Tracing Networks: Ontology-based Software in a Nutshell

Tracing NetworksTracing Networks

Yi HongDepartment of Computer ScienceUniversity of Leicester

Ontology-based software application in a Nutshell

Semantic WebSemantic Web

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“Semantic web is an evolution to the current web and provide new information representation feature.”

•Current web•Document-centric•Human readers•Syntax (Schema)•HTML, XML etc.

•Semantic web•Knowledge representation•Machine readable•Semantics (Ontology)•RDF, OWL etc

Tracing Networks programme

OntologyOntology

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What is an ontology?“An ontology is a formal specification of a conceptualization” -Thomas Gruber

Domain ontology e.g. (CIDOC-CRM for archaeology, Gene, GXO for Genetics)

Ontology

Concepts

Specified byDescribes

Modelled by

Domain

Ontology-based databaseOntology-based database

What is an ontology-based database.How it is different from a relational

database.Why use ontology? What can you do

with an ontology-based database.How to query an ontology-based

database.

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Relational database vs Ontology-Relational database vs Ontology-based databasebased database

Image on a ceramic vessel found at Sopron-Várhely

5(provided by Katharina)

Example : Image tagging and search for human representation database

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Object ID: 15 Inventory number: 443 Excavation site: Sopron-Várhely (N47.66519, E16.518044

Hungary) Human figure (individuals)

◦ rider◦ wagon guide◦ wagon rider

Animal◦ 2 horses

◦ 1 horse Material:

◦ ceramic Technology:

◦ Incised

`

etc.……….(60+ attributes)

Data structure


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Database schema

Entity-relationship diagram

Relational database (MS Access 2007)


tables, fields (columns)

Data

primary-foreign key pairs

Relational vs Ontology-based Relational vs Ontology-based databasedatabase

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Relational Database

Ontology-based Database (Triple

store) MySQL, Oracle, SQL Server,

MS Access etcJena SDB, virtuoso universal server, RDF/OWL document

Database Schema (table, field, key)

Ontology(class, property, individual)

records triples (RDF graph)

Data Structure

Basic elements

Database products

Data storage

OntologyOntology

◦Semantics Class Property Individual

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individual

classpropert

y

has value for

restrict

is instance of

OntologyOntology

Class◦ Person◦ Archaeologist

Property◦ Is a friend of◦ subClassOf◦ instanceOf

Individual◦ Alex◦ John

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Ontology example:

OntologyOntology

Subject

Predicate

Object

A Triple is:Basic element in the ontology world.contains three parts: subject, predicate and object.

OntologyOntology

Ceramic pot

was found in

Leicester

A Triple is:Basic element in the ontology world.contains three parts: subject, predicate and object.

OntologyOntologyRDF Graph A set of triples become a graph An ontology-based database is a graph

Ceramic pot

was found in

Leicester

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Object

wasFoundAtSite

IndividualFigure

Animal

Scene

Material

wasMadeFrom

hasScene

Appears On

…….

Country

isLocatedIn

Horse

subClassOf

contains

Appears On

Ontology

…….……s.

(Protégé Ontology Editor)


Appears On

…….

http://protege.stanford.edu/

Relational vs Ontology-based Relational vs Ontology-based databasedatabase

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SQL

generate

Relational Database

query

Database

Query language SPARQL

generate

query

Ontology-based Database (Triple

store)

Query Interface

Text-based keywords+ options Graph pattern

Search

Why use ontology?Why use ontology?

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Tags: cat , mouse,

• Problem with traditional keyword search


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Tags: cat , mouse,

• Problem with traditional keyword search• Ambiguous semantics

A tag is normally a freely-chosen, non-hierarchical keyword or term.

The tag can be the identical but it might have different interpretation.

What you are looking for …..


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Tags: cat , mouse,

• Problem with traditional keyword search• Ambiguous semantics

What you actually get…

The meaning of the keyword is unclear

(Can not tell what it is about by only looking at the tags… )


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Tags: cat , mouse,

• Problem with traditional keyword search• Labelling objects rather than relationship

the keyword approach is more focus on labeling objects rather than the relationship

Not way to describe the links (chasing) between them.

Describing the link between objects is as important as tagging the objects themselves


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Tags: cat , mouse, chase

• Problem with traditional keyword search• Labelling objects rather than relationship

Additional tags will not be sufficient to describe the links. By adding the third tag “chase”.

The question remains :

Who is chasing who?


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◦ Problem with traditional keyword search Difficult to describe complex and arbitrary

query

Query:

“Display images with an animal and a person on them, along with what is happening between them"

rider

horse


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How to describe this search in a query interface?

Google style?

single textbox

Not expressive enough

Library style?

Textbox with drop down list or check box

Not flexible enough

Native SQL?

SQL syntax

Learn complex syntax Knowledge of DB schema Difficult to write

What else?

Query: “Display images with an animal and a person on them, along with what is happening between them"


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◦ Problem with traditional keyword search Unable to perform automatic reasoning

rider

horse

Problems 1

Ask for : person, animalActual tags: rider, horse

Traditional search engine is based on keyword match. the tags we have here are rider and horse, if it does not contain any keywords we entered, the search engine will not return anything

It needs background knowledge to understand a rider is a person riding a horse and a horse is in fact an animal.


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◦ Single user Mode vs Collaborative Mode Degree of uncertainty User credibility and expertise

definitely a

horse!

probably a

fox ?

Domain-specific expertise index = E(d)

Degree of uncertainty = CF

horseTagged area 95%

Is a

zoologist 5 year kid

Query results visualisation Query results visualisation --Geo-mappingGeo-mappingKeyhole Markup Language (KML/KMZ)

http://code.google.co m/apis/kml/documentation/

◦ XML-based language.◦ Supports place marks, images, polygons, 3D

models, textual descriptionsCompatibility◦ Google Map◦ Google Maps for Mobile ◦ Google Earth◦ ESRI ArcGIS Explorer,

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Query results visualisation Query results visualisation - Statistical charts- Statistical chartsGoogle Chart API

◦ http://code.google.com/apis/chart/◦ Interactive Flash◦ Javascript arrays or XML files

Compatibility◦ Most mainstream browsers

Internet Explorer Firefox Safari Chrome

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Ontology-based software demoOntology-based software demo

Semantic tagging

Query by graph pattern

Integration with Google earth

Statistical charts

System ArchitectureSystem Architecture

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LinksLinksA Guide to Creating Your First Ontology

◦ By Stanford University◦ http://www.ksl.stanford.edu/people/dlm/papers/ontology-

tutorial-noy-mcguinness-abstract.htmlProtégé Ontology editor

◦ http://protege.stanford.edu/◦ Protégé tutorial

http://owl.cs.manchester.ac.uk/tutorials/protegeowltutorial/CIDOC-CRM ontology

◦ An ontology for culture and heritage domain◦ http://www.cidoc-crm.org/

KML guide and tutorial◦ http://code.google.com/apis/kml/documentation/

kml_tut.html29