1. “Think Ontologically”
Process to create a
“Think Ontologically”
A Crash Course in Ontology Modelling
for Archaeologists
Yi Hong
Department of Computer Sciences
University of Leicester

2. How we describe knowledge? …as archaeologists
Unstructured free-form text
natural language
human readable, highly expressive
no universally-agreed terminology
reflect individual interpretations and explanations of archaeological evidence
“Archaeology is the search for fact... not truth. If it's truth you're looking for, Dr. Tyree's philosophy class is right down the hall.”
Indiana Jones

3. How we describe knowledge? …as computer scientists
Formal Specification
programming language, metadata
machine readable and executable
controlled vocabulary, Limited expressivity
well-defined, highly uniform mathematical symbols and notations
“Computer language design is
just like a stroll in the park. 
Jurassic Park, that is.” -Larry Wall inventor of “Perl”

4. How people structure data traditionally..

5. Traditional Relational Database approach Table values row Fields
Record
Identified/linked by
Primary/Foreign Keys

6. Create tables & columns Link tables(foreign keys)
Process to create a database
Relational Database approach
Form
Step 1.
paper-based or electronic form
List fields (columns)
Group fields
Create tables & columns
Link tables(foreign keys)
Add records

7. Create tables & columns Link tables(foreign keys)
Process to create a database
Relational Database approach
Form
Step 2. List all fields
List fields (columns)
Inventory Number,
Excavation Date,
Site name,
Site description,
Material,
Weight,
Catalog,
Images,
Object Description
Group fields
Create tables & columns
Link tables(foreign keys)
Add records

8. Create tables & columns Link tables(foreign keys)
Process to create a database
Relational Database approach
Form
Step 3. Group fields, give a group name
List fields (columns)
Object
Inventory Number
Excavation Date
Material
Weight
Catalog
Images
Object description
Site
Site name
Site description ….
Group fields
Create tables & columns
Link tables(foreign keys)
Add records

9. Create tables & columns Link tables(foreign keys)
Process to create a database
Relational Database approach
Form
Step 4. create tables, columns
List fields (columns)
Group fields
Create tables & columns
Link tables(foreign keys)
Add records

10. Create tables & columns Link tables(foreign keys)
Process to create a database
Relational Database approach
Form
Step 4. create tables, columns with
MS Access
List fields (columns)
tables, fields (columns)
Group fields
primary-foreign
key pairs
Create tables & columns
Link tables(foreign keys)
Add records

11. Create tables & columns Link tables(foreign keys)
Process to create a database
Relational Database approach
Form
Step 4. Data entry
List fields (columns)
Group fields
Create tables & columns
Link tables(foreign keys)
Add records

12. Example Scenario : Requirement:
Design a data structure for Course Modules Selection
Relational Database Design Ontology Modeling
Requirement:
Every course module can only be taught by one Lecturer
A Lecturer can teach many courses..
An student must enrol in at least 3 courses.
Max enrolment number for a course is 100.
* Every student has a unique student ID
* Every staff has a unique staff ID

13. Relational Database Approach
* Many to many relation
Tables
Student
Form 1
Course
List
Form 2
(Lecturer)
Form 3
(Student)
Student ID
Name ….
Lecturer
Staff ID
Name ….
Course
Course ID
Course Name ….
ModuleSelection
Course ID
Staff ID
Student ID

14. Think Ontologically

15. Ontology
“An ontology is a formal specification of a conceptualization”
Thomas Gruber

16. Relational Database vs Ontological Database
Schema (SQL)
(table, field)
Ontology (RDF/OWL)
(class, property)
Define Structure
Records
Triples/ axioms
Basic elements
Products/
Editor
Relational DB
OntoDB (Triple store)
Virtuoso ,
Jena SDB, TDB
etc.
Microsoft Access, FileMaker,
Oracle, MySQL etc
Protége, SWOOP

17. Web Ontology Language No No Yes No Undefined OWA Vegetarian? Yi
Assume knowledge is completed
everything we don’t know is false
Web Ontology Language
Open World Assumption (OWA)
We know
Closed world assumption
Assume knowledge is incompleted
everything we don’t know is undefined
Yi eats
chicken tikka
boiled rice
potato salads
tofu
OWA
Data No
Vegetarian? Yi
Alessandro
Closed world assumption No
Yes
Alessandro eats
pasta
boiled rice
potato salads
hash browns
Open world assumption No
Undefined
Question:
Can vegetarian eat Tofu?
Vegetarian: someone who does not eat meat.

