Introduction to Ontologies

Reusable Specifications as Ontologies

An ontology is a partial specification of a conceptual vocabulary to be used for formulating knowledge-level theories about a domain of discourse.

The fundamental role of an ontology is to support knowledge sharing and reuse.

Example: Ontology Simple-TimeDefines classes, relations and axioms to support the modelling of time-dependent activities

Classes and Relations in Simple Time

ClassesDay-Name Day-Number Duration Hour-Number Minute-Number Month-Name Month-Number Second-Number Time-Point Calendar-Date Calendar-Year Universal-Time-Spec Time-Range Year-Number

Relations < > After After= Before Before= Disjoint-Time-Ranges During During= Equals Finishes Finishes= Meets Overlaps Overlaps= Start= Starts

Definition of Time Point

(def-class TIME-POINT (time-position) "A point in time" ((second-of :type second-in-time :max-cardinality 1 ) (minute-of :type minute-in-time :max-cardinality 1 ) (hour-of :type hour-in-time :max-cardinality 1 ) (day-of :type day-in-time :max-cardinality 1) (month-of :type month-in-time :max-cardinality 1) (year-of :type year-in-time :max-cardinality 1 )) :constraint (and (not (and (month-of ?x 2) (> (the ?day (day-of ?x ?day)) 29))) (not (and (member-of ?x (4 6 9 11)) (> (the ?day (day-of ?x ?day)) 30)))))

Ontology for medical guidelines

• What is a medical guideline?– A specification (often partial) of a protocol of care– Aims to define “best practice”– Examples

• Protocols for treating AIDS patients

• Protocols for the prevention of bed sores

• The Ontology– Defines classes, relations and axioms to support the

specification of medical guidelines – Builds on a generic medical ontology– Supports both guideline design and execution.

Advantages of Ontologies (1): Reuse

base-ontology

simple-time

common-concepts

bibliographic-datageneric-events

medical-ontology

medical-guidelines

generic-technologies

organization-ontology

Class Hierarchy for Medical Guidelines

Temporal-thing

Plan

Medical-Guideline

Therapeutic-GuidelinePreventive-Guideline Diagnostic-Guideline

Simple-time Ontology

Common ConceptsOntology

Medical-GuidelinesOntology

Advantages of Ontologies (2)

• Formal Community View– Make it possible to formalise a shared viewpoint over a

certain universe of discourse– E.g., agreement on how to model time

• Interoperability– Can support communication and cooperation between

systems developed at different sites– The ontological commitments made by a system are made

explicit– E.g., diagnostic and therapy-control medical systems may

share the same underlying generic medical ontology• e.,g., notion of pathological state, therapeutic procedure

Advantages of Ontologies (3)

• Model-based knowledge acquisition– E.g., use the medical guideline ontology to acquire

knowledge about particular medical guidelines in a structured way

• Knowledge-level validation and verification– E.g., use the medical guideline ontology to check guideline

documents

(Gruber, 1995)

Criteria for Ontology Design

• Clarity– User-centred definitions– Documentation– Alternative choices

• Coherence– Logical consistency– Coherent Style (e.g., naming conventions)

• Minimal ontological commitments– Do not impede extensibility by making unnecessary knowledge-level

commitments

• Minimal encoding bias– Do not pre-judge reuse by making symbol-level commitments

Physical Quantity = <Unit, Magnitude>

Example: <second, 5>

Example of not-so-good definition

(defrelation PHYSICAL-QUANTITY

(<=> (PHYSICAL-QUANTITY ?q)

(and (defined (quantity.magnitude ?q))

(double-float (quantity.magnitude ?q))

(defined (quantity.unit ?q))

(member (quantity.unit ?q)

(setof meter second kilogram ampere kelvin mole candela)))

Physical Quantity = <Unit, Magnitude>

Example: <second, 5>

Example of not-so-good definition

(defrelation PHYSICAL-QUANTITY

(<=> (PHYSICAL-QUANTITY ?q)

(and (defined (quantity.magnitude ?q))

(double-float (quantity.magnitude ?q))

(defined (quantity.unit ?q))

(member (quantity.unit ?q)

(setof meter second kilogram ampere kelvin mole candela)))

Encoding Bias

Unnecessary Ontological Commitment

AKT Reference Ontology

• Task: Develop a common ontology to describe academic resources

• Rationale:– Ontology to provide a common semantic basis to support

variety of AKT services– Gather data about collaborative development– Test tools– Take Integration and Collaboration seriously

AKT is a 6-year UK €11M focusing on knowledge technologies, involving 5 universities

Organization of AKT Reference Ontology

• 100% self-contained

• Two-subontologies– AKT-Support

• Frames, Sets, Numbers, Lists, Relations, Time, Micro Top Level

– AKTive-Portal• Technologies, Events, People & Organizations, Documents,

Research Areas and Projects

Publishing through D3E

Setup for collaborative ontology design

Screen 1Screen 1OntologyOntologyBrowsersBrowsers

Screen 2Screen 2Discussion/RationaleDiscussion/RationaleCapture in CompendiumCapture in Compendium

Capturing ontology design, discussions, and rationaleCapturing ontology design, discussions, and rationale

Publishing through D3E

Typology of Comments

AKT-2 Architecture

Southampton

Edinburgh.

Aberdeen.

Sheffield.

OU

OKBC Triple StoreRDF

RDF

RDF

RDF

RDF

RDF

Wilbur

Freaky

Aktive Portal Server

AKT Reference OntologyAKT Portal KB

OCML

OCML

E-print server Amilcare

News server

AKT Portal Client

AKT Reference

Ontology

Exercise: Analysis of AKT Reference Ontology

Class Medical-Guideline

(def-class medical-guideline (plan)

"Each guideline is associated with a medical

condition. It also targets a particular population"

((outcome-measure :type string)

(target-population :type population-specification)

(full-name :type string)

(associated-medical-condition :type medical-condition)

(temporal-constraints :type string)

(location-constraints

:type guideline-application-location)

(associated-documents :type document-reference)

(has-guideline-user-type :type guideline-user-type)))