national e-science centre, edinburgh 27/11/06 (ontology-based) metadata: what is it, where and how...
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National e-Science Centre, Edinburgh 27/11/06
(Ontology-based) Metadata: What is it,
Where and How can we use it, and How can we share it?
www.ontogrid.eu
Oscar CorchoUniversity of Manchester
Free text and tags also allowed
Controlled and systematicmanagement
And many other Wh-questions
2Edinburgh, 27 November 2006
Outline
Metadata, annotations... What are they and where are they used?Semantic Annotation WebSemantic Data (Integration) WebSemantic Knowledge (Reasoning) Web
Our approach to systematic metadata managementOntoGrid and S-OGSAThe S-OGSA model: Semantic BindingsS-OGSA capabilities and mechanismsOne S-OGSA scenario of use
Ongoing work Conclusions
3Edinburgh, 27 November 2006
Organisation
News
Research
Grant Application
Videocast
Events
Gene Database
Annotation assert facts using terms (metadata in RDF)Represent terms and their relationships (ontology in RDFS/OWL)
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Types of vocabularies. Formality
Lassila O, McGuiness D. The Role of Frame-Based Representation on the Semantic Web. Technical Report. Knowledge Systems Laboratory. Stanford University. KSL-01-02. 2001.
BIRNLex GO GALENAdd your vocabularies here
5Edinburgh, 27 November 2006
Metadata annotation
Different types of annotation depending on the type of vocabulary used
Based on Dublin CoreThe contributor and creator is the flight booking service “www.flightbookings.com”.The date would be January 1st, 2003, in case that the HTML page has been generated on that specific date.The description would be something like “flight details for a travel between Madrid and Seattle via Chicago on February 8th, 2004”.The document format is “HTML”.The document language is “en”, which stands for English
Based on thesauriMadrid is a reference to the term with ID 7010413 in the thesaurus, which refers to the city of Madrid in Spain.Spain is a reference to the term with ID 1000095, which refers to the kingdom of Spain in Europe.Chicago is a reference to the term with ID 7013596, which refers to the city of Chicago in Illinois, US.United States of America is a reference to the term “United States” with ID 7012149, which refers to the US nation.Seattle is a reference to the term with ID 7014494, which refers to the city of Seattle in Washington, US.
Based on ontologiesConcept instances relate a part of the document to one or several concepts in an ontology. For example, “Flight details” may represent an instance of the concept Flight, and can be named as AA7615_Feb08_2003, although concept instances do not necessarily have a name.Attribute values relate a concept instance with part of the document, which is the value of one of its attributes. For example, “American Airlines” can be the value of the attribute companyName.Relation instances that relate two concept instances by some domain-specific relation. For example, the flight AA7615_Feb08_2003 and the location Madrid can be connected by the relation departurePlace
Ontology-based document annotation: trends and open research problems. Corcho, O. International Journal of Metadata, Semantics and Ontologies 1(1):47-57. 2006
6Edinburgh, 27 November 2006
Outline
Metadata, annotations... What are they and where are they used?Semantic Annotation WebSemantic Data (Integration) WebSemantic Knowledge Web
Our approach to systematic metadata managementOntoGrid and S-OGSAThe S-OGSA model: Semantic BindingsS-OGSA capabilities and mechanismsOne S-OGSA scenario of use
Ongoing work Conclusions
7Edinburgh, 27 November 2006
Data mining
Knowledge Discovery
Smart search
Social networking
Smart portals
Agents
Information Integration and aggregation
Integration use a uniform common model in RDFConnecting through shared terms and shared instancesPreserving context and provenance
D2RR2OBIRN Mediator
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urn:data:f2urn:data:f2
urn:data1urn:data1
urn:data2urn:data2
urn:compareinvocation3urn:compareinvocation3
urn:data12urn:data12
Blast_report
[input]
[output]
[input]
[distantlyDerivedFrom]
SwissProt_seq[instanceOf]
Sequence_hit
[hasHits]
urn:hit2….urn:hit2….
urn:hit1…urn:hit1…
urn:hit50…..
urn:hit50…..
[instanceOf]
[similar_sequence_to]
Data generated by services/workflows
Concepts
[ ]
[performsTask]
Find similar sequence[contains]
Services
urn:data:3urn:data:3
urn:hit8….urn:hit8….
urn:hit5…urn:hit5…
urn:hit10…..
urn:hit10…..
