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, AR
2 University at Buffalo, Buffalo, NY
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Contents
I.
II.
III.
IV.
V.
VI.
Introduction
Terminological considerations
Creating the hierarchy of classes
Creating relations
(Instances)
Creating restrictions on classes
2
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)”.
3
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.
4
II. Terminological considerations
a. OWL/Protégé terminology
b. Preferable terminology
5
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
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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II.b Preferable terminology
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.
10
II.b Preferable terminology
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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II.b Preferable terminology
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.
12
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)
c)
d)
e)
f)
g)
What is represented by the hierarchy?
How to create a class hierarchy?
Changing OWL class names
Disjointness
Exhaustiveness
Rigidity
13
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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III.a Why work with an Upper Ontology
 Some Upper Ontologies
 Basic Formal Ontology (BFO)
 Descriptive Ontology for Linguistic and
Cognitive Engineering (DOLCE)
 Suggested Upper Merged Ontology (SUMO)
15
III.a Why work with an Upper Ontology
 How to import Upper Ontologies (or other
pre-existent ontologies) into our ontology
project?
16
Importing another ontology (e.g. an
Upper Ontology)
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18
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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.
III.b What is represented by the hierarchy?
Chordate
Mammal
Dog
Labrador
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III.b What is represented by the hierarchy?
 is_a relation
 The Protégé OWL Editor is based around a is_ahierarchy 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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III.b What is represented by the hierarchy?
 Incorrect usage of is_a, Example 1
Travel
Car Rental
Cruise Liner
Flight
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III.a What is represented by the hierarchy?
 Incorrect usage of is_a, Example 2
Organism
Bacteria
Animal
Other
Organism
Groupings
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2. What is represented by the hierarchy?
 Subclass Relation (in OWL):
 A ⊆ B ⇔ ∀x ∈ A : x ∈ B
 Proper Subclass (in Set Theory):
 A⊂B⇔A⊆B∧A≠B
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III.c How to create a class hierarchy?
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III.c How to create a class hierarchy?
 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:
35
III.c How do we create a class hierarchy?
36
III.c How do we create a class hierarchy?
37
III.c How do we create a class hierarchy?
38
III.c How do we create a class hierarchy?
39
III.c How do we create a class hierarchy?
40
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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III.d Changing OWL class names

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.
42
III.d Changing OWL class names
43
III.d Changing OWL class names
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III.d Changing OWL class names

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.d Changing OWL class names
46
III.d Changing OWL class names
47
III.d Changing OWL class names
48
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
50
III.e Disjointness
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III.e Disjointness
52
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.f Exhaustiveness
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III.f Exhaustiveness
55
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
58
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)
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Resulting Hierarchies
IV. Creating relations
Not only universals, but also relations are
represented in a hierarchy.
61
IV. Creating relations
a) Adding relations (object properties)
b) Domains & ranges
c) Characteristics of relations
62
IV.a Adding relations (object properties)
63
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
65
IV.c Characteristics of relations
 Functional
 Inverse functional
 Transitive
 Symmetric
 Asymmetric
 Reflexive
 Irreflexive
66
IV.c Characteristics of relations
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IV.c Characteristics of relations
Functional
For xRy there is only one unique possible value of
y.
Formula: (a,b) ∈ R & (a,c) ∈ R ⇒ b=c
Example: Matt hasBiologicalMother Bridget
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IV.c Characteristics of relations
Inverse functional
For xRy there is only one unique possible value of
x.
Formula: (a,b) ∈ R & (c,b) ∈ R ⇒ a=c
Example: Bridget isBiologicalMotherOf Matt
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IV.c Characteristics of relations
Transitive
If xRy and yRz then xRz
Formula: (a,b) ∈ R & (b,c) ∈ R ⇒ (a,c) ∈ R
Example: Matt hasAncestor Rudolph
Rudolph hasAncestor Francis
⇒ Matt hasAncestor Francis
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IV.c Characteristics of relations
Symmetric
If xRy, then yRx.
Formula: (a,b) ∈ R ⇒ (b,a) ∈ R
Example: Matt hasSibling Chris
⇒ Chris hasSibling Matt
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IV.c Characteristics of relations
Asymmetric
If xRy, then not (yRx).
Formula: (a,b) ∈ R ⇒ (b,a) ∉ R
Example: Chris isChildOf Bridget
Bridget isChildOf Chris
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IV.c Characteristics of relations
Reflexive
R relates x to itself.
Formula: (a,a) ∈ R
Example: Matt knows Matt
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IV.c Characteristics of relations
Irreflexive
aRb is only if a ≠ b
Formula: (a,b) R ⇔ a ≠ b
Example: Chris isChildOf Bridget
Chris isChildOf Chris
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V. (Instances)
 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.
75
VI. Creating restrictions on classes
a) General remarks
b) Necessary vs. Necessary and Sufficient
c) Types of restrictions
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VI.a General remarks
 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.)
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VI.a General remarks
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.
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VI.b Necessary vs. Necessary and Sufficient
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.
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VI.b Necessary vs. Necessary and Sufficient
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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VI.b Necessary vs. Necessary and Sufficient
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VI.c Types of restrictions
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)
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VI.c Types of restrictions
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VI.c Types of restrictions
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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VI.c Types of restrictions
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VI.c Types of restrictions
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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VI.c Types of restrictions
87
VI.c Types of restrictions
88
VI.c Types of restrictions
89
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