A Generic Software Framework for building Hybrid Ontology-Backed Models for Driving Applications...
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![Page 1: A Generic Software Framework for building Hybrid Ontology-Backed Models for Driving Applications Colin Puleston, James Cunningham, Alan Rector Bio-Health.](https://reader030.fdocuments.us/reader030/viewer/2022032604/56649e595503460f94b5343f/html5/thumbnails/1.jpg)
A Generic Software Frameworkfor building
Hybrid Ontology-Backed Modelsfor
Driving Applications
Colin Puleston, James Cunningham, Alan Rector
Bio-Health Informatics Group, University of Manchester
![Page 2: A Generic Software Framework for building Hybrid Ontology-Backed Models for Driving Applications Colin Puleston, James Cunningham, Alan Rector Bio-Health.](https://reader030.fdocuments.us/reader030/viewer/2022032604/56649e595503460f94b5343f/html5/thumbnails/2.jpg)
Hybrid-Model Demo
![Page 3: A Generic Software Framework for building Hybrid Ontology-Backed Models for Driving Applications Colin Puleston, James Cunningham, Alan Rector Bio-Health.](https://reader030.fdocuments.us/reader030/viewer/2022032604/56649e595503460f94b5343f/html5/thumbnails/3.jpg)
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
![Page 4: A Generic Software Framework for building Hybrid Ontology-Backed Models for Driving Applications Colin Puleston, James Cunningham, Alan Rector Bio-Health.](https://reader030.fdocuments.us/reader030/viewer/2022032604/56649e595503460f94b5343f/html5/thumbnails/4.jpg)
Object-Model/Ontology Interaction
![Page 5: A Generic Software Framework for building Hybrid Ontology-Backed Models for Driving Applications Colin Puleston, James Cunningham, Alan Rector Bio-Health.](https://reader030.fdocuments.us/reader030/viewer/2022032604/56649e595503460f94b5343f/html5/thumbnails/5.jpg)
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
![Page 6: A Generic Software Framework for building Hybrid Ontology-Backed Models for Driving Applications Colin Puleston, James Cunningham, Alan Rector Bio-Health.](https://reader030.fdocuments.us/reader030/viewer/2022032604/56649e595503460f94b5343f/html5/thumbnails/6.jpg)
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
![Page 7: A Generic Software Framework for building Hybrid Ontology-Backed Models for Driving Applications Colin Puleston, James Cunningham, Alan Rector Bio-Health.](https://reader030.fdocuments.us/reader030/viewer/2022032604/56649e595503460f94b5343f/html5/thumbnails/7.jpg)
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
![Page 8: A Generic Software Framework for building Hybrid Ontology-Backed Models for Driving Applications Colin Puleston, James Cunningham, Alan Rector Bio-Health.](https://reader030.fdocuments.us/reader030/viewer/2022032604/56649e595503460f94b5343f/html5/thumbnails/8.jpg)
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)
![Page 9: A Generic Software Framework for building Hybrid Ontology-Backed Models for Driving Applications Colin Puleston, James Cunningham, Alan Rector Bio-Health.](https://reader030.fdocuments.us/reader030/viewer/2022032604/56649e595503460f94b5343f/html5/thumbnails/9.jpg)
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
![Page 10: A Generic Software Framework for building Hybrid Ontology-Backed Models for Driving Applications Colin Puleston, James Cunningham, Alan Rector Bio-Health.](https://reader030.fdocuments.us/reader030/viewer/2022032604/56649e595503460f94b5343f/html5/thumbnails/10.jpg)
Why Hybrid Models?