[contains]
[instanceOf]
urn:BlastNInvocation3urn:BlastNInvocation3
urn:invocation5urn:invocation5urn:data:f1urn:data:f1[output]
New sequenceMissed sequence
[hasName][hasName]
literalsDatumCollection
[type]
LSDatum
[type]Properties
[instanceOf]
[output]
[output]
[directlyDerivedFrom]
Resource Description Framework
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Metadata Matters
Flexible and extensible self describing schemas that don’t have to be nailed down “Lets describe my data set, or the output format of my tool, that
changes all the time” Open world
“I need to comment on that experiment” “That fact is now incorrect because …”
Data fusion across different data modelscross linked by shared instances and shared concepts
Global naming schemeE.g. LSID: Life Science Identifiers
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Don’t Prescribe, Describe!!
The tyranny of the table •The tyranny of the tree
“Not everything fits in onetaxonomy” -- Maryanne Martone (US BIRN)
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Seamark Demo:
ID new drug candidates for
BRKCB-1
GO2Keyword.rdf
UniProt.rdf
GO.rdf
Keywords.rdf
Taxonomy.rdfPubMed.xml
Citation
IntAct.rdf
Organism
Enzymes.rdf
OMIM.rdf
GO2OMIM.rdf
GO2Enzyme.rdf
MIM Id
KEGG.rdf
KeywordGO2UniProt.rdf
Protein
Enzyme
ProbeSet.rdf
Gene
Probe
Pathway
Compound
Courtesy Joanne Luciano
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RDF for Proteomic Standards
http://www.naturebiotechnology.org
13Edinburgh, 27 November 2006
Outline
Metadata, annotations... What are they and where are they used?Semantic Annotation WebSemantic Data WebSemantic Knowledge (Reasoning) Web
Our approach to systematic metadata managementOntoGrid and S-OGSAThe S-OGSA model: Semantic BindingsS-OGSA capabilities and mechanismsOne S-OGSA scenario of use
Ongoing work Conclusions
14Edinburgh, 27 November 2006James Hendler Science and the Semantic Web Science 299: 520-521, 2003
Rearrangement of a DNA sequence homologous to a cell-virus junction fragment in several Moloney murine leukemia virus-induced rat thymomas
8q24PVT1
Inference Logic-based classification and validity checking using OWLRules using SWRL (Semantic Web Rule Language)RDF queries Just making connections because so much stuff is connected!
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In summary
OWL
Integration
RDF(S)
RDF
XML
Annotation
Integration
Inference
SWRL
Extensible metadata schemas that you don’t have to nail down
Controlled vocabularies
Data fusion
Expressive models
Model fusion
16Edinburgh, 27 November 2006
Outline
Metadata, annotations... What are they and where are they used?Semantic Annotation WebSemantic Data (Integration) WebSemantic Knowledge (Reasoning) Web
Our approach to systematic metadata managementOntoGrid and S-OGSAThe S-OGSA model: Semantic BindingsS-OGSA capabilities and mechanismsOne S-OGSA scenario of use
Ongoing work Conclusions
17Edinburgh, 27 November 2006
EU-STREP Project OntoGrid
Middleware for the Semantic GridP2P Metadata Storage & Querying
(Atlas).Ontology Access: WS-DAIOnt-
RDF(S)Annotation:
• Data and provenanceKnowledge Parser
• ServicesODE-SGS
Business process monitoringNegotiation Coordination
Applications Insurance SettlementSatellite Image Quality
Analysis
SEMANTIC OGSACapabilites & Behaviors for
Semantic GridsPrincipled way of realization
Disclaimer: Talking about Grid does not necessarily mean High Performance Computing and Parallelisation, but mainly management of distributed systems
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S-OGSA
Semantic-OGSA (S-OGSA) is...Our proposed Semantic Grid reference architectureA low-impact extension of OGSA
• Mixed ecosystem of Grid and Semantic Grid servicesServices ignorant of semanticsServices aware of semantics but unable to process themServices aware of semantics and able to process (part of) them
• Everything is OGSA compliant
Defined by • Information model
New entities
• CapabilitesNew functionalities
• Mechanisms How it is delivered
Model
Capabilities Mechanisms
provide/consume
expose
use
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METADATAas SemanticAnnotations
S-OGSA Model
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S-OGSA Model: Metadata is a first-class resource
Benefits of treating Metadata as a first-class resource:-- Clear AuthZ mechanisms-- Clear lifetime-- Metadata can be also distributed-- ...
