Stuart Aitken Artificial Intelligence Applications Institute

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Artificial Intelligence Applications InstituteCentre for Intelligent Systems and their Applications

Stuart Aitken

Artificial Intelligence Applications Institute

A Process Ontology for A Process Ontology for Cell BiologyCell Biology

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OutlineOutline

• Rapid Knowledge Formation (RKF) Project– RKF Project goals and domain– The Cyc knowledge based-system– RKF Tools

• Process Ontology– General approach– Formalisation– Example

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Rapid Knowledge FormationRapid Knowledge Formation

• The RKF project aims to develop tools which will allow domain experts to enter knowledge directly into the KBS.

• DARPA-funded, two teams:– CYCORP– SRI

• Organised around ‘Challenge Problems’ – Cell Biology

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RKFRKF

Aim: To enable biologists to construct an ontology/KB from a textbook source

formalise

Ontology

Alberts et al, Essential Cell Biology, 1998

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Key techniques:• The KBS has knowledge of the KA

process– Knowledge of salience– Knowledge of the requirements of an

adequate formalisation

• There is a dialogue between expert and system, which clarifies the concept being defined.

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Evaluation:

After a period of tool development,• trials are organised, both• expert performance, and• KE performance is measured,• and assessed independently.

The evaluation is extensive – over a period of 2 weeks

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The Cyc KBSThe Cyc KBS

• Cyc (Doug Lenat) is a knowledge-based system, under development since ~1984, aiming to represent common sense knowledge.

• Cyc uses a large upper-level ontology

• Uses a logical language based on first-order logic

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Concepts in the Upper Ontology:– Thing, Agent, Event– TangibleThing, InformationBearingObject– …. Dog, Book– subclass(genls), instance-of(isa)– parts, subevent, role predicates– 1600 concepts in total in the public

release (1998) - small% of Cyc

Classification:– Stuff-like vs Object-like– Individual vs Set

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• The upper-ontology supports application development:

Upper-level

Intermediate-level

Application-level

Thing

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Cyc includes:• An inference engine, • GUI, • tools for ontology development.• Until the RKF project, ontology

development was by trained knowledge engineers, working with domain experts.

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RKFRKF

New tools in Cyc:• Define a new concept, and place it

correctly in the ontology• Refine a concept definition• Define a new predicate• Assert a new fact• Define a new rule• State an analogy• Construct a new process

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RKFRKF

User interaction:• Selection of items in the interface

– Choice determined ‘intelligently’, KBS has knowledge of salience, and the KA process, this knowledge must be authored

• Browsing of the ontology• Search• Natural language dialogue

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Process ModelsProcess Models

BindsTogether Move

RNA Transcription

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Process DescriptorProcess Descriptor

Q: Name the processA: [ RNA Transcription ]Q:Select the type of Process that describes

the category best• event localised• creation or destruction event…• ‘say this:’[ _ _ _ _ _ _ ]Q: Define:• affected object: [ _ _ _ _ _ ]• location: [ _ _ _ _ _ ]• actor: [ _ _ _ _ _ ]

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Process ModelsProcess Models

Describing Processes:• Complex expressions at the instance level• Simpler to describe in terms of types

Upper-level

Intermediate-level

subevent(Event,Event)doneBy(Event,Agent)

ForAll ?E ?F ?G implies(subevent(?E,?G) and isa(?E,BindsTogether)subevent(?F,?G) and isa(?F,Move))before(startOf(?E),startOf(?F))

Application-level?

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Script VocabularyScript Vocabulary

The Script theory defines the semantics of Type-Level assertions

(typePlaysRoleInScene RNATranscription DNAMolecule BindsTogether objectActedOn)

• Requires rules for identity– Can require complex reasoning

• Good for user input• Can be extended to cover pre and

postconditions of actions

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ScriptsScripts

subevents

BindsTogether

e

Move

f

RNA Transcription

Forall subevents f of t, of type Move,and all subevents e of t, of type BindsTogether,(startsAfterStartingof f e) where t is of type RNATranscription

t

startsAfterStartingOfInScript

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ScriptsScripts

Type playing role

N

BindsTogetherNucleotide

e

Types:

objectActedOn

Instance:

For some n in N, (objectActedOn e n)

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New Script VocabularyNew Script Vocabulary

• Pre and Post conditions

BindsTogether

N

R

N

RnottouchingDirectly connectedTo

(preconditionOfScene-negated BindsTogether touchingDirectly <Ribonucleotide Nucleotide>)

(postconditionOfScene BindsTogether connectedTo <Ribonucleotide Nucleotide>)

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New Script VocabularyNew Script Vocabulary

N R

Some ?n in N, some ?r in R(not(touchingDirectly ?n ?r))

Some ?n in N, some ?r in R(connectedTo ?n ?r)

BindsTogetherNucleotide Ribonucleotide

e

Types:

roleroleSet ofInstances:

Precondition: Postcondition:

identity

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Script VocabularyScript Vocabulary

• The Script vocabulary forms an ‘intermediate level’, which

• lies behind the Process descriptor GUI (i.e. the textboxes)

• Not, in itself, a taxonomy of processes, but allows processes to be described in detail.

• Defining the subclass relation is just one task.

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Vaccinia Virus Life CycleVaccinia Virus Life Cycle

• The vaccinia virus life cycle was selected as an example of a complex model to formalise as a set of Scripts.

• The model includes actions, decomposition, ordering, objects-playing-roles and pre/postconditions

• It is a good test for the Script vocabulary

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Vaccinia Virus Life CycleVaccinia Virus Life Cycle

mRNATranscription-Early

ViralGeneTranslation-Early

MovementOfProtein

Temporal:



MovementOfProtein



MovementOfProtein

Participants

Conditions:

Outputs:messengerRNA

Inputs:messengerRNA

Pre:spatiallySubsumes Cell VirusCore

Post:spatiallySubsumes CellCytoplasm Vitf2

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EvaluationEvaluation

• 8 biologists were selected, and trained in the tools, 4 per team

• The knowledge to be formalised was selected (chapter 7 in Alberts)

• The knowledge base was allowed to contain ‘pump-priming’ knowledge

• The biologists entered knowledge , using the tools, then tested it against a set of questions,

• Ontology/KB was revised

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EvaluationEvaluation

Results (outline)• A huge amount of data was collected,

but analysis is complex (IET Inc)• Domain experts were able to develop

ontologies after ‘light’ training• Knowledge engineers out-perform

domain experts in ontology construction

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SummarySummary

‘Power Tools’ for ontology development are being implemented and tested in the RKF project.

• A Script/Process vocabulary has been developed and applied to processes in cell biology, covering:– Temporal order– Participants– Pre/postconditions– Repetition

Documents

Stuart Aitken Artificial Intelligence Applications Institute