![Page 11: A Generic Software Framework for building Hybrid Ontology-Backed Models for Driving Applications Colin Puleston, James Cunningham, Alan Rector Bio-Health.](https://reader030.fdocuments.us/reader030/viewer/2022032604/56649e595503460f94b5343f/html5/thumbnails/11.jpg)
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
![Page 12: A Generic Software Framework for building Hybrid Ontology-Backed Models for Driving Applications Colin Puleston, James Cunningham, Alan Rector Bio-Health.](https://reader030.fdocuments.us/reader030/viewer/2022032604/56649e595503460f94b5343f/html5/thumbnails/12.jpg)
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…
![Page 13: A Generic Software Framework for building Hybrid Ontology-Backed Models for Driving Applications Colin Puleston, James Cunningham, Alan Rector Bio-Health.](https://reader030.fdocuments.us/reader030/viewer/2022032604/56649e595503460f94b5343f/html5/thumbnails/13.jpg)
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…
![Page 14: A Generic Software Framework for building Hybrid Ontology-Backed Models for Driving Applications Colin Puleston, James Cunningham, Alan Rector Bio-Health.](https://reader030.fdocuments.us/reader030/viewer/2022032604/56649e595503460f94b5343f/html5/thumbnails/14.jpg)
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
![Page 15: A Generic Software Framework for building Hybrid Ontology-Backed Models for Driving Applications Colin Puleston, James Cunningham, Alan Rector Bio-Health.](https://reader030.fdocuments.us/reader030/viewer/2022032604/56649e595503460f94b5343f/html5/thumbnails/15.jpg)
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
![Page 16: A Generic Software Framework for building Hybrid Ontology-Backed Models for Driving Applications Colin Puleston, James Cunningham, Alan Rector Bio-Health.](https://reader030.fdocuments.us/reader030/viewer/2022032604/56649e595503460f94b5343f/html5/thumbnails/16.jpg)
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
![Page 17: A Generic Software Framework for building Hybrid Ontology-Backed Models for Driving Applications Colin Puleston, James Cunningham, Alan Rector Bio-Health.](https://reader030.fdocuments.us/reader030/viewer/2022032604/56649e595503460f94b5343f/html5/thumbnails/17.jpg)
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
![Page 18: A Generic Software Framework for building Hybrid Ontology-Backed Models for Driving Applications Colin Puleston, James Cunningham, Alan Rector Bio-Health.](https://reader030.fdocuments.us/reader030/viewer/2022032604/56649e595503460f94b5343f/html5/thumbnails/18.jpg)
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
![Page 19: A Generic Software Framework for building Hybrid Ontology-Backed Models for Driving Applications Colin Puleston, James Cunningham, Alan Rector Bio-Health.](https://reader030.fdocuments.us/reader030/viewer/2022032604/56649e595503460f94b5343f/html5/thumbnails/19.jpg)
Higher-Level Model Architecture
![Page 20: A Generic Software Framework for building Hybrid Ontology-Backed Models for Driving Applications Colin Puleston, James Cunningham, Alan Rector Bio-Health.](https://reader030.fdocuments.us/reader030/viewer/2022032604/56649e595503460f94b5343f/html5/thumbnails/20.jpg)
Higher-level interaction orchestrated by Interaction Model…
Object Model
Static Model(SNAP/SPAN)
Interaction Model
EKSAccessSystem
Temporal Abstraction
System
![Page 21: A Generic Software Framework for building Hybrid Ontology-Backed Models for Driving Applications Colin Puleston, James Cunningham, Alan Rector Bio-Health.](https://reader030.fdocuments.us/reader030/viewer/2022032604/56649e595503460f94b5343f/html5/thumbnails/21.jpg)
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
![Page 22: A Generic Software Framework for building Hybrid Ontology-Backed Models for Driving Applications Colin Puleston, James Cunningham, Alan Rector Bio-Health.](https://reader030.fdocuments.us/reader030/viewer/2022032604/56649e595503460f94b5343f/html5/thumbnails/22.jpg)
Driving Applications
![Page 23: A Generic Software Framework for building Hybrid Ontology-Backed Models for Driving Applications Colin Puleston, James Cunningham, Alan Rector Bio-Health.](https://reader030.fdocuments.us/reader030/viewer/2022032604/56649e595503460f94b5343f/html5/thumbnails/23.jpg)
•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
![Page 24: A Generic Software Framework for building Hybrid Ontology-Backed Models for Driving Applications Colin Puleston, James Cunningham, Alan Rector Bio-Health.](https://reader030.fdocuments.us/reader030/viewer/2022032604/56649e595503460f94b5343f/html5/thumbnails/24.jpg)
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
![Page 25: A Generic Software Framework for building Hybrid Ontology-Backed Models for Driving Applications Colin Puleston, James Cunningham, Alan Rector Bio-Health.](https://reader030.fdocuments.us/reader030/viewer/2022032604/56649e595503460f94b5343f/html5/thumbnails/25.jpg)
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)
![Page 26: A Generic Software Framework for building Hybrid Ontology-Backed Models for Driving Applications Colin Puleston, James Cunningham, Alan Rector Bio-Health.](https://reader030.fdocuments.us/reader030/viewer/2022032604/56649e595503460f94b5343f/html5/thumbnails/26.jpg)
Software
![Page 27: A Generic Software Framework for building Hybrid Ontology-Backed Models for Driving Applications Colin Puleston, James Cunningham, Alan Rector Bio-Health.](https://reader030.fdocuments.us/reader030/viewer/2022032604/56649e595503460f94b5343f/html5/thumbnails/27.jpg)
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.
![Page 28: A Generic Software Framework for building Hybrid Ontology-Backed Models for Driving Applications Colin Puleston, James Cunningham, Alan Rector Bio-Health.](https://reader030.fdocuments.us/reader030/viewer/2022032604/56649e595503460f94b5343f/html5/thumbnails/28.jpg)
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
![Page 29: A Generic Software Framework for building Hybrid Ontology-Backed Models for Driving Applications Colin Puleston, James Cunningham, Alan Rector Bio-Health.](https://reader030.fdocuments.us/reader030/viewer/2022032604/56649e595503460f94b5343f/html5/thumbnails/29.jpg)
Further demos available on request– please ask!
Software soon available on-line(Technical Supplement will provide details)