© Geodise Project, University of Southampton, 2001-2004.http://www.geodise.org/
Semantic Web based Content Enrichment and Knowledge Reuse
in e-ScienceFeng Tao, Liming Chen, Nigel Shadbolt, Fenglian Xu, Simon
Cox, Colin Puleston, Carole Goble
University of SouthamptonUniversity of Manchester
U.K.
Presenter: Barry TAO
© Geodise Project, University of Southampton, 2001-2004.http://www.geodise.org/
Overview
• Background and purpose – EDSO, Resource, knowledge support
• A layered semantic infrastructure– Protégé + OWL, Ontology, Jena, Annotator and Advisor
• Life cycle of semantic web base KM– Knowledge capture, binding and reuse
• Illustration of various tools– Generic Protégé tool, Function Annotator, Knowledge advising
service, knowledge toolbox in Matlab, etc.
• Summary
© Geodise Project, University of Southampton, 2001-2004.http://www.geodise.org/
Background and purposes
• e-Science – Large scale science– Distributed global collaboration on data, computation and knowledge
• Grid based EDSO– Engineering Design Search & Optimisation– Resources of distributed computation, distributed storage and distributed knowledge– Toolbox of Grid enabled Matlab functions
• Describe and share resources using Ontology and Semantic Grid technologies– Components: Matlab functions – the toolbox, – Domain knowledge: optimisation methods, valid configurations, etc.
• Provide knowledge through reusing the semantics– Retrieval of the semantics (direct use)– Advice (more advanced usage)
On function configuration On workflow composition (driven by semantic matching)
– Web services, distributed and service oriented architecture
© Geodise Project, University of Southampton, 2001-2004.http://www.geodise.org/
Layered Semantic Web Infrastructure
• EDSO Domain Ontology– Concepts and relations in a domain– Obtained through KA– Represented in OWL
• Generic Ontology/Semantics manipulation
– Protégé with Owl plug-in– Ontology further refined and populated in
protégé
• Geodise knowledge services/demonstrators
– Function Annotator– Semantic Retrieval GUI– Knowledge advisor service
• Geodise Apps integrated with knowledge
– Knowledge toolbox in Matlab– WCE standalone tool– DSE standalone tool
Applicationswith integratedKnowledge support
ProtégéOWL plug-inEditing GUI
SemanticDriven GUI
FunctionAnnotator
KnowledgeAdvisor/Service
HP Jena Ontology API
Jena normal model Jena +DIG reasoner
Domain ontology of EDSO in OWL(OWL-Lite, OWL-DL or OWL-full)
Geodise Components Generic ComponentsKeys
KnowledgeToolbox
Workflow CompositionEnvironment (WCE)
Domain ScriptEditor (DSE)
© Geodise Project, University of Southampton, 2001-2004.http://www.geodise.org/
Knowledge Life cycle
• Knowledge Capturing– Knowledge Acquisition, building
Ontologies
• Knowledge Binding– Annotation : Creating instances of
ontological concepts– Protégé editor, function annotator
• Knowledge Modeling – Specification of useful knowledge:
Semantic retrieval, advice on function configuration and assembly
• Knowledge Reusing– Semantic based function query and
knowledge advisor
• Illustration follows
Protégé with OWL Plug-in Function annotator
BuildingOntologies
Generatinginstances
Inst
ance
Sto
ring
OW
L file
Reuse over the OWL ontology model
Ontology drivenDL-based query
Semantic matchingbased knowledge advisor
Jena API
© Geodise Project, University of Southampton, 2001-2004.http://www.geodise.org/
Knowledge Capturing
• Knowledge Acquisition– From Domain experts and
