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Briefings in Bioinformatics Advance Access published online on March 12, 2009
Briefings in Bioinformatics, doi:10.1093/bib/bbp004
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© The Author 2009. Published by Oxford University Press. For Permissions, please email: journals.permissions@oxfordjournals.org

Life sciences on the Semantic Web: the Neurocommons and beyond*

Alan Ruttenberg, Jonathan A. Rees, Matthias Samwald and M. Scott Marshall

Corresponding author. Dr M. Scott Marshall, Informatics Institute, University of Amsterdam, Amsterdam, The Netherlands. Tel: +31(0)20 5257522; Fax: +31(0)20 5257490; E-mail: marshall{at}science.uva.nl

Translational research, the effort to couple the results of basic research to clinical applications, depends on the ability to effectively answer questions using information that spans multiple disciplines. The Semantic Web, with its emphasis on combining information using standard representation languages, access to that information via standard web protocols, and technologies to leverage computation, such as in the form of inference and distributable query, offers a social and technological basis for assembling, integrating and making available biomedical knowledge at Web scale. In this article, we discuss the use of Semantic Web technology for assembling and querying biomedical knowledge from multiple sources and disciplines. We present the Neurocommons prototype knowledge base, a demonstration intended to show the feasibility and benefits of using these technologies. The prototype knowledge base can be used to experiment with and assess the scalability of current tools and methods for creating such a resource, and to elicit issues that will need to be addressed in order to expand the scope and use of it. We demonstrate the utility of the knowledge base by reviewing a few example queries that provide answers to precise questions relevant to the understanding of disease. All components of the knowledge base are freely available at http://neurocommons.org/, enabling readers to reconstruct the knowledge base and experiment with this new technology.

Keywords: Semantic Web, ontology, data integration, life science, medicine, neuroscience

Submitted: September 18, 2008. Received (in revised form): January 14, 2009.


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[Abstract] [Full Text] [PDF]


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