1 introduction to ontology development and tools part i: first steps in ontology development icbo...

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Introduction to Ontology Development and Tools

Part I: First Steps in Ontology Development

ICBO 2011, Buffalo, July 26, 2011

Mathias Brochhausen1 & Amanda Hicks2

1 UAMS, Little Rock, AR2 University at Buffalo, Buffalo, NY

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Contents

I. IntroductionII. Terminological considerationsIII. Creating the hierarchy of classesIV. Creating relationsV. (Instances) VI. Creating restrictions on classes

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I. Introduction

What is Protégé?

We are concerned here with ‟Protégé-OWL editor”.

‟The Protégé-OWL editor enables users to build ontologies for the Semantic Web, in particular in the W3C‘s Web Ontology Language (OWL)”.

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I. Introduction 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 4.1 in this and the following hands-on exercise.

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II. Terminological considerations

a. OWL/Protégé terminology

b. Preferable terminology

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IIa.OWL/Protégé terminology

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. 6

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II.a OWL/Protégé terminology

Properties: ‟binary relation between individuals”

Object Properties; Examples: is_part_of,

is_kissing

Datatype Properties; Examples:

has_DateValue, has StringValue

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II.a OWL/Protégé terminology

Individuals: ‟represent objects in the domain we

are interested in”. Examples: me, the Pentagon

in Washington, Jane Doe‘s lung.

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II.b Preferable terminology

a) Instance: An individual or particular which instantiates a universal; Examples: me, the Pentagon in Washington, Jane Doe‘s lung b) Universal: A universal is something that is shared in common by all those particulars which are its instances, Examples: Animal, Human being, Building, Human lung

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c) Attributive Collection: An attributive collection is a collection (a set) of particulars which share a common property; Examples: All patients suffering from breast cancer in the Mayo Clinic in 2009, all humans who have been tested positive for HIV, all bacteria in the petri dish over there.

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d) Relation: Relations exist mutually between universals and universals, between universals and particulars, and between particulars and particulars; Examples: is_subtype_to, is_part_of, is_instance_of, is_kissing

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However,... Throughout the presentation I will say

“classes” to keep the creation of the hierachy free from possible ontological issues about universals vs. attributive collections.

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III. Creating the hierarchy of classes

a) Why work with an Upper Ontology? Importing another ontology (e.g. an Upper Ontology) Basic Formal Ontology-a primer

b) What is represented by the hierarchy?c) How to create a class hierarchy?d) Changing OWL class namese) Disjointnessf) Exhaustivenessg) Rigidity

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III.a Why work with an Upper Ontology

Upper Ontologies…

...support consistency. ...foster harmonization and modularization. …help you to get into the right frame of mind.

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Some Upper Ontologies

Basic Formal Ontology (BFO) Descriptive Ontology for Linguistic and

Cognitive Engineering (DOLCE) Suggested Upper Merged Ontology (SUMO)

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How to import Upper Ontologies (or other pre-existent ontologies) into our ontology project?

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Importing another ontology (e.g. an Upper Ontology)

BFO - Entities

Continuant - a heart, the color of a tomato, the mass of a cloud

Occurrent - the life of an organism, a surgical operation, a conversation a heart, a table, a collection of stones

BFO - Continuants

Dependent Continuant - the color of a tomato, the mass of a cloud

Independent Continuant - a heart, a chair, the Northern Hemisphere of the Earth

Spatial Region - Dimensions Zero - Three

BFO - Dependent Continuants

Generically Dependent Continuant - a PDF file, a musical score

Specifically Dependent Continuant - the color of a tomato, the disposition of fish to decay, the role of being a doctor

BFO - Specifically Dependent Continuants

Quality - the color of a tomato, the mass of a cloud

Realizable Entity -

Disposition - fragility, solubility

Function - of the heart, to pump blood; of the a computer, to compute.

Role - being a doctor, being pet, being student

BFO - Independent Continuants

Material Entity - a heart, a table, a collection of stones

Object Boundary - end points of a line, the surface of the skin

Site - A particular room, Maria’s nostril

BFO - Material Entities

Fiat Object Part - the upper lobe of the left lung, The Northern Hemisphere

Object - a heart, a chair, a lung, an apple

Object Aggregate - a collection of bacteria, a collection of stones

BFO - Occurents

Processual Entity - a conversation, the life of an organism

Spatiotemporal Region - any part of space-time

Temporal Region - any interval of time

BFO - Processual Entities

Fiat Process Part - The worst part of a rainstorm, the middle of a meal

Proccess - sleeping, cell division,

Process Aggregate - chewing gum and walking at the same time.