domain documents.– Build in Protégé with OWL
Plug-in– Concepts
Classes
– Relationships Hierarchy Property slots
• Result– OWL format ontology
© Geodise Project, University of Southampton, 2001-2004.http://www.geodise.org/
Function Annotation (Knowledge Binding)
• Generating semantic instances– Binding ontology with semantics content– Populating the semantic web based knowledge base
• Supporting Tools– Through Protégé editor
High flexibility (can generate instances of any ontology concept) sometimes tedious
– Through a customized function annotator Automatic parsing Lack of flexibility (only deal with functions at the moment)
– We use both
© Geodise Project, University of Southampton, 2001-2004.http://www.geodise.org/
With Protégé
• Creating + maintaining the ontology
• Generating semantic instances
– Instantiating abstract nodes defined in ontology
– Filling ontology driven forms with semantic content
© Geodise Project, University of Southampton, 2001-2004.http://www.geodise.org/
With Function Annotator
• Customised for Matlab functions
– Automatic parsing Matlab function source
• Instantiating abstract nodes defined in ontology
• Semi-automatic filling of the ontology driven forms
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© Geodise Project, University of Southampton, 2001-2004.http://www.geodise.org/
Knowledge Reuse
• Semantic retrieval – Retrieve semantics from the knowledge repository (Entity Semantics)
• Inference– Direct – “a subClassOf b” , “b subClassOf c”– Inferred – “a subClassOf c”
• Advice– Function assembly (Service composition)– Function configuration (Parameter tuning)
• Service Oriented Architecture – Service side: Semantics processing and domain specific knowledge
generation mechanisms with web service interfaces– Client side: light weight, generic web service invoking, returns XML
© Geodise Project, University of Southampton, 2001-2004.http://www.geodise.org/
Function/workflowRepository (Archive)
Service-oriented Semantics Application Scenario
Geodise Functions
Function Ontology
Function Annotator
Grid Fabrics
Semantic/Knowledge support middleware
OntologyServices
AdvisorServices
InstanceServices ….
Engineering Design Community
The Proposed Browser-based
Function/workflowExplorer
Geodise
Matlab EnvWCEOtherapplications
If we want to leverage and harvest the maximum benefit of Semantic web, i.e. effective discovery, machine-enabled (processible, understandable) interoperability and automation, and the Grid, i.e. resource sharing, this is one of the realisations.
The choice is up to the users!
© Geodise Project, University of Southampton, 2001-2004.http://www.geodise.org/
Towards Service Oriented Paradigm
• Server (in the middle)– Semantic layer– Interfaces at different level
Web service Java APIs
Server side Knowledge Service Light weight client side(Applications)
Web service
OWL/Jena OntologyModel
Jena AP
Semantic MatchingEngine and Knowledge
Advisor API
KnowledgeToolbox
GD API
Matlab
Java Virtual Machine
Other java applications thatconsume the knowledge
Workflow CompositionEnvironment (WCE)
Domain Script Editor
Function Annotator
DL-based FunctionQuery GUI
Migrate to
WCE
© Geodise Project, University of Southampton, 2001-2004.http://www.geodise.org/
Towards Service Orientated Paradigm
• Other java applications (to the left)
– Consume the service via Knowledge service APIs
– WCE, DSE, FA, DL-FQ– To be moved to client side in
the right?