18. “Think Ontologically”
Outside the box
Ontology
Class
restrict
Instance of
Property
Individual
has value for
Identified/linked by
(URI) Uniform Resource Identifier

19. Identify domain concepts Organise classes into hierarchies
Class (Concept)
“Think Ontologically”
Identify domain concepts
Class (Concept)
A template of definition of
a particular kind of object
Organise classes into hierarchies
Identify properties
Object properties
Data type properties
Add triples

20. Identify domain concepts Organise classes into hierarchies
Class (Concept)
“Think Ontologically”
Identify domain concepts
Class (Concept)
A template of definition of
a particular kind of object
Organise classes into hierarchies
e.g. Person, Ceramic Pot , Excavation Site, Color
Identify properties
Object properties
Data type properties
Add triples

21. Describe Class with Description Logic
“Think Ontologically”
Examples
“Circular terracotta loom weight”
“Excavation site”
“Settlement”
Description Logic

22. Identify domain concepts Organise classes into hierarchies
Individual
“Think Ontologically”
Identify domain concepts
Individual (object)
Individuals are instance of class
Organise classes into hierarchies
Example:
Identify properties
Red is an instance of Color
Object properties
Data type properties
Instance of
Red
Color
Add triples

23. Identify domain concepts Organise classes into hierarchies
Individual
“Think Ontologically”
Identify domain concepts
Individual (object)
Individuals are instance of class
Organise classes into hierarchies
Example:
Identify properties
Alessandro is an instance Person
Object properties
Data type properties
Instance of
Alessandro
Person
Add triples

24. Identify domain concepts Organise classes into hierarchies
Individual
“Think Ontologically”
Identify domain concepts
Individual (object)
Individuals are instance of class
Organise classes into hierarchies
Example:
Identify properties
“A two holes disc loom weight found at Satriano” is an instance of loom weight
Object properties
Data type properties
Instance of
Add triples

25. Identify domain concepts Organise classes into hierarchies
Vessel(Bowl)
Ceramic vessel
wooden vessel
Class Hierarchy
“Think Ontologically”
Identify domain concepts
Class hierarchy
(subclass: “IS A” relationship)
Organise classes into hierarchies
Vessel(Bowl)
Ceramic vessel
supercalss
Identify properties
Wooden vessel
Vessel(Bowl)
Object properties
Data type properties
sub class of
sub class of
subclass
wooden vessel
Ceramic vessel
Add triples

26. Identify domain concepts Organise classes into hierarchies
Class Hierarchy
“Think Ontologically”
Identify domain concepts
Class hierarchy
multiple inheritance
Organise classes into hierarchies
Craft worker
Woman
Identify properties
sub class of
sub class of
Female Craft worker
Object properties
Data type properties
Add triples

27. Identify domain concepts Organise classes into hierarchies
Class Hierarchy
“Think Ontologically”
Identify domain concepts
Class hierarchy
multiple inheritance
Organise classes into hierarchies
Man
Woman
Identify properties
sub class of
sub class of
Object properties
Data type properties ??
Add triples
Disjoined class

28. University of Leicester
Common mistakes in organising class hierarchy
“Think Ontologically”
Example: Ontology for Education
(1)
(2)
University
University
University
National University
Staff
University of Leicester
Student
University of Glasgow
Private University
…..
…..
…..
Person
Staff
Student
“Sub class ”relationship
must be “is a” relationship
UoL is an indiviual of class University , not a class

29. Identify domain concepts Organise classes into hierarchies
Property
“Think Ontologically”
e.g. Person, Excavation Site, Ceramic Pot, Color
Identify domain concepts
Property
an element that takes a value and is associated with an object. It defines attributes of a concept and relations between concepts.
Data type property
Object property
Organise classes into hierarchies
Class hierarchy (sub class)
Identify properties
Vessel(Bowl)
Ceramic vessel
wooden vessel
Object properties
Data type properties
Add triples

30. Identify domain concepts Organise classes into hierarchies
Data Type Property
“Think Ontologically”
e.g. Person, Excavation Site, Ceramic Pot, Color
Identify domain concepts
Data type property
(attribute)
A Data type property is an element that takes a value and is associated with an object (properties for which the value is a data literal)
Organise classes into hierarchies
Class hierarchy (sub class)
Identify properties
Vessel(Bowl)
Ceramic vessel
wooden vessel
String
Number
Date …
Object properties
Data type properties
Add triples

