A generic software framework for building hybrid ontology backed models for driving applications
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A Generic Software Framework for building Hybrid Ontology-Backed Models for Driving Applications. Colin Puleston , James Cunningham , Alan Rector Bio-Health Informatics Group, University of Manchester. Hybrid-Model Demo. Demo Shows…. Object Model (Java) provides central structure

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A Generic Software Framework for building Hybrid Ontology-Backed Models for Driving Applications

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A generic software framework for building hybrid ontology backed models for driving applications

A Generic Software Frameworkfor buildingHybrid Ontology-Backed ModelsforDriving Applications

Colin Puleston, James Cunningham, Alan Rector

Bio-Health Informatics Group, University of Manchester


Hybrid model demo

Hybrid-Model Demo


Demo shows

Demo Shows…

  • Object Model (Java) provides central structure

  • OWL Ontology provides detailed domain knowledge

  • Dynamic model updates:

    • Orchestrated by Object Model

    • Based on interaction with ontology + classifier


Object model ontology interaction

Object-Model/Ontology Interaction


A generic software framework for building hybrid ontology backed models for driving applications

Ontological knowledge comes from set of External Knowledge Sources (EKS)…

Object Model

Object Model accesses EKS and associated inference mechanismsvia mediating interface

…has no knowledge of any EKSformat

…and no knowledge of any inference mechanisms

EKS Access System

OWL-Access

Protege-Ac.

FaCT++

Domain Knowledge Sources

(ontologies, databases, etc.)


A generic software framework for building hybrid ontology backed models for driving applications

Ontological knowledge comes from set of External Knowledge Sources (EKS)…

Object Model has no prior knowledge of any EKS contents…

…other than an expectation that a small number of ‘key-entities’ will be represented somewhere

…and that mappings will be provided via a configuration file

Object Model

EKS Access System

OWL-Access

Protege-Ac.

FaCT++

Domain Knowledge Sources

(ontologies, databases, etc.)


A generic software framework for building hybrid ontology backed models for driving applications

Object Model

field-value updated

Cancer

C1

selected

Get concept-hierarchy for

<problem-type-identifier>

Update field-set +

constraints for

Create instance of

C1a

C1

Cancer

C1

EKS Access System


A generic software framework for building hybrid ontology backed models for driving applications

Concept-Instance state update (OWL Implementation)…

Concept-Instance

Concept-Instance

Instance-of

Cancer

Instance-of

Cancer

Field

Root

Value

locus

Locus

Breast

Field

Root

Value

stage

BC+s

Stage2

locus

Breast

Locus

stage

Stage2

subSt.

BC2+ss

BC2+ss

BC+s

Update

(via ‘sanctioning’ mechanism)

To OWL Description

Stage2BreastCancer

EquivalentTo:

BreastCancer

and stage some Stage2

SubClassOf:

subStage some (SubStageA

or SubStageB…)

Cancer

and locus some Breast

and stage some Stage2

Classify


A generic software framework for building hybrid ontology backed models for driving applications

Note

  • EKS Access System allows ‘compositional’ concepts such as BreastCancer and Stage2BreastCancer to be hidden from Object Model

  • …Hence: No need for classification during execution of queries constructed via Object Model

  • …Hence: Relatively efficient (SPARQL-based) querying of large numbers of individual records


Why hybrid models

Why Hybrid Models?


A generic software framework for building hybrid ontology backed models for driving applications

For simple GLIMPSE model of time…

Cancer

Breast

Stage2

SubStageA

type

locus

stage

subStage

Problem-Glimpse

...simple one-to-one correspondence between Object Model and EKS Access System

Concept-Instance

Instance-of

Cancer

Field

Root

Value

locus

Locus

Breast

stage

BC+s

Stage2

subSt.

BC2+ss

BC2+ss


A generic software framework for building hybrid ontology backed models for driving applications

But… full SNAP/SPAN model of time involves non-ontologically-specifiable interaction…

Cancer

Breast

type

locus

Problem-History

snapshot

snapshot

snapshot

Problem-Snapshot

Problem-Snapshot

Problem-Snapshot

stage

stage

stage

subStage

Stage1

Stage1

Stage3

SubStageA


A generic software framework for building hybrid ontology backed models for driving applications

Including interaction with a Temporal Abstraction System…

Stage1

Stage3

Stage1

Stage3

start

end

min

max

Temporal-Abstractions

Cancer

Breast

type

locus

stage

Problem-History

snapshot

snapshot

snapshot

Problem-Snapshot

Problem-Snapshot

Problem-Snapshot

stage

stage

stage

subStage

Stage1

Stage1

Stage3

SubStageA


A generic software framework for building hybrid ontology backed models for driving applications

