National e-Science Centre, Edinburgh 27/11/06

1. Free text and tags also allowed (Ontology-based) Metadata: What is it, Where and How can we use it, and How can we share it? www.ontogrid.eu And many other Wh-questions Controlled and systematicmanagement Oscar Corcho University of Manchester Oscar.Corcho@manchester.ac.uk National e-Science Centre, Edinburgh 27/11/06

2. Outline • Metadata, annotations... What are they and where are they used? • Semantic Annotation Web • Semantic Data (Integration) Web • Semantic Knowledge (Reasoning) Web • Our approach to systematic metadata management • OntoGrid and S-OGSA • The S-OGSA model: Semantic Bindings • S-OGSA capabilities and mechanisms • One S-OGSA scenario of use • Ongoing work • Conclusions Edinburgh, 27 November 2006

3. Annotation assert facts using terms (metadata in RDF) Represent terms and their relationships (ontology in RDFS/OWL) News Videocast Grant Application Research Events Organisation Gene Database Edinburgh, 27 November 2006

4. Types of vocabularies. Formality GO Add your vocabularies here  BIRNLex GALEN 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. Edinburgh, 27 November 2006

5. Metadata annotation Ontology-based document annotation: trends and open research problems. Corcho, O. International Journal of Metadata, Semantics and Ontologies 1(1):47-57. 2006 • Different types of annotation depending on the type of vocabulary used Based on Dublin Core The 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 thesauri Madrid 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 ontologies Concept 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 Edinburgh, 27 November 2006

6. Outline • Metadata, annotations... What are they and where are they used? • Semantic Annotation Web • Semantic Data (Integration) Web • Semantic Knowledge Web • Our approach to systematic metadata management • OntoGrid and S-OGSA • The S-OGSA model: Semantic Bindings • S-OGSA capabilities and mechanisms • One S-OGSA scenario of use • Ongoing work • Conclusions Edinburgh, 27 November 2006

7. Integration use a uniform common model in RDF Connecting through shared terms and shared instances Preserving context and provenance Agents Smart portals Data mining Social networking Smart search Knowledge Discovery Information Integration and aggregation D2R R2O BIRN Mediator Edinburgh, 27 November 2006

8. Resource Description Framework [instanceOf] urn:data1 SwissProt_seq [similar_sequence_to] [input] urn:hit1… [performsTask] [instanceOf] urn:BlastNInvocation3 urn:hit2…. [contains] [output] Find similar sequence urn:hit50….. urn:data2 Sequence_hit urn:data12 [input] [hasHits] [instanceOf] urn:compareinvocation3 Blast_report [directlyDerivedFrom] [distantlyDerivedFrom] [instanceOf] [output] urn:hit5… urn:data:3 urn:hit8…. [contains] Data generated by services/workflows [output] urn:hit10….. [output] urn:data:f1 urn:invocation5 [ ] Properties [type] [hasName] urn:data:f2 Concepts [type] [hasName] Services Missed sequence DatumCollection New sequence LSDatum literals Edinburgh, 27 November 2006

9. 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 models • cross linked by shared instances and shared concepts • Global naming scheme • E.g. LSID: Life Science Identifiers Edinburgh, 27 November 2006

10. Don’t Prescribe, Describe!! • The tyranny of the table • The tyranny of the tree “Not everything fits in onetaxonomy” -- Maryanne Martone (US BIRN) Edinburgh, 27 November 2006

11. Seamark Demo: ID new drug candidates for BRKCB-1 GO2Keyword.rdf Keywords.rdf ProbeSet.rdf Keyword GO2OMIM.rdf GO2UniProt.rdf Protein Gene Probe MIM Id OMIM.rdf IntAct.rdf GO.rdf GO2Enzyme.rdf UniProt.rdf Enzyme Organism Citation Compound Taxonomy.rdf Enzymes.rdf PubMed.xml KEGG.rdf Pathway Courtesy Joanne Luciano Edinburgh, 27 November 2006

12. RDF for Proteomic Standards Edinburgh, 27 November 2006 http://www.naturebiotechnology.org

13. Outline • Metadata, annotations... What are they and where are they used? • Semantic Annotation Web • Semantic Data Web • Semantic Knowledge (Reasoning) Web • Our approach to systematic metadata management • OntoGrid and S-OGSA • The S-OGSA model: Semantic Bindings • S-OGSA capabilities and mechanisms • One S-OGSA scenario of use • Ongoing work • Conclusions Edinburgh, 27 November 2006

14. Inference Logic-based classification and validity checking using OWL Rules using SWRL (Semantic Web Rule Language) RDF queries Just making connections because so much stuff is connected! Rearrangement of a DNA sequence homologous to a cell-virus junction fragment in several Moloney murine leukemia virus-induced rat thymomas 8q24 PVT1 Edinburgh, 27 November 2006 James Hendler Science and the Semantic Web Science 299: 520-521, 2003

15. In summary SWRL Expressive models Inference Model fusion OWL Controlled vocabularies RDF(S) Data fusion Integration Integration Extensible metadata schemas that you don’t have to nail down RDF Annotation XML Edinburgh, 27 November 2006

16. Outline • Metadata, annotations... What are they and where are they used? • Semantic Annotation Web • Semantic Data (Integration) Web • Semantic Knowledge (Reasoning) Web • Our approach to systematic metadata management • OntoGrid and S-OGSA • The S-OGSA model: Semantic Bindings • S-OGSA capabilities and mechanisms • One S-OGSA scenario of use • Ongoing work • Conclusions Edinburgh, 27 November 2006

