co-ode/hyontuse jisc/epsrc 1 why i need both owl/dls & frames alan rector medical informatics...

1O p en G A L E N

CO-ODE/HyOntUse JISC/EPSRC

Why I need both OWL/DLs & FramesWhy I need both OWL/DLs & Frames

Alan Rector Alan Rector Medical Informatics GroupMedical Informatics Group

Bio Health Informatics ForumBio Health Informatics ForumDepartment of Computer ScienceDepartment of Computer Science

University of ManchesterUniversity of Manchester

[email protected]@cs.man.ac.uk

oiled.man.ac.ukoiled.man.ac.uk

www.bhif.man.ac.ukwww.bhif.man.ac.ukwww.mig.man.ac.ukwww.mig.man.ac.uk

2O p en G A L E N


CO-ODE/HyOntUseCO-ODE/HyOntUseBringing Protégé and OWL/OilEd Bringing Protégé and OWL/OilEd

TogetherTogether

OilEdThe de factostandard editor forDAML+OIL/OWL/logic-based ontologies

Protégé:The de facto standard environmentfor frames

Plus methodsfromOpenGALENPEN&PAD& AKT

Not as easy as it looks!

3O p en G A L E N


Very Brief History of OWLVery Brief History of OWL

• OIL – European approach – Description Logics in Frame Clothing– Initial OilEd - Manchester

DAML – DARPA Agent Markup Language– DARPA

• DAML+OIL – First joined up approach- EU+DARPA

• OWL– Emerging W3C WebOnt Standard

• 3 Flavours – Lite, DL, and Full – & still evolving – I work mostly with the subset of DL that works with existing classifiers

• De facto standard way to apply logic-based ontologies– OilEd still the main editor but new efforts e.g. PROTÉGÉ-OilEd/OWL tab

coming

4O p en G A L E N


Why I need both OWL/DLs and Why I need both OWL/DLs and FramesFrames

• Build real large-scale knowledge intensive applications“Ontology Anchored Knowledge Bases”– Fractal Adaptation

• “Rebuild PEN&PAD introduction”– GRAIL is essentially a hybrid Frame/DL system

• Build robust auditable applications– Get the ontology right– Meta data and provenance

• Achieve sufficient abstraction for re-use– From application ontologies to domain ontologies

• Get the right answer to the intended question– Do I mean “Is it possible” or “Is it true”?– Do only what is needed

5O p en G A L E N


Specific Information

on Individuals

Data store

Why I need both OWL/DLs & Why I need both OWL/DLs & FramesFrames

• To Build Knowledge Intensive applications– Knowledge bases anchored on ontologies

supporting information resources– Meta data with everything

Contingent

KnowledgeKnowledgeBase

Necessaryknowledge Ontology

Meta Data

Annotation

6O p en G A L E N


Why I need OWL/DLsWhy I need OWL/DLs• Maintain large, complex ontologies/terminologies

– Parsimonious ontologies - “Conceptual lego” • Avoid combinatorial explosions

– Strong semantics for Reasoning about Subsumption & Normalisation• Modularity• Avoid inheritance conflicts (“Nixon Diamonds”)

• …but it lacks– Meta data– Defaults & exceptions– Reflective queries– Reasoning/Querying with individuals – Other forms of reasoning – arithmetic, coordinate/unit transformation, …

• …and it does too much – Complete reasoning about what is possible when I need

predictable reasoning about what is true• Domain & range checks

7O p en G A L E N


Why I need Frames/ProtégéWhy I need Frames/Protégé

• Manage Metadata, Contingent knowledge & Individuals– Knowledge about Knowledge– Defaults & exceptions – classic frame reasoning– Individuals– Reflective queries – ask about the knowledge base

itself

• Hybrid reasoning– Easy to integrate special purpose solutions for special

purpose problems– Easy to extend expressiveness for queries

• …but it lacks– Parsimonious representation – No “Lego”– Strong semantics for subsumption

• Reasoning about what is possible rather than just what is

8O p en G A L E N


I need to experiment with I need to experiment with much more metadatamuch more metadata

“Provenance, provenance, “Provenance, provenance, provenance”provenance”

9O p en G A L E N


Maintaining large Ontologies: Maintaining large Ontologies: Conceptual LegoConceptual Lego

“SNPolymorphism of CFTRGene causing Defect in MembraneTransport of ChlorideIon causing Increase in Viscosity of Mucus in CysticFibrosis…”

“Hand which isanatomicallynormal”

OpenGALEN & OWL

10O p en G A L E N


What’s in a “Logic based ontology”?What’s in a “Logic based ontology”?

