weigh at least 2,000 kg


All
Elephant
s are either
African_Elephant
s or
Indian_Elephant
s


No individual can be both a
Herbivore

and a
Carnivore


Structure of an Ontology

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Manchester

Ontogenesis Network Tutorial

A semantic continuum

[Mike Uschold, Boeing Corp]

Shared
human
consensus

Implicit

Text
descriptions

Pump: “a device for
moving a gas or liquid
from one place or
container to another”

Informal

(explicit)

Semantics
hardwired;

used at runtime

Formal

(for humans)

Semantics
processed and
used at runtime

(pump has


(superclasses (…))

Formal

(for machines)


Less ambiguity


Better inter
-
operation


More robust


less hardwiring


More difficult



Further to the right


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Ontogenesis Network Tutorial

Pizza

Margherita

Pizza

Vegetarian

Pizza

Spicy Beef

Pizza

Pizza

Topping

Vegetable

topping

Tomato

topping

Mozzarella

topping

Cheese

topping

Pizza_base

Deep

dish base

Regular

base

A simple ontology: Pizzas

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Manchester

Ontogenesis Network Tutorial


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

Ontology Design and
Deployment

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Ontogenesis Network Tutorial

Example Ontology

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Ontogenesis Network Tutorial


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

Many languages use “object
oriented” model based on:

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Manchester

Ontogenesis Network Tutorial

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)

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Manchester

Ontogenesis Network Tutorial


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

Why it’s hard (1)

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Manchester

Ontogenesis Network Tutorial


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 it’s hard (2)

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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


Why its hard (3)

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Ontogenesis Network Tutorial


“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” …

Vocabulary

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Ontogenesis Network Tutorial

Ontologies

Software
agents

Problem
-
solving
methods

Domain
-
independent

applications

Databases

Declare

structure

Knowledge

bases

Provide

domain

description

The
“Semantic

Web”

An Ontology should be just
the Beginning