© University of Manchester Intermediate Representations Taming the complexity monster(s) Dr Jeremy...

© University of Manchester

Intermediate RepresentationsTaming the complexity monster(s)

Dr Jeremy Rogers

Manchester University

[email protected]

BioHealthInformaticsGroup

OpenGALEN


Ontology EngineeringComplexity Monsters

►Computation

►The Domain

►Artefacts

►Understanding


Domain ComplexityMedicine is big

►Very large and inherently complex►975,354 distinct UMLS concepts

►but this is still too small


Domain ComplexityMedicine is big

UMLS: 975,000 different medical concepts

1980 1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003

Concepts

150,000

100,000

50,000

200,000

250,000

300,000

Pathology II (1980)(V 3.0) (V 3.1) (V 3.2) (V 3.3) (V 3.4) (V 3.5)

SNOMED II (1979)

SNOMED International

SNOMED RT (Beta)

(V 3.0)(V 3.1) (V 3.2)

(V 3.3)

(V 3.4)(V 3.5)

SNOMED CT

344,000 (Jan 2003)


Domain ComplexityMedicine is changing

New entities defined…Charcot-Marie-Tooth

1:2500 genetically determined peripheral neuropathy

1975 (ICD) - one code

1996 (Steadmans) – 3 codes

2003 (OMIM) – 46 phenotypic variants, 39 identified locus

…old ones consigned to history


Domain ComplexityBut this is tip of iceberg…

► 15496 OMIM UIDs (1 Feb 2006)

► Conditions probably or definitely at least partly genetically determined, including:► 107700 Appendicitis

► 600631 Bed Wetting

► 604324 Adult Acne

► 177900 Psoriasis

► 103780 Alcoholism

► 188890 Tobacco Addiction

► 606349 Pathologic Gambling

► 119915 Cluster Headache

► 607504 Benign Sexual Headache

► 220700 Deafness

► 125480 Depression/Mania

► 109200 Male pattern baldness

► 179600 Raynaud Disease

10000 -

5000 -

15000 -

1965 1970 1975 1980 1985 1990 1995 2000 2005

10,000

14,737

15,496


Domain ComplexityMultiple User Views

►Different Purpose► [Physician] – where is the pain (and the lesion)?

► [Pharmacologist] – what is physiology of pain receptors and conduction?

► [Neurologist] – in phantom limb pain, how is pain perceived?

►Different focus► Ontology for diabetic Sx:

►Abscess:Locus(finger, hand, forearm, arm, shoulder, neck, face, scalp, chest, abdomen, back, thigh, calf, shin, forefoot or toe)

► Ontology for diabetic Rx:

►Penicillin – IndicatedFor – Abscess:Locus(Skin)

► Ischaemia:Locus(finger, hand, forearm, arm, shoulder, neck, face, scalp, chest, abdomen, back, thigh, calf, shin, forefoot or toe)


Domain ComplexityNeeds of external KBs

►Need for lots of rules► Form on [Hand] should have options [left, right]

► Form on [Palm of hand] should have options [left, right]

► Form on [Finger] should have options [left, right]

► Form on [Thumb] should have options [left, right]

► Form on [First metacarpal] should have options [left, right]

► Etc. etc.

►Obscure categories required for parsimony► ALL Forms on [mirror-imaged body structures] OR [their subparts]

should have option ANY [laterality]

► ALL Forms on [respiratory disease] should have options [cough, wheeze]

► ALL Forms on [symptoms] should have option ANY [severity]


Domain ComplexityPolyhierarchies

►Requirement for multiaxial classification►World is used to monoaxial classification

►Very large domain very large polyhierarchies

►Impossible to accurately construct by hand

►Inherently confusing to navigate

►The smallprint, if made explicit, overwhelms us


Artefactual ComplexityUnreadable notations

(ClinicalSituation which <isCharacterisedBy (presence which isExistenceOf (ContractionProcess which <isSpecificFunctionOf SphincterAniMuscle hasImmediateConsequence Pain hasIntentionality (Intentionality which hasAbsoluteState involuntary) hasDuration (Duration which hasAbsoluteState longTerm) hasTemporalPattern (TemporalPattern which hasAbsoluteState ongoing) >)) isCharacterisedBy (presence which isExistenceOf (UrgeToVoidUrineOrFaeces which hasProcessActivity (ProcessActivity which hasQuantity (Level which hasMagnitude highLevel)))) isCharacterisedBy (presence which isExistenceOf AbdominalStraining) >)

<owl:Class rdf:about="#InjectionOfContrastMedium"> <owl:equivalentClass> <owl:Class> <owl:intersectionOf rdf:parseType="Collection"> <owl:Restriction> <owl:onProperty> <owl:ObjectProperty rdf:about="#acts_on"/> </owl:onProperty> <owl:someValuesFrom> <owl:Class rdf:ID="RadioopaqueContrastMedium"/> </owl:someValuesFrom> </owl:Restriction> <owl:Class rdf:about="#Injecting"/> </owl:intersectionOf> </owl:Class> </owl:equivalentClass> </owl:Class>