• Primitive concepts - in a hierarchy– Described but not defined

• Properties - relations between concepts– Also in a hierarchy

• Descriptors - property-concept pairs

Fra

mes

OW

L / D

Ls

–qualified by “some”, “only”, “at least”, “at most”

Defined concepts–Made from primitive concepts and descriptors

Axioms–disjointness, further description of defined concepts

A Reasoner–to organise it for you

Meta dataContingent Knowledge

•Defaults & Exceptions

Reflective queriesIndividualsHybrid reasoning

11O p en G A L E N


Encrustation

+ involves: MitralValve

Thing

+ feature: pathological

Structure

+ feature: pathological

+ involves: Heart

OWL/Logic Based Ontologies: The OWL/Logic Based Ontologies: The basicsbasics

Thing

Structure

Heart MitralValve EncrustationMitralValve* ALWAYS partOf: Heart

Encrustation* ALWAYS feature: pathological

Feature

pathological red

+ (feature: pathological)

red

+ partOf: Heart

red

+ partOf: Heart

Primitives Descriptions Definitions Reasoning Validating

12O p en G A L E N


The Key: Normalising (untangling) The Key: Normalising (untangling) OntologiesOntologies

StructureFunction

Part-wholeStructure Function

Part-w

hole

13O p en G A L E N


The Key: Normalising (untangling) The Key: Normalising (untangling) OntologiesOntologies

Making each meaning explicit and separateMaking each meaning explicit and separatePhysSubstance Protein ProteinHormone Insulin Enzyme Steroid SteroidHormone Hormone ProteinHormone^ Insulin^ SteroidHormone^ Catalyst Enzyme^

Hormone = Substance & playsRole-HormoneRoleProteinHormone = Protein & playsRole-HormoneRoleSteroidHormone = Steroid & playsRole-HormoneRoleCatalyst = Substance & playsRole CatalystRoleInsulin playsRole HormoneRole

...and helping keep argument rational and meetings short!

Enzyme ?=? Protein & playsRole-CatalystRole

PhysSubstance Protein ‘ ProteinHormone’ Insulin ‘Enzyme’ Steroid ‘SteroidHormone’ ‘Hormone’ ‘ProteinHormone’ Insulin^ ‘SteroidHormone’ ‘Catalyst’ ‘Enzyme’

… ActionRole PhysiologicRole HormoneRole CatalystRole …

… Substance BodySubstance Protein Insulin Steroid …

14O p en G A L E N


The benefitsThe benefitsAvoiding combinatorial explosionsAvoiding combinatorial explosions

• The “Exploding Bicycle” From “phrase book” to “dictionary + grammar” – 1980 - ICD-9 (E826) 8 – 1990 - READ-2 (T30..) 81– 1995 - READ-3 87– 1996 - ICD-10 (V10-19 Australian) 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

15O p en G A L E N


The benefits:The benefits:ModularisationModularisation

Bridging Scales and Bridging Scales and context with context with OntologiesOntologies

GenesSpecies

Protein

Function

Disease

Protein coded bygene in humans

Function ofProtein coded bygene in humans

Disease caused by abnormality inFunction ofProtein coded bygene in humans

Gene in humans

16O p en G A L E N


Benefits: Fractal Indexing on multiple Benefits: Fractal Indexing on multiple axesaxes

• Indefinite customisation from a finite knowledge base

• Consistent application of policies– “Fail soft” – always produce something plausible

• Multiple axes of specialisationNormalised ontologies produce few inheritance conflicts– Condition– Use case

• Task• User type• Setting

– Medium• Browser, PDA, WAP, Thick client, …

17O p en G A L E N


Example: Fractal tailoring of Example: Fractal tailoring of Forms/Guidelines/Procedures Forms/Guidelines/Procedures

• Cough – Initial evaluation in general practice– routine evaluation in general practice

• routine evaluation by nurse in general practice– Home monitoring

• Cough in patient with TB – as above– In chest clinic

• In Dr Jones’ chest clinic– In Dr Jones’ chest clinic seen by a trainee

100 diseases x 10 complications x 5 settings x 5 user types x 5 tasks 25000 situations

Do you really want to enumerate them by hand? maintain them?

