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

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

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

P1

S1

O1

P2

S2

P2

O2

• 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}

• 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

Units in seconds

Source: Chong et al. VLDB 2005

• Map relationships to terms using RDF triples
• ‘Mandible’, sameAs’, ‘Jaw’
• ‘Maxilla’, ‘partOf’, ‘Jaw’

• “Find me all DICOM images that contain the term ‘Jaw’”

• Map relationships to terms using RDF triples
• ‘Mandible’, sameAs’, ‘Jaw’
• ‘Maxilla’, ‘partOf’, ‘Jaw’

• “Find me all papers that contain the term ‘Jaw’”

• 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

Source: Stephens et al. J Web Semantics 2006

Source: Stephens et al. J Web Semantics 2006

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

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

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

Image Source: Semantic Technologies Conference 2006

• 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

Molecules to nervous system

Numerous Web resources

Effective data sharing &

integration needed

Disease Focus

Huntingtons

Alzheimers

Parkinsons

• 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

• 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

• 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

• 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