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Applications of Semantic Web Technology in the Life Sciences Susie Stephens Principal Product Manager, Life Sciences, Or PowerPoint Presentation
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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, Oracle
  • Coordinator BioRDF Subgroup, HCLSIG, W3C
  • susie.stephens@oracle.com
outline
Outline
  • Oracle’s RDF Data Model
  • Applications of Oracle’s Technology
  • BioRDF Overview and Tasks
  • Challenges & Future Work
oracle rdf data model

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}
sparql like query capability
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
enterprise functionality
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

image search
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’”
text search
Text Search
  • Map relationships to terms using RDF triples
  • ‘Mandible’, sameAs’, ‘Jaw’
  • ‘Maxilla’, ‘partOf’, ‘Jaw’
  • “Find me all papers that contain the term ‘Jaw’”
data integration
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
seamark navigator use case aggregation of data
Seamark Navigator Use Case Aggregation of Data

Source: Stephens et al. J Web Semantics 2006

seamark navigator use case faceted browser interface
Seamark NavigatorUse CaseFaceted Browser Interface

Source: Stephens et al. J Web Semantics 2006

pathways use case mapping pathway to biopax format
Pathways Use CaseMapping Pathway to BioPAX Format

Source: http://www.symbionicproject.org/Data/Events/Course_2005/Persico.pdf

stanford university use case web interface
Stanford University Use CaseWeb Interface

Source: http://pkb.stanford.edu/

eli lilly use case
Eli Lilly Use Case

Source: http://www.olsug.org/wiki/images/d/df/AWL.pdf

university of texas health science center use case
University of Texas Health Science Center Use Case

Image Source: Semantic Technologies Conference 2006

biordf charter
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
neuroscience focus
Heterogeneous Data

Molecules to nervous system

Numerous Web resources

Effective data sharing &

integration needed

Disease Focus

Huntingtons

Alzheimers

Parkinsons

Neuroscience Focus
challenges
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
future work
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
summary
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
further information
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