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Introduction to Ontology Development and Tools Part I: First Steps in Ontology Development

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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 – PowerPoint PPT presentation

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Title: Introduction to Ontology Development and Tools Part I: First Steps in Ontology Development


1
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

2
Contents
  1. Introduction
  2. Terminological considerations
  3. Creating the hierarchy of classes
  4. Creating relations
  5. (Instances)
  6. Creating restrictions on classes

3
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 W3Cs Web Ontology Language (OWL).

4
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
5
II. Terminological considerations
  1. OWL/Protégé terminology
  2. Preferable terminology

6
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
7
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

7
8
II.a OWL/Protégé terminology
Individuals ?represent objects in the domain we
are interested in. Examples me, the Pentagon in
Washington, Jane Does lung.
8
9
II.b Preferable terminology
  • Instance An individual or particular which
    instantiates a universal Examples me, the
    Pentagon in Washington, Jane Does lung
  • 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

9
10
II.b Preferable terminology
  • 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
11
II.b Preferable terminology
  • 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

11
12
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
13
III. Creating the hierarchy of classes
  • Why work with an Upper Ontology?
  • Importing another ontology (e.g. an Upper
    Ontology)
  • Basic Formal Ontology-a primer
  • What is represented by the hierarchy?
  • How to create a class hierarchy?
  • Changing OWL class names
  • Disjointness
  • Exhaustiveness
  • Rigidity

14
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.

15
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)

16
III.a Why work with an Upper Ontology
  • How to import Upper Ontologies (or other
    pre-existent ontologies) into our ontology
    project?

17
Importing another ontology (e.g. an Upper
Ontology)
18
(No Transcript)
19
(No Transcript)
20
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
21
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
22
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
23
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
24
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, Marias nostril
25
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
26
BFO - Occurents
Processual Entity - a conversation, the life of
an organism Spatiotemporal Region - any part of
space-time Temporal Region - any interval of time
27
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
28
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 infants
life Scattered Spatiotemporal Region - the
spatiotemporal region occupied by all games of
the World Cup. Temporal Regions have a parallel
hierarchy.
29
III.b What is represented by the hierarchy?
Chordate
Mammal
Dog
Labrador
30
III.b What is represented by the hierarchy?
  • 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.

31
III.b What is represented by the hierarchy?
  • Incorrect usage of is_a, Example 1

Travel
Cruise Liner
Flight
Car Rental
32
III.a What is represented by the hierarchy?
  • Incorrect usage of is_a, Example 2

Organism
Animal
Other Organism Groupings
Bacteria
33
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

34
III.c How to create a class hierarchy?

35
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

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.c How do we create a class hierarchy?
41
III.d Changing OWL class names
  • Basically, there are two things that we need to
    keep separate
  • URI/IRI
  • Class label

42
III.d Changing OWL class names
  • URI/IRI (Uniform Resource Identifier/International
    ized 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.

43
III.d Changing OWL class names
44
III.d Changing OWL class names
45
III.d Changing OWL class names
  • rdfslabel
  • 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).

46
III.d Changing OWL class names
47
III.d Changing OWL class names
48
III.d Changing OWL class names
49
III.e Disjointness
  • No member of A is a member of B.
  • A n B Ø
  • A n 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)!

50
III.e Disjointness
51
III.e Disjointness
52
III.e Disjointness
53
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)!

53
54
III.f Exhaustiveness
55
III.f Exhaustiveness
56
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.

57
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.

58
III.f Rigidity
59
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)

60
Resulting Hierarchies
61
IV. Creating relations
Not only universals, but also relations are
represented in a hierarchy.
62
IV. Creating relations
  1. Adding relations (object properties)
  2. Domains ranges
  3. Characteristics of relations

62
63
IV.a Adding relations (object properties)
64
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.

64
65
IV.b Domains ranges
66
IV.c Characteristics of relations
  • Functional
  • Inverse functional
  • Transitive
  • Symmetric
  • Asymmetric
  • Reflexive
  • Irreflexive

67
IV.c Characteristics of relations
68
IV.c Characteristics of relations
Functional For xRy there is only one unique
possible value of y. Formula (a,b) ? R (a,c)
? R ? bc Example Matt hasBiologicalMother
Bridget
68
69
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 ? ac Example Bridget
isBiologicalMotherOf Matt
69
70
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
70
71
IV.c Characteristics of relations
Symmetric If xRy, then yRx. Formula (a,b) ? R
? (b,a) ? R Example Matt hasSibling Chris ?
Chris hasSibling Matt
71
72
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
72
73
IV.c Characteristics of relations
Reflexive R relates x to itself. Formula (a,a)
? R Example Matt knows Matt
73
74
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
74
75
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.

76
VI. Creating restrictions on classes
  • General remarks
  • Necessary vs. Necessary and Sufficient
  • Types of restrictions

77
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.)

78
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.
79
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.

80
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.

81
VI.b Necessary vs. Necessary and Sufficient
82
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)

83
VI.c Types of restrictions
84
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)

85
VI.c Types of restrictions
86
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)

86
87
VI.c Types of restrictions
88
VI.c Types of restrictions
89
VI.c Types of restrictions
90
Sources
  • Bechhofer 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/protegeo
    wltutorial/
  • 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_Onto
    logies.pdf
  • Spear AD (2006) Ontology for the Twenty First
    Century An Introduction with Recommendations.
  • http//www.ifomis.org/bfo/documents/manual.pdf

90
91
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_Onto
    logies.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
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