Ontology development in protégé-آنتولوژی در پروتوغه

In The Name Of Allah

Instructor: Dr.Ghasem-Aghaie

Presentation: Mohammad Sadegh Salehi

Ontology Development in

Protégé

Protégé – Winter 2014

Session 1: Ontology And OWL Basics, Syntatic Web,

Problem of Syntatic Web,

Semantic Web,

Ontology and Pizza Example,

OWL,

Session 2: Protégé & Protégé-OWL, What is Protégé?

Protégé and OWL,

Pizza in Protégé ,

Agenda

Ontology and OWL


Hard Work using the Syntactic Web…

Find images of Tim Bray and Alan Rector…

Tim Bray

Sun

Microsystems

Rev. Alan M.

Gates,

Associate

Rector of the

Church of the

Holy Spirit,

Lake Forest,

Illinois

Prof Alan

Rector,

University of

Manchester,

Medical

Informatics

Group


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

Finding and using “web services” Book me a holiday next weekend somewhere warm, not too far

away, and where they speak French or English


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…



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 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…



…

What information can a machine see…


What is the Problem?Solution: XML markup with “meaningful” tags?

<name>

</name>

<location>

</location>

<date> </date>

<slogan> </slogan>

<participants>

</participants>

<introduction>

… </introduction>

<speaker> </speaker>

<bio> </bio>…


What is the Problem?But What About… Machine sees…

<>

</>

<>

</>

<> </>

<> </>

<>

</>

<>

…

</>

<> </>

<> </>

<> </>

<> </>


Need to Add “Semantics”

Use Ontologies to specify meaning of annotationsOntologies provide a vocabulary of terms

New terms can be formed by combining existing ones

Meaning (semantics) of such terms is formall specified

Can also specify relationships between terms in


Our Domain

Pizzas have been used in Manchester tutorials for years,

Tutorial developed by BioHealth Informatics Group in Manchester,


Pizzas…

are fun

are internationally known

are highly compositional

are limited in scope

are fairly uncontroversial


Pizzas Ontology …

PizzaPizza Topping Pizza_base

Vegetarian

Pizza Vegetable

Topping

Margareta

PizzaTomato

Topping

Cheese

Topping

Spicy Beef

Pizza

Mozzarella

Topping

Deep

Dish base

Regular

base


Is the Web Ontology Language…

is a standard – Web Ontology Language

comes in 3 flavours (lite, DL and full) we are using OWL DL (Description Logic)

DL = decidable fragment of First Order Logic (FOL)

Is used for capturing knowledge in a machine understandable way

Review of OWL


OWL helps us …

Describe something, rather than just name it.

Class (BlueThing) does not mean anything

Class (BlueThing completeowl:Thing

restriction (hasColour someValuesFrom (Blue)))


OWL is a syntax independent language that has several common representations

– Abstract Syntax

– N3

– RDF/XML

OWL Syntax


One of the clearer human-readable syntaxes

OWL Syntax: Abstract Syntax

Class(SpicyPizza complete

annotation(rdfs:label "PizzaTemperada"@pt)

annotation(rdfs:comment "Any pizza that has a spicy topping

is a SpicyPizza"@en)

Pizza

restriction(hasTopping someValuesFrom(SpicyTopping))

)


OWL Constructs

Person Country

= class (concept)

Animal

= individual (instance)

Belgium

Paraguay

China

Latvia

Elvis

Hai

Holger

Kylie

S.Claus

Rudolph

Flipper

= property (relationship)

Protégé & Protégé-OWL


Developed by Stanford Medical Informatics,

Has a large user community (approx 300k),

Free, open source ontology editor and knowledge-base framework.

What is Protégé?


Based on Java, is extensible,

Provides a plug-and-play environment

Supported by a strong community of developers and academic, government and corporate users

What is Protégé?(Cont.)


Keep in mind that Protégé is...

...not a programming language.

...only a tool. It will not prevent you from making mistakes.

Notice that we will be referring to Protégé 4.3 in this and the following hands-on exercise.

What is Protégé?(Cont.)


Create a new ontology from scratch

Download and extend an existing ontology

Export ontologies in a variety of formats

OWL

RDF

XML Schema

What can you do with Protégé?


