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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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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.
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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.
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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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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)
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III.a Why work with an Upper Ontology
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)
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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.
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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.
III.b What is represented by the hierarchy?
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Incorrect usage of is_a, Example 1
III.b What is represented by the hierarchy?
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.c How do we create a class hierarchy?
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III.c How do we create a class hierarchy?
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III.c How do we 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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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.
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III.d Changing OWL class names
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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
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III.d Changing OWL class names
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III.d Changing OWL class names
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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.f Exhaustiveness
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III.f Exhaustiveness
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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
IV.c Characteristics of relations
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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
IV.c Characteristics of relations
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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
IV.c Characteristics of relations
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Symmetric
If xRy, then yRx.Formula: (a,b) ∈ R ⇒ (b,a) ∈ RExample: Matt hasSibling Chris
⇒ Chris hasSibling Matt
IV.c Characteristics of relations
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Asymmetric
If xRy, then not (yRx).Formula: (a,b) ∈ R ⇒ (b,a) ∉ RExample: Chris isChildOf Bridget
Bridget isChildOf Chris
IV.c Characteristics of relations
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Reflexive
R relates x to itself. Formula: (a,a) ∈ R Example: Matt knows Matt
IV.c Characteristics of relations
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Irreflexive
aRb is only if a ≠ b Formula: (a,b) R ⇔ a ≠ bExample: Chris isChildOf Bridget
Chris isChildOf Chris
IV.c Characteristics of relations
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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.
VI.b Necessary vs. Necessary and Sufficient
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VI.b Necessary vs. Necessary and Sufficient
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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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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)
VI.c Types of restrictions
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VI.c Types of restrictions
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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)
VI.c Types of restrictions
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VI.c Types of restrictions
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VI.c Types of restrictions
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VI.c Types of restrictions
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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.
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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
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