Process Boundary - death

Processual Context - a war is the context of battles

BFO - Spatiotemporal Regions

Connected Spatiotemporal Region - spatiotemporal region of the life of an organism

Spatiotemporal Instant - the spatiotemporal location of an instant of an organisms life

Spatiotemporal Interval - the spatiotemporal region of the first year of an infant’s life

Scattered Spatiotemporal Region - the spatiotemporal region occupied by all games of the World Cup.

Temporal Regions have a parallel hierarchy.

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III.b What is represented by the hierarchy?

Labrador

Dog

Mammal

Chordate

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is_a relation

The Protégé OWL Editor is based around a is_a-hierarchy of the entities in a given domain.

Start with thinking about your domain and its is_a-hierachy, draw a sketch.

Make sure to use formal is_a relations (subclass relations) exclusively to build your hierarchy.


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Incorrect usage of is_a, Example 1


Travel

Cruise LinerCar Rental Flight

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Incorrect usage of is_a, Example 2

III.a What is represented by the hierarchy?

Organism

AnimalBacteria Other Organism Groupings

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Subclass Relation (in OWL):

A ⊆ B ⇔ ∀x ∈ A : x ∈ B

Proper Subclass (in Set Theory):

A ⊂ B ⇔ A ⊆ B ∧ A ≠ B

2. What is represented by the hierarchy?

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III.c How to create a class hierarchy?

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A shortcut to create a hierarchy from a list

You might find yourself in a situation where you have a list of terms referring to classes to be represented in your ontology.

Example:

III.c How to create a class hierarchy?

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III.c How do we create a class hierarchy?

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III.d Changing OWL class names

Basically, there are two things that we need to keep separate:

URI/IRI

Class label

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URI/IRI (Uniform Resource Identifier/Internationalized Resource Identifier)

The full URI consists of a locator and a name (e.g. the class name).

Every URI is unique ( no classes with ➯the same URI allowed within one ontology).

Every class has exactly one URI.

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rdfs:label

String value It is possible (though not advisable) to

annotate two classes in one ontology with the same label.

One class can have any number of labels (synonyms, terms in multiple languages).

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III.e Disjointness

No member of A is a member of B.

A ∩ B = ∅ A ∩ B ⇔ (∀x) (x ∈ A & x ∉ B) For universals or types: No instance of A

is an instance of B. When building a taxonomy in OWL

disjointness needs to be explicitly stated (Open World Assumption)!

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III.e Disjointness

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III.e Disjointness

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III.e Disjointness

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III.f Exhaustiveness

At times we want to express that a certain level of a hierarchy is exhaustive, viz. the represented subclasses are all subclasses of their superclass. B & C are exhaustive of A ⇔

( x) x ∀ ∈ A & (x ∈ B x ∨ ∈C)

When building a taxonomy in OWL exhaustiveness needs to be explicitly stated (Open World Assumption)!

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III.g Rigidity

A universal is rigid if it is essential to its instances.

An essential universal is one that necessarily holds for all of its instances.

“Cat” is rigid; “Pet” is not.

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III.f Rigidity

Types vs. Roles

Types are rigid sortals. Roles are non-rigid sortals.Sortals describe what sort of thing a concept

represents.– e.g., “cat”, “milk”, and “doctor” are sortals.– e.g., “red”, “heavy”, and “singing” are not.– Sortals usually correspond to nouns.

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III.f Rigidity

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III.f Rigidity

Rigidity tagging

portion of matter-R drug

+R antibiotic+R chemical compound

+R oil -R nutriment (a source of material to nourish the body)

Resulting Hierarchies

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IV. Creating relationsNot only universals, but also relations are represented in a hierarchy.

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IV. Creating relationsa) Adding relations (object properties) b) Domains & rangesc) Characteristics of relations

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IV.a Adding relations (object properties)

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IV.b Domains & ranges

In OWL all relations are binary and are sets of ordered pairs.

So in “aRb”, “a” is in the domain and “b” is in the range.

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IV.b Domains & ranges

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IV.c Characteristics of relations Functional Inverse functional Transitive Symmetric Asymmetric Reflexive Irreflexive

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IV.c Characteristics of relations

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Functional

For xRy there is only one unique possible value of y.

Formula: (a,b) ∈ R & (a,c) ∈ R ⇒ b=cExample: Matt hasBiologicalMother Bridget


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Inverse functional

For xRy there is only one unique possible value of x.

