The Integration of Biological Data Using Semantic Web Technologies Susie Stephens Principal Product Manager, Life Sciences Oracle

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Presentation transcript:

The Integration of Biological Data Using Semantic Web Technologies Susie Stephens Principal Product Manager, Life Sciences Oracle

Outline Complexity of Biological Data Oracles RDF Data Model Life Sciences Use Cases

The Complexity of Biological Data

Source: PhRMA & FDA 2003 Pharmaceutical Productivity

RDF Triples in Life Sciences

The Semantic Web Vision Source: Stephens et al. J Web Semantics 2006

Outline Life Sciences Data Oracles RDF Data Model Use Cases

Oracle and RDF: Motivation Customer requests RDF (and OWL) are maturing Oracle supports open standards Complements Oracles information management approaches Ability to leverage existing technologies

Oracle RDF Data Model RDF Triples: {S 1, P 1, O 1 } {S 1, P 2, O 2 } {S 2, P 2, O 2 } S1S1 O1O1 O2O2 S2S2 P2P2 P2P2 P1P1 Support for RDF and RDFS Object-relational implementation Subjects and objects are re-used Links represent complete RDF triples

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

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

Map relationships to terms using RDF triples -Mandible, sameAs, Jaw -Maxilla, partOf, Jaw Image Search Find me all DICOM images that contain the term Jaw

Text Search Find me all papers that contain the term Jaw Map relationships to terms using RDF triples -Mandible, sameAs, Jaw -Maxilla, partOf, Jaw

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

Oracle Database Enterprise Edition 10g Release 2 Download the Database!

Outline Life Sciences Data Oracles RDF Data Model Use Cases

Source: Stanford University Use Case

Source: Eli Lilly Use Case

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

Source: BioRDF

Summary The Semantic Web provides the ability to more easily integrate heterogeneous data Oracle has a scalable, secure, highly- available RDF Data Model Adoption of Semantic Web technologies is accelerating Make your data sharable, make it available in RDF