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Applications of Semantic Web Technology in the Life Sciences Susie Stephens Principal Product Manager, Life Sciences, Or

Applications of Semantic Web Technology in the Life Sciences Susie Stephens Principal Product Manager, Life Sciences, Oracle Coordinator BioRDF Subgroup, HCLSIG, W3C susie.stephens@oracle.com. Outline. Oracle’s RDF Data Model Applications of Oracle’s Technology BioRDF Overview and Tasks

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Applications of Semantic Web Technology in the Life Sciences Susie Stephens Principal Product Manager, Life Sciences, Or

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  1. Applications of Semantic Web Technology in the Life Sciences • Susie Stephens • Principal Product Manager, Life Sciences, Oracle • Coordinator BioRDF Subgroup, HCLSIG, W3C • susie.stephens@oracle.com

  2. Outline • Oracle’s RDF Data Model • Applications of Oracle’s Technology • BioRDF Overview and Tasks • Challenges & Future Work

  3. Oracle’s RDF Data Model

  4. P1 S1 O1 P2 S2 P2 O2 Oracle RDF Data Model • Support for RDF and RDFS • Object-relational implementation • Subjects and objects are re-used • Links represent complete RDF triples • RDF Triples: • {S1, P1, O1} • {S1, P2, O2} • {S2, P2, O2}

  5. SPARQL-like Query Capability • A table function allows a graph query to be embedded in a SQL query • Searches for an arbitrary pattern against the RDF data • Includes inferencing based on RDF, RDFS, and user-defined rules

  6. Enterprise Functionality • Real Application Clusters (RAC), Security • Multi-threaded, parallel processing, indexed, etc. • Performance testing with UniProt Units in seconds Source: Chong et al. VLDB 2005

  7. Image Search • Map relationships to terms using RDF triples • ‘Mandible’, sameAs’, ‘Jaw’ • ‘Maxilla’, ‘partOf’, ‘Jaw’ • “Find me all DICOM images that contain the term ‘Jaw’”

  8. Text Search • Map relationships to terms using RDF triples • ‘Mandible’, sameAs’, ‘Jaw’ • ‘Maxilla’, ‘partOf’, ‘Jaw’ • “Find me all papers that contain the term ‘Jaw’”

  9. Data Integration • SQL / RDBMS • Concise, efficient transactions • Transaction metadata is embedded or implicit in the application or database schema • XQuery / XML • Transaction across organizational boundaries • XML wraps the metadata about the transaction around the data • SPARQL / RDF • Information sharing with ultimate flexibility • Enables semantics as well as syntax to be embedded in documents

  10. Applications of Oracle’s Technology

  11. Seamark Navigator Use Case Aggregation of Data Source: Stephens et al. J Web Semantics 2006

  12. Seamark NavigatorUse CaseFaceted Browser Interface Source: Stephens et al. J Web Semantics 2006

  13. Pathways Use CaseMapping Pathway to BioPAX Format Source: http://www.symbionicproject.org/Data/Events/Course_2005/Persico.pdf

  14. Stanford University Use CaseWeb Interface Source: http://pkb.stanford.edu/

  15. Eli Lilly Use Case Source: http://www.olsug.org/wiki/images/d/df/AWL.pdf

  16. University of Texas Health Science Center Use Case Image Source: Semantic Technologies Conference 2006

  17. BioRDF Overview

  18. BioRDF Charter • Build a life sciences demo that spans from bench to bedside using RDF & OWL to help scientist better understand the value of the Semantic Web • Explore the effectiveness of current tools for making data available as RDF • Document our finding to help accelerate the adoption of the Semantic Web by others

  19. Heterogeneous Data Molecules to nervous system Numerous Web resources Effective data sharing & integration needed Disease Focus Huntingtons Alzheimers Parkinsons Neuroscience Focus

  20. The BioRDF Meadow

  21. BioRDF Tasks

  22. Challenges & Future Work

  23. Challenges • Semantic Web & Database communities differ • View that moving to the ‘Semantic Web’ is a huge jump • Lack of awareness that the database can be downloaded for free • Maturity of standards and tools • Assigning URIs to public data sources • Gluing ontologies together • Not much data is available in RDF

  24. Future Work • Continue to enhance Oracle’s products • Explore hybrid approaches • Further work to explore scalability • BioRDF to convert more data sets to RDF • Build the BioRDF demo

  25. Summary • Oracle has a scalable, secure, highly-available RDF Data Model • Oracle continues to enhance technology for the Semantic Web • Many organizations are already using Semantic Web solutions • BioRDF is a community effort to solve many of the challenges

  26. Further Information • Oracle’s Semantic Technologies Web sites • http://www.oracle.com/technology/industries/life_sciences • http://www.oracle.com/technology/tech/semantic_technologies • BioRDF • http://w3.org/2001/sw/hcls • http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup

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