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BioHealth Informatics Group QA of Ontologies QA of Ontologies OWL Tutorial December 6 th 2005

BioHealth Informatics Group QA of Ontologies OWL Tutorial December 6 th 2005

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Page 1: BioHealth Informatics Group QA of Ontologies OWL Tutorial December 6 th 2005

BioHealthInformaticsGroup

QA of OntologiesQA of Ontologies

OWL Tutorial

December 6th 2005

Page 2: BioHealth Informatics Group QA of Ontologies OWL Tutorial December 6 th 2005

BioHealthInformaticsGroup

The GIGO ProblemThe GIGO Problem

Logic may be necessary

But it is not sufficient

Can not validate all possibleinferences in advance

Instead must prove:Reasoner is soundAxioms are correctInduction does the rest

Page 3: BioHealth Informatics Group QA of Ontologies OWL Tutorial December 6 th 2005

BioHealthInformaticsGroup

Barriers to Ontology QABarriers to Ontology QA

►Absolute Measures►No ‘Gold Standard’

►Mutual cross validation only as good as the parts

►Manual checking error-prone

►and can’t measure HOW error prone because of (1)

►Comparitive Measures►Better than worse does not imply good

►Relative Measures►Provides unequivocal evidence of improvement

►But not of proximity to goal

►Falling error detection rate does not imply none exist

Page 4: BioHealth Informatics Group QA of Ontologies OWL Tutorial December 6 th 2005

BioHealthInformaticsGroup

Types of Axiom QualityTypes of Axiom Quality

Philosophical Rigour

Ontological commitment

Content correctness

Fitness for purpose

Page 5: BioHealth Informatics Group QA of Ontologies OWL Tutorial December 6 th 2005

BioHealthInformaticsGroup

Philosophical RigourPhilosophical Rigour

►2500 years of research

►Theories of time, mereonomy, containment►Often FOL, so not computable

►Similar upper level ontologies ►DOLCE, BFO

►But not 100% agreement: Realist vs Cognitivist

Page 6: BioHealth Informatics Group QA of Ontologies OWL Tutorial December 6 th 2005

BioHealthInformaticsGroup

Ontological commitmentOntological commitment

►Formally specified semantic equivalence►Logical transformation to canonical form

►Semantically equivalent but no logical transform

► ‘Fixation of femur by means of inserting pins’

► ‘Insertion of pins to fixate the femur’

►Metamodel rules/commitments►Arbitrary choice of preferred form

►Conventions to be applied throughout ontology

►And by all applications that use it

Page 7: BioHealth Informatics Group QA of Ontologies OWL Tutorial December 6 th 2005

BioHealthInformaticsGroup

Content correctnessContent correctness

► Metadata Provenance, lexical annotations etc

► Truth► ‘Structure of labial vein’ is-a ‘Superficial vein of face’

► Completeness – ambiguity and omission► Thymus secretes Thymosin; Thymosin is-a Hormone

…but omits Thymus is-a endocrine gland

► Conciseness► Redundant inclusion of inferrable axioms

► Consistency – contradictory, duplicated, circular► endocrine surgery vs endocrine surgeons

► Traumatic unilateral amputationUnilateral traumatic amputation

Page 8: BioHealth Informatics Group QA of Ontologies OWL Tutorial December 6 th 2005

BioHealthInformaticsGroup

Fitness for PurposeFitness for Purpose

► Best theories no guarantee of usability or utility

► Lab experiences no predictor of field behaviour

► All for nothing, if user can’t use it► Interrater variability

Page 9: BioHealth Informatics Group QA of Ontologies OWL Tutorial December 6 th 2005

BioHealthInformaticsGroup

Fitness for Purpose:Fitness for Purpose: Inter-rater variabilityInter-rater variability

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Headcloth

Cloth

Scarf

Model Person

Woman

Adults

Standing

Background

Brown

Blue

Chemise

Dress

Tunics

Clothes

Suitcase

Luggage

Attache case

Brass Instrument

French Horn

Horn

Tuba

Page 10: BioHealth Informatics Group QA of Ontologies OWL Tutorial December 6 th 2005

BioHealthInformaticsGroup

Fitness for Purpose:Fitness for Purpose: Inter-rater variabilityInter-rater variability

► Miscoding ► Code meaning is inappropriate to thing being described

► Instrument definitely not a french horn

► Missed coding► Not coding something that could be coded

► No code for the table/platform

► Overcoding► Code meaning is more detailed than justified

► Can the gender really be determined?

► Undercoding► Code meaning is less detailed than justified

► Brass Instument vs Tuba

Page 11: BioHealth Informatics Group QA of Ontologies OWL Tutorial December 6 th 2005

BioHealthInformaticsGroup

Fitness for PurposeFitness for Purpose

What ontological properties..What ontological properties..

► Increase usablility and utility?

► Are a prerequisite for them?

► Decrease usability or utility?

Page 12: BioHealth Informatics Group QA of Ontologies OWL Tutorial December 6 th 2005

BioHealthInformaticsGroup

Ontology QAOntology QAHow much quality do we need?How much quality do we need?

Perfection is unattainable

Trade-offs between quality and…Performance

Cost

Maintainability

Usability

Acceptance

Utility

Page 13: BioHealth Informatics Group QA of Ontologies OWL Tutorial December 6 th 2005

BioHealthInformaticsGroup

Need for CQI, not final QANeed for CQI, not final QAAssure the Assure the pprocess rocess notnot the product the product

Use/Test cases & exemplars

REVIEWExplore

consequences

APPLYQI

Algorithm

DEVISEQI

Algorithm

ASSESSIdentifyproblems