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Optimization
Execution Management
Resourcemanagement
Data
Security
Information Management
Infrastructure Services
Application 1 Application N
OG
SA
Sem
antic
-OG
SA
Semantic Services
S-OGSA Capabilities: From OGSA to S-OGSA
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Optimization
Execution Management
Resourcemanagement
Data
Security
Information Management
Infrastructure Services
Application 1 Application N
OG
SA
Sem
antic
-OG
SA
Semantic Services
S-OGSA Capabilities: From OGSA to S-OGSA
Ontology
ReasoningKno
wle
dge
Metadata
Annotation
Sem
antic
bin
ding
Semantic Provisioning Services
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S-OGSA Patterns. Semantic Aware and Capable Service
Deployed in Globus Toolkit 4
Lifetime
MetadataService
Service
ResourceMetadataSeekingClient
Properties
Others…
Access/Query Semantic Bindings1Semantics
1.1
Farm out request
Semantic aware interface
OntologyService
24Edinburgh, 27 November 2006
S-OGSA Scenario. Satellite Image Quality Analysis
Scenes: Routine operations Metadata generation Report retrieving
Satellite Routine Operations
Satellite LifeCycle: Launch and Early Orbit
Phase (~ 3 days) Calibration and Validation
campaign (~ 6-9 months) Routine operations (~ 5-9
years) Satellite de-orbiting.
Product processing continues
25Edinburgh, 27 November 2006
Outline
Metadata, annotations... What are they and where are they used?Semantic Annotation WebSemantic Data (Integration) WebSemantic Knowledge (Reasoning) Web
Our approach to systematic metadata managementOntoGrid and S-OGSAThe S-OGSA model: Semantic BindingsS-OGSA capabilities and mechanismsOne S-OGSA scenario of use
Ongoing work Conclusions
26Edinburgh, 27 November 2006
S-OGSA Metadata Access/Management Protocols
SB Factory
Client
Semantic Binding
Metadata Query
SBSB
SB
create
Query w/o Inference, UpdateContent
Query( over unified view)
WS-RP: Get/Set/Query Properties
WS-Addressing: epr
RDFRDF
create
query
Inspect-props . . .
query
Semantic Binding Service Suite
WS-RL: Destroy , SetTerminationTime
WS-RL ++: archive
WS-Notif: Subscribe / Notify
27Edinburgh, 27 November 2006
S-OGSA Metadata Lifecycle
Metadata is normally in stable situation
If the entity it refers to or the knowledge entity it uses change, then it may move to a stale situationChecks neededPossibly reannotation
Metadata can be archived or deleted from the system
Stable
Stale
GEchanged
KEchanged
Archived Deleted
“Periodically, we will have to reannotate everything” -- Maryanne Martone (US BIRN)
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Data Integration
Information integration from gLite and GT4 information servicesBDIIRGMAMDS
Trade-off between...Continuous update or on-
demand access, fresh information
Consolidated data but possibly non-fresh information
29Edinburgh, 27 November 2006
Outline
Metadata, annotations... What are they and where are they used?Semantic Annotation WebSemantic Data (Integration) WebSemantic Knowledge (Reasoning) Web
Our approach to systematic metadata managementOntoGrid and S-OGSAThe S-OGSA model: Semantic BindingsS-OGSA capabilities and mechanismsOne S-OGSA scenario of use
Ongoing work Conclusions
30Edinburgh, 27 November 2006
Conclusions
Metadata can be used for many purposesSimply for the sake of annotation
• Reuse and sharing Look at the Web 2.0 successFor integration
• Open and flexible schemas. Describe, not prescribeFor reasoning
• Complex applications
S-OGSA Metadata as a first-class citizen Semantic BindingSemantic Binding Service already available for use
• Robust metadata management• Distributed
Metadata lifecycle
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Access to S-OGSA
PublicationsAn overview of S-OGSA: a Reference Semantic Grid
Architecture. Corcho O, Alper P, Kotsiopoulos I, Missier P, Bechhofer S, Goble C. Journal of Web Semantics 4(2):102-115. June 2006
Source code http://www.ontogrid.net/, For Downloading DistributionsAccess to CVS
Connection type: pserveruser: ontogridpassword: not neededHost: rpc262.cs.man.ac.ukPort: 2401Repository path: /local/ontogrid/cvsrootmodule: prototype
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Questions
Thank you for your attention!
Questions?
Acknowledgements Carole Goble OntoGrid team members at Manchester
• Pinar Alper, Ioannis Kotsiopoulos, Sean Bechoffer, Ian Dunlop, Wei Xing
OntoGrid Consortium
National e-Science Centre, Edinburgh 27/11/06
(Ontology-based) Metadata: What is it,
Where and How can we use it, and How can we share it?
www.ontogrid.eu
Oscar CorchoUniversity of Manchester