31. Identify domain concepts Organise classes into hierarchies
Data Type Property
“Think Ontologically”
e.g. Person, Excavation Site, Ceramic Pot, Color
Identify domain concepts
Data type property
(attribute)
A Data type property is an element that takes a value and is associated with an object (properties for which the value is a data literal)
Organise classes into hierarchies
Class hierarchy (sub class)
Identify properties
Vessel(Bowl)
Ceramic vessel
wooden vessel
e.g. Ceramic Pot
Object properties
Data type properties
Weight: 1.4kg
Description: “Beautiful”
Year of Excavation: 1980
Add triples

32. Identify domain concepts Organise classes into hierarchies
Object Property
“Think Ontologically”
e.g. Person, Excavation Site, Ceramic Pot, Color
Identify domain concepts
Object Property
(relation)
An Object property is a direct binary relation between two classes
Organise classes into hierarchies
Class hierarchy (sub class)
Identify properties
Vessel(Bowl)
Ceramic vessel
wooden vessel
was found at
Object properties
Data type properties
Pot
Site
owned by
Person
Add triples

33. Identify domain concepts Organise classes into hierarchies
Property
“Think Ontologically”
e.g. Person, Excavation Site, Ceramic Pot, Color
Identify domain concepts
Property hierarchy
Organise classes into hierarchies
has parent
Class hierarchy (sub class)
Identify properties
has mother
Vessel(Bowl)
Ceramic vessel
wooden vessel
has father
Object properties
Data type properties
Add triples

34. Identify domain concepts Organise classes into hierarchies
Domain & Range
“Think Ontologically”
e.g. Person, Excavation Site, Ceramic Pot, Color
Identify domain concepts
Property
Domain:
A domain of a property limits the individuals to which the property can be applied.
Range:
The range of a property limits the individuals that the property may have as its value
Organise classes into hierarchies
Class hierarchy (sub class)
Identify properties
Vessel(Bowl)
Ceramic vessel
wooden vessel
Object properties
Data type properties
Add triples

35. Domain & Range “Think Ontologically” Range: Property Domain: owned by
A domain of a property limits the individuals to which the property can be applied.
Range:
The range of a property limits the individuals that the property may have as its value
owned by
teaches
teaches
Artefact
Person
Teacher
Student
domain
range

36. Domain & Range “Think Ontologically” Range:
Domain & range can be the same class
Property
Domain:
A domain of a property limits the individuals to which the property can be applied.
Range:
The range of a property limits the individuals that the property may have as its value
Is a friend of
Class Person
Is a friend of
Is a friend of

37. Cardinality “Think Ontologically” Cardinality
cardinality specifies the occurances of a relationship
A property can have:
Exact cardinality
Min cardinality
Max cardinality
has_CFS _Id
exactly 1
Univ Staff
has_child
min 1
child
Mother
has_passenger
Bus
max 60

38. Inverse Property “Think Ontologically” Property (P1) owned by
One property may be stated to be the inverse of another property.
If the property P1 is stated to be the inverse of the property P2, then if X is related to Y by the P2 property, then Y is related to X by the P1 property
(P1) owned by
Person
Pot
(P2) has_personal_belongings
(p1)hasParent
Child
Parent
(p2) hasChild

39. Characteristics of a property
Data Type
Property
Transitive Property
Property
Symmetric Property
Object
Property
Functional Property
InverseFunctional Property
…………

40. Characteristics of a property
Functional Property
has husband
Inverse Functional Property
If John has a driving licence (No.)
biologicalMotherOf

41. Characteristics of a property
Transitive Property
is part of
is part of
EBA 1
Early Bronze Age
Bronze Age
3300 – 3000 BC BC BC
is part of
Symmetric Property
overlaps with
Iron Age
Roman period
overlaps with

42. Many other properties ….

43. Identify domain concepts Organise classes into hierarchies
Triple
e.g. Person, Excavation Site, Ceramic Pot, Color
Identify domain concepts
Triple (RDF triple)
A Triple is conventionally written in the order
subject,
predicate,
object.
The predicate is also known as the property of the triple.
Organise classes into hierarchies
Class hierarchy (sub class)
Identify properties
Vessel(Bowl)
Ceramic vessel
wooden vessel
Object properties
Data type properties
Add triples

44. Triple Outside the box Basic element
contains three parts: subject, predicate and object.
e.g. Person, Excavation Site, Ceramic Pot, Color
Property
Class hierarchy (sub class)
Predicate
Vessel(Bowl)
Ceramic vessel
wooden vessel
Subject
Object
Individual
Individual

