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
Challenges & Future Work
Oracle’s RDF Data Model
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:
P1
S1
O1
P2
S2
P2
• {S1, P1, O1}
• {S1, P2, O2}
O2
• {S2, P2, O2}
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
• 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
“Find me all DICOM images that contain the
term ‘Jaw’”
• Map relationships to
terms using RDF triples
- ‘Mandible’, sameAs’, ‘Jaw’
- ‘Maxilla’, ‘partOf’, ‘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
Applications of Oracle’s
Technology
Seamark Navigator Use Case
Aggregation of Data
Source: Stephens et al. J Web Semantics 2006
Seamark Navigator Use Case
Faceted Browser Interface
Source: Stephens et al. J Web Semantics 2006
Pathways Use Case
Mapping Pathway to BioPAX Format
Source: http://www.symbionicproject.org/Data/Events/Course_2005/Persico.pdf
Stanford University Use Case
Web Interface
Source: http://pkb.stanford.edu/
Eli Lilly Use Case
Source: http://www.olsug.org/wiki/images/d/df/AWL.pdf
University of Texas Health
Science Center Use Case
Image Source: Semantic Technologies Conference 2006
BioRDF Overview
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
The BioRDF Meadow
BioRDF Tasks
Challenges & Future Work
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
•
•
•
•
•
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
• Oracle has a scalable, secure, highlyavailable 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
• 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