17. EU-STREP Project OntoGrid • SEMANTIC OGSA • Capabilites & Behaviors for Semantic Grids • Principled way of realization • Middleware for the Semantic Grid • P2PMetadata Storage & Querying (Atlas). • Ontology Access: WS-DAIOnt-RDF(S) • Annotation: • Data and provenance • Knowledge Parser • Services • ODE-SGS • Business process monitoring • Negotiation • Coordination • Applications • Insurance Settlement • Satellite Image Quality Analysis Disclaimer: Talking about Grid does not necessarily mean High Performance Computing and Parallelisation, but mainly management of distributed systems Edinburgh, 27 November 2006

18. S-OGSA • Semantic-OGSA (S-OGSA) is... • Our proposed Semantic Grid reference architecture • Alow-impact extension of OGSA • Mixed ecosystem of Grid and Semantic Grid services • Services ignorant of semantics • Services aware of semantics but unable to process them • Services aware of semantics and able to process (part of) them • Everything is OGSA compliant • Defined by • Information model • New entities • Capabilites • New functionalities • Mechanisms • How it is delivered Model provide/ consume expose Capabilities Mechanisms use Edinburgh, 27 November 2006

19. S-OGSA Model METADATAas Semantic Annotations Edinburgh, 27 November 2006

20. 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 -- ... Edinburgh, 27 November 2006

21. S-OGSA Capabilities: From OGSA to S-OGSA Application 1 Application N Security Optimization Data OGSA Execution Management Semantic-OGSA Semantic Services Resource management Information Management Infrastructure Services Edinburgh, 27 November 2006

22. S-OGSA Capabilities: From OGSA to S-OGSA Semantic Provisioning Services Semantic binding Knowledge Metadata Ontology Annotation Reasoning Application 1 Application N Security Optimization Data OGSA Execution Management Semantic-OGSA Semantic Services Resource management Information Management Infrastructure Services Edinburgh, 27 November 2006

23. S-OGSA Patterns. Semantic Aware and Capable Service • Deployed in Globus Toolkit 4 Ontology Service Metadata Service Farm out request 1.1 Properties Lifetime 1 Metadata Seeking Client Access/Query Semantic Bindings Semantics Resource Service Others… Semantic aware interface Edinburgh, 27 November 2006

24. S-OGSA Scenario. Satellite Image Quality Analysis Satellite Routine Operations Scenes: • Routine operations • Metadata generation • Report retrieving 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 Edinburgh, 27 November 2006

25. Outline • Metadata, annotations... What are they and where are they used? • Semantic Annotation Web • Semantic Data (Integration) Web • Semantic Knowledge (Reasoning) Web • Our approach to systematic metadata management • OntoGrid and S-OGSA • The S-OGSA model: Semantic Bindings • S-OGSA capabilities and mechanisms • One S-OGSA scenario of use • Ongoing work • Conclusions Edinburgh, 27 November 2006

26. S-OGSA Metadata Access/Management Protocols Semantic Binding Service Suite create SB Factory create WS-Addressing: epr SB Semantic Binding SB WS-RP: Get/Set/Query Properties query Client SB WS-Notif: Subscribe / Notify RDF Inspect-props . . . WS-RL: Destroy , SetTerminationTime WS-RL ++: archive Query w/o Inference, UpdateContent query Query( over unified view) Metadata Query Edinburgh, 27 November 2006

27. S-OGSA Metadata Lifecycle Stable Stale GE changed KE changed Archived Deleted • 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 situation • Checks needed • Possibly reannotation • Metadata can be archived or deleted from the system “Periodically, we will have to reannotate everything” -- Maryanne Martone (US BIRN) Edinburgh, 27 November 2006

28. Data Integration • Information integration from gLite and GT4 information services • BDII • RGMA • MDS • Trade-off between... • Continuous update or on-demand access, fresh information • Consolidated data but possibly non-fresh information Edinburgh, 27 November 2006

29. Outline • Metadata, annotations... What are they and where are they used? • Semantic Annotation Web • Semantic Data (Integration) Web • Semantic Knowledge (Reasoning) Web • Our approach to systematic metadata management • OntoGrid and S-OGSA • The S-OGSA model: Semantic Bindings • S-OGSA capabilities and mechanisms • One S-OGSA scenario of use • Ongoing work • Conclusions Edinburgh, 27 November 2006

30. Conclusions • Metadata can be used for many purposes • Simply for the sake of annotation • Reuse and sharing  Look at the Web 2.0 success • For integration • Open and flexible schemas. Describe, not prescribe • For reasoning • Complex applications • S-OGSA • Metadata as a first-class citizen  Semantic Binding • Semantic Binding Service already available for use • Robust metadata management • Distributed • Metadata lifecycle Edinburgh, 27 November 2006

31. Access to S-OGSA • Publications • An 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 Distributions • Access to CVS Connection type: pserver user: ontogrid password: not needed Host: rpc262.cs.man.ac.uk Port: 2401 Repository path: /local/ontogrid/cvsroot module: prototype Edinburgh, 27 November 2006

32. 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 Edinburgh, 27 November 2006

33. (Ontology-based) Metadata: What is it, Where and How can we use it, and How can we share it? www.ontogrid.eu Oscar Corcho University of Manchester Oscar.Corcho@manchester.ac.uk National e-Science Centre, Edinburgh 27/11/06