45. Triple Populating ontology Triple Graph
A set of triples become a graph
An ontology-based database is a graph
was destroyed by
house
fire

46. Example Scenario : Requirement:
Design a data structure for Course Modules Selection
Requirement:
Every course module can only be taught by one Lecturer
A Lecturer can teach many courses..
An student must enrol in at least 3 courses.
Max enrolment number for a course is 100.
* Every student has a unique student ID
* Every staff has a unique staff ID

47. Ontological approach
Identify concepts
Student
Course
Lecturer

48. Ontological approach Organise classes into hierarchies Student
Lecturer
Course

49. Making relationships explicit and clear
Organise classes into hierarchies
Person
Lecturer
Student
Course
Enable reuse of domain knowledge

50. Ontological approach Enable reuse of domain knowledge
Can be taken from
other ontology
Ontological Approach
Person
Lecturer
Student
Course
Enable reuse of domain knowledge

51. Ontological approach Add Data Type Property Ontological Approach Name…
Staff ID …
Person
Lecturer
Student
Student ID
Course …
Course ID
Add Data Type Property

52. Ontological approach Add Object Property Ontological Approach Name …
Staff ID …
Person
Lecturer
Student
Student ID
Course …
Course ID
Add Object Property

53. Ontological approach Object Property Ontological Approach Name …
Staff ID …
Person
Lecturer
Student
Student ID
Course …
Course ID
Object Property

54. Ontological approach Add ObjectProperty Object Property
Person
Lecturer
Student
Course
Object Property

55. Ontological approach Add ObjectProperty Object Property
Person
Lecturer
teaches
Student
Course
Object Property

56. Ontological approach Add ObjectProperty Object Property
Person
Lecturer
teaches
Student
enrol in
Course …
Object Property

57. Ontological approach Add ObjectProperty Object Property
Person
Lecturer
teaches
Course
enrol in
Student
Object Property

58. Ontological approach Add Inverse Property Object Property
Person
Lecturer
teaches
is taught by
Course
has registered student
enrol in
Student
Object Property

59. Ontological approach Specify cardinality Object Property
Person
Lecturer
teaches =1
is taught by =1
Course
has registered student
min. 3
max. 100
enrol in
Student
Object Property

60. Ontological approach Identify type of property Object Property
Person
Lecturer
teaches =1
(functional)
is taught by
(inverseFunctional) =1
Course
has registered student
min. 3
max. 100
enrol in
Student
Object Property

61. Ontological approach Done! Object Property Ontological Approach Person
Lecturer
teaches =1
(functional)
is taught by
(inverseFunctional) =1
Course
has registered student
min. 3
max. 100
enrol in
Student
Object Property

62. Ontological approach Add triple Ontological Approach course C1
lecturer
student L1
enrol in
teaches
Add triple

63. Ontological approach Add triple Ontological Approach course C1
lecturer
teaches
student L1
enrol in
teaches
Add triple

64. Ontological approach Add triple Ontological Approach enrol in S1
course C1
lecturer
teaches
student L1
enrol in
teaches
Add triple

65. Ontological approach Add triple Why use ontology? Ontological Approach
course C1 C2 S2
lecturer C3 S3
student C4 L1
enrol in C5
teaches L2
Add triple

66. Explore implicit relationship
Ontological Approach S1
course C1
lecturer
studied under the
supervision of
student L1
enrol in
if Student S studies course C
if Lecturer L teaches course C
teaches
Reasoning

67. Explore implicit relationship
course
Deductive reasoning
enrolled S1
lecturer
if Student S enrolled in course C C1
AND
Lecturer L teaches course C
THEN
Student S studied under the
supervision of L
student
teaches
studied under the
supervision of
enrol in L1
teaches
(?s rdf:type Student) (?s rdf:type Student)(?s enrolled ?c) (?l teaches ?c)
(?s studies_under the supervision of ?l)
studied under the
supervision of
Reasoning

68. Classification Reasoning Class hierarchy course C2 C2 C2 lecturer
Person
Lecturer
student C1 L1
Lazy Lecturer
enrol in
Hardworking Lecturer
Define Hardworking Lecturer:
A Lecturer who teach more than 4 courses using
Description Logic
teaches
Student
Class(Hardworking Lecturer, subClassOf(Restriction(hasCourse, min-cardinality(4))))
Reasoning

69. Protégé Try it? Download Protége 3.4.7 Download example in this slide:
Ontology Editor
Download Protége 3.4.7
Download example in this slide:
Try it?