Homepage http://protege.stanford.edu/

Download http://protege.stanford.edu/download/protege/4.3/installanywh

ere/

Documentation http://protegewiki.stanford.edu/index.php/Protege4UserDocs

Plugins http://code.google.com/p/co-ode-owl-

plugins/downloads/list?can=3

Get Protégé

http://protege.stanford.edu/download/protege/4.0/installanywhere/

http://protege.stanford.edu/download/protege/4.3/installanywhere/

http://protegewiki.stanford.edu/index.php/Protege4UserDocs

http://code.google.com/p/co-ode-owl-plugins/downloads/list?can=3


Protégé Overview


Classes in OWL

Classes: ‟OWL classes are interpreted as sets.”

Primitive Classes: ‟Classes that only have necessary

conditions”; Example: Animal, Cat…

Defined Classes: ‟A class that has at least one necessary

and sufficient condition”; Example: All things that are biped

and lack feathers.


Classes in Protégé

All classes are subclasses of Thing

Classes overlap by default!

Can use tools menu to create class hierarchies


Properties in OWL

Object Properties

Relationships between two individuals

Correspond to relationships in UML

Examples: is_part_of, is_kissing

Datatype Properties

Relationships between an individual and data values

Correspond to attributes in UML

Examples: has_DateValue, has StringValue


Properties in Protégé

Object or data type

Properties can have

Subproperties

Inverse properties


Protégé Tabs

Protégé tabs


Protégé OWL plugin: Tabs

Used in this tutorial

Changing the GUI

Populating the

model

Top-level

functionality

Extensions

(visualisation)


Classes Tab


ClassesTab: Asserted Class Hierarchy

Subsumption hierarchy (superclass/subclass)

Structure as asserted by the ontology engineer

Create and Delete classes (actually subclasses!!)

Everything is a subclass of owl:Thing

Search for class


ClassesTab: Class Editor


ClassesTab: 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)


Create Classes

1. Click the “Create Class” button

(this is above the class hierarchy)

A new class will be created as a subclass of owl:Thing

2. Type in a new name “DomainConcept” over the default

(return updates the hierarchy)

3. Req. for later labs: document your class using the rdfs:comment field

4. Create another class called “Pizza” using the same method

You will notice that Pizza has been created as a subclass of

DomainConcept as this was the class selected when the button was

pressed. You can also right-click any class and select “Create Class”

5. Create two more subclasses of DomainConcept called “PizzaTopping”

and “PizzaBase”.

Any mistakes, use the “Delete Class” button next to “Create Class”

Start with your empty ontology


Concept: Disjointness

All classes could potentially overlap

Pizza Ice Cream

= individual

This means an individual could be both a Pizza and a

IceCream at the same time.



If we state that classes are disjoint

This means an individual cannot be both a Pizza and a Ice

Cream at the same time

We must do this explicitly in the interface

Pizza Ice Cream

= individual



Add siblings as disjoint

Add new disjoint Remove disjoint siblings

List of disjoint classes


ClassesCreate Pizza Ontology classes

Pizza

PizzaBase

PizzaTopping


ClassesPizza Toppings classes

Using the Tools->“Create class Hierarchy…”

CheeseTopping◦ MozzarellaTopping

◦ ParmezanTopping

MeatTopping◦ HamTopping

◦ PepperoniTopping

◦ SalamiTopping

◦ SpicyBeefTopping

SeafoodTopping◦ AnchovyTopping

◦ TunaTopping

VegetableTopping◦ OliveTopping

◦ OnionTopping

◦ PepperTopping

◦ TomatoTopping

Meaning: All individuals that are members of the class TomatoTopping are members of the class VegetableTopping and members of the class PizzaTopping…


Creating Properties

Properties can be in a hierarchy

Search for property

Create property


Creating Properties

There can be at most one individual (range)

that is related to the domain individual

via the property: “hasMother”

The inverse property is functional:

“hasMother → hasChild”

P(A,B) and P(B,C) -> P(A,C)

If a property P is transitive, and the property

relates individual A to individual B, and also

individual B to individual C: “hasAncestor”