<owl:Class rdf:ID="ContrastCTScan"> <owl:equivalentClass> <owl:Class> <owl:intersectionOf rdf:parseType="Collection"> <owl:Restriction> <owl:onProperty> <owl:TransitiveProperty rdf:about="#has_part"/> </owl:onProperty> <owl:someValuesFrom> <owl:Class rdf:ID="InjectionOfContrastMedium"/> </owl:someValuesFrom> </owl:Restriction> <owl:Class rdf:about="#XrayComputedTomography"/> </owl:intersectionOf> </owl:Class> </owl:equivalentClass> </owl:Class>

(XrayComputedTomography which hasPart (Injecting which actsOn RadioopaqueContrastMedium))name ContrastCTScan


Artefactual ComplexityWorkarounds

►Limitations in formalism Workarounds


Cognitive Complexity

►Scale of task►Multiple authors

►Quality control and assurance

►Formal ontologies require great precision►Poor debugging tools

►Natural Language can misdirect


Complexity Effect on the user

Syntactic confusion – I can’t read this

Navigational Confusion – I don’t need most of this

Navigational Uncertainty – where am I ?

Editorial Uncertainty – atom or primitive ?

Editorial Confusion – what recipe ?


#1 Challenge for Ontology Engineering:

Hide the complexity


Intermediate Representations

From this to this…(SurgicalDeed which

isCharacterisedBy (performance whichG

isEnactmentOf (Dividing whichG <

playsClinicalRole SurgicalRole

actsSpecificallyOn HeartValve

hasSubprocess (TemporalFeature which <

isSpecificImmediateConsequenceOf VolitionalAct

involves Heart

hasSpecificConsequence (BodyProcess which <

isSpecificFunctionOf Heart

hasProcessActivity (ProcessActivity which

hasQuantity (Level which

hasMagnitude undetectedLevel)) >)

hasPathologicalStatus pathological >)>)))

MAIN replacing

ACTS_ON heart valve

HAS_ FEATURE induced arrest of heart

(And back again)


Demonstration

CLAW


Syntactic confusion

Navigational Confusion

Navigational uncertainty

Editorial confusion

Editorial uncertainty

USER DIFFICULTIES

Syntactic Compression

Semantic Compression

No Brackets

No Keywords

Ontological Compression

Simpler Schemas

Fewer Concepts

Monohierarchy of concepts

Fewer Links

Defer semantic choices

Simplified constraints

Syntactic confusion



Editorial confusion


USER DIFFICULTIES

TECHNIQUES FOR SIMPLIFICATION

Semantic Expansion

Ontological Expansion

Syntactic expansion

Syntactic Compression

Semantic Compression

No Brackets

No Keywords

Ontological Compression

Simpler Schemas

Fewer Concepts

Monohierarchy of concepts

Fewer Links

Defer semantic choices

Simplified constraints

Syntactic confusion



Editorial confusion


Restore Brackets

Restore Keywords

Semantic Substitution

Semantic Normalisation

USER DIFFICULTIES

TECHNIQUES FOR SIMPLIFICATION

STEPS IN REWRITE TO TARGET

REPRESENTATION

HOW?


Intermediate RepresentationSemantic Expansion

MAIN excision action

HAS_APPROACH transethmoidal

SITE pituitary structure

transethmoidal

leg

excision - action

pituitary structure

open

partial

etc.

‘DESCRIPTORS’

(Route which passesThrough EthmoidSinus)

LowerExtremity

Excising

PituitaryGland

surgicallyOpen

partial

GALEN Common Reference Model

HAS_APPROACH

ACTS_ON

SITE

HAS_EXTENT

HAS_LOCATION

IS_PART_OF

etc.

‘LINKS’

... hasSubprocess (Approaching hasMeans ...

...hasSubprocess (Approaching hasMeans

(Route passesThrough ...

...hasSubprocess (Approaching hasMeans

(TranstubalRoute hasDirection...

GALEN Common Reference Model


Intermediate Representation Context sensitive substitution

(SurgicalDeed whichisMainlyCharacterisedBy (performance whichG

isEnactmentOf ((Excising which playsClinicalRole SurgicalRole) whichG <hasSpecificSubprocess (SurgicalApproaching whichG

hasPhysicalMeans ((Route which passesThrough EthmoidBone)))actsSpecificallyOn PituitaryGland>)))

hasProjection (('READ' schemeVersion 'default') code '71000' 'code');extrinsically hasDissectionRubric 'READ 71000 Transethmoidal hypophysectomy'.

RUBRIC ‘Transethmoidal hypophysectomy’

SOURCE ‘READ’ CODE ‘71000’

MAIN excision action

HAS_APPROACH transethmoidal

SITE pituitary structure

Descriptor Mappings

Link Mappings


Intermediate Representation Supporting Infrastructure

Dissection

Library

Expanded Dissections

Mapping

Descriptors

Links

Expansion Algorithm

Existing Classification Dissections

New Descriptors

New Links

ClaW: Check &

Iterate

Derived Classification

GRAIL Expansion

compare

So where did the complexity go?


Demonstration

TIGGER


Demonstration

DOPAMINE


Drug Ontology & Dopamine


Demonstration

CLINERGY2

© University of Manchester Intermediate Representations Taming the complexity monster(s) Dr Jeremy...

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