18O p en G A L E N


PEN&PADPEN&PADFractal Tailoring of ‘fail soft’ Fractal Tailoring of ‘fail soft’

formsforms

19O p en G A L E N


20O p en G A L E N


Idiopathic Hypertensionin our co’s Phase 2 study

Fractal tailoring forms for clinical trialsFractal tailoring forms for clinical trials

Hypertension

Idiopathic Hypertension

In our company’s studies

In Phase 2 studies

Hypertension

Idiopathic Hypertension`

In our company’s studies

In Phase 2 studies

21O p en G A L E N


Other Fractal Indexing TasksOther Fractal Indexing Tasks

• Mapping to between coding systems and ontologies– From logical to alogical systems – e.g. ICD10

• All ICD “excludes” come automatically

– Drug interactions and contraindications and usage

• Contingent knowledge – not part of necessary nature of drug

– Help systems• Gather all relevant information from all levels

– Selecting relevant guidelines and trial protocols

22O p en G A L E N


But it is not trivialBut it is not trivial• OWL and Frame paradigms are more different than they look

– OWL is concerned with axioms– Protégé is concerned with facts

• Structure of graph– OWL focuses on restrictions

• Roughly the allowed classes/existent classes facets• Class-instance distinction principled• …

– Protégé focuses on values• Meaning of a class value ambiguous – used differently in different

applications• Class instance distinction application dependent• …

• OWL supports ONLY an ontology & one kind of reasoning– Protégé supports knowledge bases & potentially many kinds of

querying• but not OWL’s open world reasoning!

23O p en G A L E N


Classifying and QueryingClassifying and QueryingOnly doing the reasoning Only doing the reasoning

necessarynecessary• Classifying – OWL, DLs, …

– What must be true or false • In any extension of this “world” consistent with axiomsaxioms

– related to modal logics

– Negation = impossibility (“unsatisfiability”)• “Open World”

– Computationally expensive• Limits expressivity• Persistent

• Querying – PAL, Query tab, SQL, …– What is true or false

• In this “world” about which we know factsfacts– Negation = failure

• “Closed World”– Computationally relatively cheap (usually)

• Ephemeral

24O p en G A L E N


Classifying and Querying:Classifying and Querying:The Pizza ExampleThe Pizza Example

MyPizza ==Pizza hasTopping Peppers hasTopping Mushrooms

Is MyPizza a vegetarian pizza?– Classification/OWL:

• “No” – not necessarily, you haven’t said it doesn’t have meat

– Negation as impossibility» open world

– Querying/Database• “Yes” – I can’t find any meat

– Negation as failure» closed world

25O p en G A L E N


User Oriented Ontology DevelopmentUser Oriented Ontology DevelopmentCO-ODE & HyOntUseCO-ODE & HyOntUse

• New projects under the UK JISC/EPSRC joint initiative on Semantic Web & Autonomic Computing Initiative parallel with US NLM/NCI funding– Collaboration - Manchester, Stanford,

Southampton/Epistemics

• Integrate – Bridge the Gaps– Frames & Metaknowledge – Protégé

• Plug & Play environment– Visualisation, DAGs, Constraints, …

– Logic based domain ontologies – DAML+OIL/OWL/OilEd• User oriented debugging and visualisation

– Views & Perspectives – GALEN– User oriented design / Knowledge Elicitation

–AKT/Southampton

26O p en G A L E N


CO-ODE/HyOntUse ConsortiumCO-ODE/HyOntUse Consortium• Manchester CS

– With thanks to Sean Bechhofer, Carole Goble, …http://oiled.man.ac.ukhttp://oiled.man.ac.uk

• Stanford Medical Informatics– With thanks to Holger Knublauch, Ray Fergerson, …

• Southampton Advanced Knowledge Technologies– With thanks to Nigel Shadbolt & Clive Embury (Epistemics)

• …and all of you– Help to improve usability, visualisation, applications, …, …

• Help us – Help yourselves – Join in – Invite others!Help us – Help yourselves – Join in – Invite others!

PS – Post Doc Needed!

co-ode/hyontuse jisc/epsrc 1 why i need both owl/dls & frames alan rector medical informatics...

Documents

coodehyontuse jiscepsrc

provenance slide

subsumption reasoning

domain ontologies

hybrid reasoning easy

predictable reasoning

complete reasoning

ontology right meta