Visual Analysis of the Web of Linked Data: The S*QL Plugin for Cytoscape
Share this Session:
  Eric Neumann   Eric Neumann
Executive Director
Clinical Semantics Group
    James McGurk
Clinical Scientist
Daiichi Sankyo Pharma Development


Wednesday, June 23, 2010
04:30 PM - 05:00 PM

Level:  Technical - Intermediate

Many applications have been created that interact with RDF: some query RDF via SPARQL endpoints, while others help visualize RDF data. Yet coupling both functions is essential in order to support interactive analytics on RDF content. Furthermore, RDF technologies should attempt to work with existing software that has a large community base. An example of this in the life sciences is the open-source Cytoscape application, which has a strong following and allows scientists to view and analyze complex gene and protein relations via rich graphs.

We describe here the S*QL plug-in technology which extends the Cytoscape architecture to handle RDF querying and visualization by supporting these analytic processes:

  • Query both SPARQL and RDBM (SQL) endpoints
  • Visualize multiple data sources
  • Propose and examine patterns within a single data space
  • Examine implications of selected patterns across multiple displays, data tables
  • Export selections with descriptive (semantic) meta-data
We apply S*QL to pathway data (BioPax) as well as Clinical Trials data.

Eric K. Neumann is Executive Director of the Clinical Semantics Group, a consulting firm that advices on and develops intelligent clinical systems for the pharmaceutical industry based on applications of semantic standards. He has also been the founder and chair of the W3C Semantic Web Healthcare and Life Science Interest Group (HCLSIG), which brings together industry leaders to advance semantic web applications. Dr. Neumann was Global Head of Knowledge Management for Scientific and Medical Affairs within Sanofi-Aventis, which covered all functions of global R&D. In 2005, Dr. Neumann developed BioDash, the first Drug Discovery Semantic Web dashboard, and is currently working on technologies for the rapid mapping of legacy databases onto Enterprise Semantic Infrastructures. Dr. Neumann is an expert in knowledge-based methods for the pharmaceutical industry, going back two decades while at Bolt, Beranek, and Newman. Dr. Neumann holds an S.B. degree from the Massachusetts Institute of Technology, and a PhD in neurobiology and developmental genetics from Case Western Reserve University.

Dr. Jim McGurk is Director of Informatics at Daiichi Sankyo Pharma Development. In his role Jim is responsible for implementing systems for Translational Medicine and Clinical Pharmacology concentrating on platforms for modeling and simulation, pharmacogenomics and biomarker discovery. Jim has more than 15 years of experience as a laboratory scientist and informatician in the pharmaceutical industry. He has a Ph.D. in neuroscience from The Rockefeller University.

Close Window