P(A,B) -> P(B,A)

If a property P is symmetric, and the property

relates individual A to individual B : “hasSibling”


Properties in Protégé


RestrictionsDefinition

A restriction describes an anonymous (unnamed) class◦ The set of subclasses and individuals that satisfy

the given restriction

Applies to◦ Classes

◦ Object Properties

◦ Datatype Properties


RestrictionsAdd restrictions

Specify that Pizza only has one PizzaBase◦ Add a cardinality restriction to Pizza on hasBase to exactly one

PizzaBase◦ Add to the superclasses section “hasBase exactly 1 PizzaBase”

Specify that Pizza has at least one PizzaTopping◦ Add an existencial restriction to Pizza on hasTopping to

PizzaToppings◦ Add to the superclasses section “hasTopping some PizzaTopping”

Create a value restriction to specify that MozzarellaTopping has Italy as its country of origin◦ Create hasCountryOfOrigin object property with Country as range◦ Add to the superclass section “hasCountryOfOrigin value Italy”

With Protégé 4.3

Using a Reasoner


Reasoner - Definition

A piece of software able to infer logical consequences from a set of asserted facts or axioms


Reasoner -Used for

Consistency checking◦ Test whether a class could have instances

Classification◦ A classifier takes a class hierarchy and places a class in the class

hierarchy

◦ Task of turning implicit definitions already present in the hierarchy as explicit


Reasoner- Protégé 4.3 support

Built-in support◦ Pellet (http://clarkparsia.com/pellet)

◦ FaCT ++(http://owl.man.ac.uk/factplusplus/)

Connection to external reasoners through a DIG interface

http://clarkparsia.com/pellet

http://owl.man.ac.uk/factplusplus/


Reasoner - Pellet vs FaCT++

FaCT++Pellet

Open-source Java OWL DL reasoner

Support expressivity of SROIQ(D)

Supports SWRL rules

Available through AGPL version 3 licence

Latest version is 2.0.0 rc5

Support in Protégé for 1.5 version

New generation and C++ implementation of FaCT

Support expressivity of SROIQ(D)

No support for Rules Available through GNU

public license Latest version is 1.2.3 Support in Protégé for

1.2.3 version



Pizzas and other ontologies are available from: www.co-ode.org/ontologies/

W3C Documentation http://www.w3.org/2001/sw/BestPractices/

Ian Horrocks, Sean Bechhofer: http://www.cs.man.ac.uk/~horrocks/Slides/Innsbruck-tutorial/

Practical Guide To Building OWL Ontologies Using Prot´eg´e 4 and CO-ODE Tools, Mathew Horridge, Edition 1.2, 2009,university of manchester

Refrences


http://www.co-ode.org/ontologies/

http://www.w3.org/2001/sw/BestPractices/

http://www.cs.man.ac.uk/~horrocks/Slides/Innsbruck-tutorial/


Pizzas…

Most often it is not the domain expert that formalises their knowledge

Because of the complexity of the modelling task 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…


Ontology in Linguistics

Concept

Form

/ SymbolReferent

“semiotic

triangle”activates Relates to

“Tank“

[Ogden, Richards, 1923]

Stands for

“a concept, is the

mediator that relates

the symbol to its

object” John F Sowa


Datatype PropertiesAdd datatype properties

Create a hasCalorificContentValue datatype property with integer as range

Create a hasBaseProperty for PizzaBase (domain)◦ Create a hasWidth datatype sub-property of hasBaseProperty with

integer as range◦ Create a hasThickness datatype sub-property of hasBaseProperty

with float as range

Change characteristics to Functional of the datatype properties◦ hasCalorificContentValue◦ hasWidth◦ hasThickness


Datatype Properties


Object Properties


Object PropertiesCreate some Object Properties

isIngredientOf◦ isToppingOf

◦ isBaseOf

hasIngredient◦ hasTopping

◦ hasBase

Pizza IngredientsIngredients that make up

the Pizza


Structure of an Ontology

Ontologies typically have two distinct components: Terminology

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 > 20 years

Background knowledge/constraints on the domain: Axioms 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

Engineering

Ontology development in protégé-آنتولوژی در پروتوغه