Hence, more complex mappings between Object Model and EKS Access System…

Concept-Instance

Instance-of

Cancer

Field

Root

Value

locus

Locus

Breast

stage

BC+s

Stage1

Cancer

Breast

type

locus

Problem-History

snapshot

Problem-Snapshot

stage

Stage1


A generic software framework for building hybrid ontology backed models for driving applications

Hence, more complex mappings between Object Model and EKS Access System…

Concept-Instance

Instance-of

Cancer

Field

Root

Value

locus

Locus

Breast

stage

BC+s

Stage1

Cancer

Breast

type

locus

Problem-History

snapshot

Problem-Snapshot

stage

Stage1


A generic software framework for building hybrid ontology backed models for driving applications

Hence, more complex mappings between Object Model and EKS Access System…

Concept-Instance

Instance-of

Cancer

Field

Root

Value

locus

Locus

Breast

stage

BC+s

Stage3

subSt.

BC2+ss

SSA

Cancer

Breast

type

locus

Problem-History

snapshot

Problem-Snapshot

stage

subStage

Stage3

SubStageA


A generic software framework for building hybrid ontology backed models for driving applications

Hence, more complex mappings between Object Model and EKS Access System…

Stage1

Stage3

Stage1

Stage3

start

end

min

max

Temporal-Abstractions

Cancer

Breast

type

locus

stage

Problem-History

Concept-Instance

…also involving Temporal Abstraction System

Temporal-Abstractor-Set

Instance-of

Cancer

+

Field

Root

Value

Field

Type

locus

Locus

Breast

stage

ORDINAL

stage

BC+s

???


Hybrid models summary

Hybrid Models Summary

  • Non-ontologically specifiable interaction

  • Hence, hybrid models of some type required

  • Advantages of Object-Model based solution:

    • Relatively simple

    • Flexible

    • Coherent

    • Domain-specific API


Higher level model architecture

Higher-Level Model Architecture


A generic software framework for building hybrid ontology backed models for driving applications

Higher-level interaction orchestrated by Interaction Model…

Interaction Model

EKS

Access

System

Temporal Abstraction System

Static Model

(SNAP/SPAN)

Object Model


A generic software framework for building hybrid ontology backed models for driving applications

Additional Processing Mechanismsdistinct from Interaction Model - do not contribute to shape of model itself

Interaction Model

EKS

Access

System

Temporal Abstraction System

Static Model

(SNAP/SPAN)

Additional Processing Mechanisms

Object Model


Driving applications

Driving Applications


A generic software framework for building hybrid ontology backed models for driving applications

Basic Source Representation provided by collection of domain-specific Java classes…

7

  • Domain-specific API

  • Interaction Model intrinsic to domain classes (extending generic patterns where applicable)

V

4.3

W

B

A

E

D

X

C

Z

2

Y

8/1/97

Object of (domain-specific) class A

Relationship represented by object of classLink

A

Field on object


A generic software framework for building hybrid ontology backed models for driving applications

Automatic translation into domain-neutral Network Representation…

  • Domain-neutralsemantic network representation

  • Interaction Model translated into a set of ‘listeners’

  • All translation specification is by individual classes

7

V

4.3

W

B

A

E

D

X

C

Z

2

Y

8/1/97

Relationship represented by object of class Link

Object of class Node - representing instance of concept ‘A’

A


A generic software framework for building hybrid ontology backed models for driving applications

Query formulation via extended version of Network Representation…

  • Extensions for…

  • Insertion of logical operators

  • Specification of data-value constraints (including temporal constraints)

  • Specification of temporal-abstractions over dynamically defined time-periods (not shown)

?p

D

> ?p

A

C

Z

OR

B

OR

NOT

Y

F

E

X

< (?p + ?q) / 2

?q


Software

Software


A generic software framework for building hybrid ontology backed models for driving applications

Core Model-Builder provides generic EKS-interaction mechanisms, skeleton interaction-patterns, etc.

Chronicle Model-Builder provides core SNAP/SPAN representation, interaction with Temporal Abstraction System, chronicle-specific interaction-patterns, etc.

Patient Chronicle Model

Temporal

Abstraction

System

Chronicle Model-Builder

Core Model-Builder

EKS Access System

OWL-Access

Protege-Ac.


A generic software framework for building hybrid ontology backed models for driving applications

GUIs (Domain-Neutral)

Record Browser

Model Browser

Query Formulator

Data-Creation Tools (Domain-Specific)

Patient Chronicle Simulator

Model

Patient Record Chronicliser

Query

Engine

Temporal Abstraction

Extension

Storage Manager

EHR Store

RDF Store

Data-Storage/Query System (Domain-Neutral)


A generic software framework for building hybrid ontology backed models for driving applications

Further demos available on request– please ask!Software soon available on-line(Technical Supplement will provide details)


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