BioHealthInformaticsGroup Advanced OWL Tutorial 2005

Ontology Engineering in OWL

Alan Rector & Jeremy Rogers

BioHealthInformaticsGroup

OpenGALEN

Ontology Engineering:The ‘ontology’ is just the beginning

‘Ontologies’‘Ontologies’

Software agents

Software agents Problem-

solving methods

Problem-solving

methods Domain-independent applications

Domain-independent applications

DatabasesDatabasesDeclarestructure

Knowledgebases

Knowledgebases

Providedomain

description

The “Semantic

Web”

The “Semantic

Web”

We know it is wrong – but why?

► Do we really mean wrong?

► Many upper ontologies► Some very abstract, some less so

► Dolce/OntoClean my favourite current compromise besides

► See Guarino and Welty: http://www.loa-cnr.it/DOLCE.html

► doc paper is a readable summary if you can get past the vocabulary

► Also Guarino’s home page

► Others

► SUO (Standard Upper Ontology)

► John Sowa’s work – see Google

► OpenCyc

► OpenGALEN

► There is no one way!► No matter how much some people want to make it a matter of dogma

Ontology Layers: What’s it for?

CooperationCooperation on the on the Domain ContentDomain Content Ontologies Ontologies to enable…to enable…

CooperationCooperation on on TopTop Domain OntologiesDomain Ontologies to enable…to enable…

CooperationCooperation on the on the Upper OntologiesUpper Ontologies to enable …. to enable ….

The The Meta OntologyMeta Ontology is to enable… is to enable…

CooperationCooperation on on Information systems & Information systems & resources resources

InformationInformation systems & systems & resources resources

Databases, RDFDatabases, RDFInstance stores, …Instance stores, …(“individuals”)(“individuals”)

Where do DLs fit in?

Domain Content Ontologies

TopTop Domain Domain OntologiesOntologies

Upper OntologiesUpper Ontologies

DLs?DLs?(“classes”)(“classes”)

Meta OntologyMeta Ontology FoL /FoL /HoLHoL

Principles

► How to describe the things in a domain & how to arrange and maintain those descriptions

► Just enough to describe what needs to be described ► No distinction without a difference!

► Properties are as important as Classes/Entities/Concepts

► If an upper level category does not act as a domain or range constraint or have some other engineering effect, why represent it?

► Exclude things that will be dealt with by other means or given► “Concrete domains”

► Time and place

► Designed to record what an observer has recorded at a given place and time

► Non_physical – e.g. agency

► Causation – except in sense of “aetiology”

► Implemented Ontology in a standard framework ► For today: OWL/DLs

► Must be implemented and support a large ontology

Principles 2

►Minimal commitment► Don’t make a choice if you don’t have to

►Understandable► Experts an make distinctions repeatably/reliably

►Able to infer classification top domain concepts► ‘Twenty questions’ – to neighbourhood

►Upper ontology primarily composed of ‘open dichotomies’► Open to defer arguments such as whether Collectives of Physical

things are physical

Issues for ‘ontology engineering’

► Utility► What’s it for? - Scope and Limitations

► Application tools

► Understandability & reliability► Can people use it consistently

► Matching level of abstraction to human use

►“Patterns”

►“Intermediate representations”, “Macros”, …

► Soundness► Logical consistency

► Sound inferences about domain

► Evolution and maintenance► Modularisation

► Debugging

► Parsimony

► Collaboration and Standards

Fundamental issue

► Knowledge is fractal► All terminologies are combinatorially large

►2 severitities * 2 durations * 2 varieties * 2 circumstances

► 24 = 16 leaf nodes

►34 = 81 potential entities

► Most problems have more than 2 at each step

►Can only catalogue a few of the descriptions to be used

►Can’t predict which in advance of use

►Experience shows get at most 50% right

►And there is a Zipf distribution for the rest

Limit combinatorial explosions

►“The Exploding Bicycle”►1980 - ICD-9 (E826) 8

►1990 - READ-2 (T30..) 81

►1995 - READ-3 87

►1996 - ICD-10 (V10-19) 587►V31.22 Occupant of three-wheeled motor vehicle injured in collision with pedal

cycle, person on outside of vehicle, nontraffic accident, while working for income

► and meanwhile elsewhere in ICD-10

►W65.40 Drowning and submersion while in bath-tub, street and highway, while engaged in sports activity

►X35.44 Victim of volcanic eruption, street and highway, while resting, sleeping, eating or engaging in other vital activities

Combinatorial explosion leads to complex polyhierarchies

► Humans find polyhierarchies hard to maintain► Experience suggests errors increase with number of parents

►1-2 10%-15% 2-4 20%-25% >4 >35%

►Only MEDDRA seems to have cracked it

► Compositional ‘ontologies’ with formal classification provide a ‘compiler’ to manage polyhierarchies as collections of mono-hierarchies

Issues for TodayOne day selection from two-three days tutorial

► Assume► Introduction to OWL & Protégé-OWL

►At least the first part of Protégé-OWL tutorial http://www.co-ode.org/resources/tutorials/ProtegeOWLTutorial.pdf

►Will review Value Partitions pattern

► Will deal with► Engineering issues and combinatorial explosion for Domain Ontologies

► A common pattern and the use of debugging tools

► Basic architecture for an “Ontology Based Knowledge Resource”

► Modularisation and Normalisation► Why and when to use a classifier

► General questions

► Additional material on the web at:► www.co-ode.org`

http://www.w3.org/2001/sw/BestPractices/http://www.w3.org/2001/sw/BestPractices/OEP/