Server side Knowledge Service
Web service
OWL/Jena OntologyModel
Jena AP
Semantic MatchingEngine and Knowledge
Advisor API
GD API
Light weight client side(Applications)
KnowledgeToolbox
Matlab
Java Virtual Machine
Other java applications thatconsume the knowledge
Workflow CompositionEnvironment (WCE)
Domain Script Editor
Function Annotator
DL-based FunctionQuery GUI
Migrate to
WCE
© Geodise Project, University of Southampton, 2001-2004.http://www.geodise.org/
Towards Service Orientated Paradigm
• Client (to the right)– Matlab PSE– Knowledge Toolbox
Matlab Java Web service consumer
• Illustrations follows …
Server side Knowledge Service
Web service
OWL/Jena OntologyModel
Jena AP
Semantic MatchingEngine and Knowledge
Advisor API
GD API
Light weight client side(Applications)
KnowledgeToolbox
Matlab
Java Virtual Machine
Other java applications thatconsume the knowledge
Workflow CompositionEnvironment (WCE)
Domain Script Editor
Function Annotator
DL-based FunctionQuery GUI
Migrate to
WCE
© Geodise Project, University of Southampton, 2001-2004.http://www.geodise.org/
Semantics Retrieval• Examples
• Get all optimisation methods (below)
• Get semantics of a particular optimisation method (right)
• Integration Support dynamic GUI generation
© Geodise Project, University of Southampton, 2001-2004.http://www.geodise.org/
Function Query GUI
© Geodise Project, University of Southampton, 2001-2004.http://www.geodise.org/
Advice on Function Assembly(Integrated in Matlab – Knowledge Toolbox)
• Goal– Function assembly– What can be deploy
next and before?
• Mechanism– Matlab Java
WSDL Web service
– Function semantic interface
– Semantic matching
• Pre-requirements– Function has been
annotated– Semantics available
in the instance store
© Geodise Project, University of Southampton, 2001-2004.http://www.geodise.org/
Advice on Function Configuration
You are using #genetic algorithm search#. Additional control parameters have been added.You may need still to configure the following control parameters:.GA_NPOP GA_ALPHA GA_DMAX GA_DMIN GA_NBIN GA_NBREED GA_NCLUST GA_NRANDM GA_PBEST GA_PCROSS GA_PENAL GA_PINVRT GA_PMUTNT GA_PRPTNL GA_PSEED
% get the default beam structure
beam = createBeamStruct (4)
% analyze the OMETH and advice on its additional control parameter (with default value)
beamcontrol = gdk_options(beam)
% check semantics
gdk_semantics(‘GD_NPOP’)
% further configure these control parameters
… …
% run options
s = OptionsMatlab (beamcontrol)
1
2
3
© Geodise Project, University of Southampton, 2001-2004.http://www.geodise.org/
Advice on Function Assembly(Integrated in WCE – workflow advisor)
Select a function and request advice
Function assembly advice
© Geodise Project, University of Southampton, 2001-2004.http://www.geodise.org/
Advice on Function Assembly(Integrated in Domain Script Editor)
Function configuration advice
Function assembly advice
Ontology and semantics Domain script editing area
© Geodise Project, University of Southampton, 2001-2004.http://www.geodise.org/
Related Work
• Protégé with OWL plug-in– Open source ontology editor, widely used– OWL plug-in built on Jena
• Jena, HP– Originally designed as RDF oriented– OWL support added on at the top layer– Various types of ontology modes: OWL_MEM, OWL_DL_MEM, etc.– Inference is available through graph manipulating
• OilED+Ontoview, UoM– OilEd developed for building DAML+OIL ontology– Ontoview is a simplified view/editing tool and API– Adapted for DL based reasoning over Instance Store
© Geodise Project, University of Southampton, 2001-2004.http://www.geodise.org/
Summary & Conclusions
• Purpose and background of KM in EDSO• A layered semantic infrastructure
– Protégé + OWL, Ontology, Jena, Annotator and Advisor• Life cycle of semantic web base KM
– Knowledge capture, binding and reuse• Demonstrations of various tools
• Long process• Preparation of ontologies and semantics instances are important• Integration is not easy• Reusing in a smart way is the key (reuse in engineer’s favorite PSE)
© Geodise Project, University of Southampton, 2001-2004.http://www.geodise.org/
Future Work
• Allow engineers to curate knowledge themselves in their favorite PSE (more integration)
WSE, Matlab
• Synchronization Engineers’ need to Maintain local knowledge of their own Selectively synchronize local knowledge with centralized knowledge
• Target more resources– Workflow– Grid fabrics
• More interfaces to the knowledge repository– More advanced advice on OptionsMatlab in Matlab– Function Browser
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