HCLSIG BioRDF Subgroup/Meetings/2006-01-26 BioRDF at F2F

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Seeding the Semantic Web

Date: January 26, 2006

Participants: Olivier Bodenreider, Kei Cheung, Roger Cutler, Brian Gilman, Joanne Luciano, Brian Osborne, Alan Ruttenburg, Matt Shanahan, Susie Stephens, Charles Tilford.

Project Goal: To build a life sciences demo using RDF and OWL to get a stronger understanding as to the work required, to explore the effectiveness of current tools, and to document our finding to help accelerate the adoption of the Semantic Web by others.


  • The demo will primarily take advantage of data sets from the NCBI. However, additional data sets will be required with time as the ultimate goal is to build a demo that spans from ‘bench to bedside’.
  • The demo will focus on the domain area of neuroscience, in order to be able to build upon the ongoing work in Scientific Commons and SWANS.
  • The main focus of the demo is on the integration of many data sets, although scalability is also of interest.

Stage 1 (3 month goals)

  • Identify the initial data sources to be used in the demo.
  • Explore additional data sources that would be required for the demo to span ‘bench to bedside’.
  • Learn about GRDDL, SPARQL, OWL, etc.
  • Increase knowledge of neuroscience.
  • Set up a Wiki for communication.

Stage 2 (6 months goals)

  • Transform data into RDF from Word, Excel, XML, Relational, etc.
  • Analysis of semantic requirements (connect to ontology sub-group).
  • Move from screen scraping to an API.
  • Create documents that describe work undertaken, and observations.

Stage 3 (12 months goals)

  • Use ontologies with the demo.
  • Answer scientific questions and hopefully glean new scientific insights through using the demo.
  • Validate the effectiveness of the data integration.