Formula: (a,b) ∈ R & (c,b) ∈ R ⇒ a=cExample: Bridget isBiologicalMotherOf Matt


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Transitive

If xRy and yRz then xRz Formula: (a,b) ∈ R & (b,c) ∈ R ⇒ (a,c) ∈ RExample: Matt hasAncestor Rudolph

Rudolph hasAncestor Francis ⇒ Matt hasAncestor Francis


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Symmetric

If xRy, then yRx.Formula: (a,b) ∈ R ⇒ (b,a) ∈ RExample: Matt hasSibling Chris

⇒ Chris hasSibling Matt


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Asymmetric

If xRy, then not (yRx).Formula: (a,b) ∈ R ⇒ (b,a) ∉ RExample: Chris isChildOf Bridget

Bridget isChildOf Chris


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Reflexive

R relates x to itself. Formula: (a,a) ∈ R Example: Matt knows Matt


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Irreflexive

aRb is only if a ≠ b Formula: (a,b) R ⇔ a ≠ bExample: Chris isChildOf Bridget

Chris isChildOf Chris


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In general, instances should not be represented by an domain ontology. However, Protégé enables representing instances (named individuals).For specific ontologies (e.g. application ontologies) it can be inevitable and necessary to specify individuals.

V. (Instances)

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a) General remarksb) Necessary vs. Necessary and Sufficientc) Types of restrictions

VI. Creating restrictions on classes

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All restrictions we put on universal or attributive collection A are universal statements, viz. all instances of A are in the relation the restriction specifies. ( x) (x ∀ ∈ A) & ((x, y) ∈ P) (The quantifier for y is to be specified by the formulation of the restriction.)

VI.a General remarks

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So, if I put the restriction “has_sibling human being” on the class “human being”, I am stating that ALL human beings have siblings.

Which, of course, is wrong.

VI.a General remarks

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Practical OWL formulation: Necessary: All members of the OWL class

in question fulfill the condition specified by the restriction.

Necessary and Sufficient: If there is an entity in the domain fulfilling the condition specified by the restriction it is a member of the OWL class in question.

VI.b Necessary vs. Necessary and Sufficient

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Examples: Necessary: If building dams is a necessary

condition for an organism to be a beaver, all instances of beaver need to be building dams.

Necessary and Sufficient: If biped and featherless is a necessary and sufficient condition for being human, every animal that is biped and featherless is human.


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Existential Restriction All members of A stand in the relation R to

at least one member of B. ( x) ( y) (x ∀ ∃ ∈ A) & (y ∈ B) & ((x, y) ∈ R)

VI.c Types of restrictions

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Universal Restriction All members of A stand in the relation R

only with members of B. ( x) ( y) (x ∀ ∃ ∈ A) & ((x, y) ∈ R) (y ⇒ ∈ B)


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Cardinality Restrictions Three types: Exact Cardinality, min

Cardinality, max Cardinality Allow to specify that All x ∈ A are related to exactly n (y ∈ B) All x ∈ A are related to at least n (y ∈ B) All x ∈ A are related to at maximally n (y ∈

B)


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SourcesBechhofer S, van Harmelen F, Hendler J, et al. (2004) OWL Web Ontology Language Reference. http://www.w3.org/TR/owl-ref/

Guarino N, Welty C (2004) An Overview of OntoClean. Handbook on Ontologies. Ed. Staab S, Studer R, pp.151-172.

Hazewinkel M (2002) Encyclopedia of Mathematics. Berlin.

http://eom.springer.de/default.htm

Horrocks M (2009) A Practical Guide To Building OWL Ontologies Using Protégé 4 and CO-ODE Tools, Edition 1.2. University of Manchester, Manchester, UK.

http://owl.cs.manchester.ac.uk/tutorials/protegeowltutorial/

Smith B, Kusnierczyk W, Schober D, Ceusters W (2006) Towards a reference terminology for ontology research and development in the biomedical domain. (2006). Proc. of KR-MED 2006. http://ontology.buffalo.edubfoTerminology_for_Ontologies.pdf

Spear AD (2006) Ontology for the Twenty First Century: An Introduction with Recommendations.

http://www.ifomis.org/bfo/documents/manual.pdf

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http://www.w3.org/TR/owl-ref/


http://owl.cs.manchester.ac.uk/tutorials/protegeowltutorial/

http://ontology.buffalo.edubfoTerminology_for_Ontologies.pdf/

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Sources (page 2):• Smith B, Kusnierczyk W, Schober D, Ceusters W (2006) Towards a reference terminology for ontology research and development in the biomedical domain. (2006). Proc. of KR-MED 2006. http://ontology.buffalo.edubfoTerminology_for_Ontologies.pdf

• Spear AD (2006) Ontology for the Twenty First Century: An Introduction with Recommendations. http://www.ifomis.org/bfo/documents/manual.pdf

• Hazewinkel M (2002) Encyclopedia of Mathematics. Berlin.http://eom.springer.de/default.htm 91


1 introduction to ontology development and tools part i: first steps in ontology development icbo...

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preferable terminology

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owlprotg terminology

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particulars examples

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hierarchy of classes