a generic software framework for building hybrid ontology-backed models for driving applications...
TRANSCRIPT
A Generic Software Frameworkfor building
Hybrid Ontology-Backed Modelsfor
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
• OWL Ontology provides detailed domain knowledge
• Dynamic model updates:– Orchestrated by Object Model– Based on interaction with ontology +
classifier
Object-Model/Ontology Interaction
EKS Access System
Object Model accesses EKS and associated inference mechanisms via mediating interface
…has no knowledge of any EKS format
…and no knowledge of any inference mechanisms
FaCT++
OWL-Access Protege-Ac.
Domain Knowledge Sources(ontologies, databases, etc.)
Ontological knowledge comes from set of External Knowledge Sources (EKS)…
Object Model
EKS Access System
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
FaCT++
OWL-Access Protege-Ac.
Domain Knowledge Sources(ontologies, databases, etc.)
Ontological knowledge comes from set of External Knowledge Sources (EKS)…
Object Model
EKS Access System
Object Model
Get concept-hierarchy
for<problem-
type-identifier>
Create instance
of C1 C1a
Update field-set +
constraints for
Cancer
Cancer selectedfield-value updated
C1
C1
Concept-Instance state update (OWL Implementation)…
Concept-Instance
Field Root Value
Cancer
locus Locus Breast
Instance-of
stage BC+s Stage2
subSt. BC2+ss BC2+ss
Concept-Instance
Field Root Value
Cancer
locus Locus Breast
Instance-of
stage BC+s Stage2
Cancerand locus some Breastand stage some Stage2
Stage2BreastCancerEquivalentTo: BreastCancer and stage some Stage2SubClassOf: subStage some (SubStageA or SubStageB…)
To OWL Description
Classify
Update(via ‘sanctioning’ mechanism)
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?
type locus
Problem-Glimpse
Cancer Breast
subStagestage
Stage2 SubStageA
For simple GLIMPSE model of time…
...simple one-to-one correspondence between Object Model and EKS Access System
Concept-Instance
Field Root Value
Cancer
locus Locus Breast
Instance-of
stage BC+s Stage2
subSt. BC2+ss BC2+ss
stage
type locus
snapshot snapshot snapshot
stage subStagestage
Problem-History
Problem-Snapshot
Problem-Snapshot
Problem-Snapshot
Stage1 Stage1 Stage3 SubStageA
Cancer Breast
But… full SNAP/SPAN model of time involves non-ontologically-specifiable interaction…
min max
stage
type locus stage
snapshot snapshot snapshot
stage subStagestage
Problem-History
Problem-Snapshot
Temporal-Abstractions
Problem-Snapshot
Problem-Snapshot
Stage1 Stage3
Stage1 Stage1 Stage3 SubStageA
Cancer Breast
start end
Stage1 Stage3
Including interaction with a Temporal Abstraction System…
stage
type locus
snapshot
Problem-Snapshot
Stage1
Cancer Breast
Concept-Instance
Field Root Value
Cancer
locus Locus Breast
Instance-of
stage BC+s Stage1
Hence, more complex mappings between Object Model and EKS Access System…
Problem-History
type locus
snapshot
stage
Problem-Snapshot
Stage1
Cancer Breast
Concept-Instance
Field Root Value
Cancer
locus Locus Breast
Instance-of
stage BC+s Stage1
Hence, more complex mappings between Object Model and EKS Access System…
Problem-History
type locus
Cancer Breast
Concept-Instance
Field Root Value
Cancer
locus Locus Breast
Instance-of
stage BC+s Stage3
subSt. BC2+ss SSA
snapshot
subStagestage
Problem-Snapshot
Stage3 SubStageA
Hence, more complex mappings between Object Model and EKS Access System…
Problem-History
min max
type locus stage
Temporal-Abstractions
Stage1 Stage3
Cancer Breast
start end
Stage1 Stage3
Concept-Instance
Field Root Value
Cancer
locus Locus Breast
Instance-of
stage BC+s ???
Temporal-Abstractor-Set
+ Field Type
stage ORDINAL
…also involving Temporal Abstraction System
Hence, more complex mappings between Object Model and EKS Access System…
Problem-History
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 interaction orchestrated by Interaction Model…
Object Model
Static Model(SNAP/SPAN)
Interaction Model
EKSAccessSystem
Temporal Abstraction
System
Additional Processing Mechanisms distinct from Interaction Model - do not contribute to shape of model itself
Object Model
Static Model(SNAP/SPAN)
Additional Processing
Mechanisms
Interaction Model
EKSAccessSystem
Temporal Abstraction
System
Driving Applications
•Domain-specific API
•Interaction Model intrinsic to domain classes (extending generic patterns where applicable)
Basic Source Representation provided by collection of domain-specific Java classes…
A
B
E
C
D
V
ZX
Y
W
7
4.3
28/1/97
Field on objectAObject of (domain-specific) class A
Relationship represented by object of class Link
Automatic translation into domain-neutral Network Representation…
•Domain-neutral semantic network representation
•Interaction Model translated into a set of ‘listeners’
•All translation specification is by individual classes
A
B
E
C
D
V
ZX
Y
W
7
4.3
28/1/97
A Object of class Node - representing instance of concept ‘A’
Relationship represented by object of class Link
B
C
D
E
Z
X
Y
?q
?p
OR
F
OR
< (?p + ?q) / 2
> ?pA
NOT
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)
Software
Patient Chronicle Model
EKS Access System
Core Model-Builder
Chronicle Model-Builder TemporalAbstraction
System
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.
OWL-Access Protege-Ac.
Model
Storage Manager
RDF Store
Data-Storage/Query System (Domain-Neutral)
GUIs (Domain-Neutral)
Record Browser
Model Browser
Query Formulator
Patient Record Chronicliser
EHR Store
Data-Creation Tools (Domain-Specific)
Patient Chronicle Simulator
QueryEngine
Temporal AbstractionExtension
Further demos available on request– please ask!
Software soon available on-line(Technical Supplement will provide details)