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Briefings in Bioinformatics Advance Access published online on May 25, 2007
Briefings in Bioinformatics, doi:10.1093/bib/bbm016
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© The Author 2007. Published by Oxford University Press. For Permissions, please email: journals.permissions@oxfordjournals.org

Improving life sciences information retrieval using semantic web technology

Dennis Quan

Corresponding author. Dennis Quan, IBM, 555 Bailey Avenue, San Jose, CA 95141 USA; E-mail: dennisq{at}us.ibm.com

The ability to retrieve relevant information is at the heart of every aspect of research and development in the life sciences industry. Information is often distributed across multiple systems and recorded in a way that makes it difficult to piece together the complete picture. Differences in data formats, naming schemes and network protocols amongst information sources, both public and private, must be overcome, and user interfaces not only need to be able to tap into these diverse information sources but must also assist users in filtering out extraneous information and highlighting the key relationships hidden within an aggregated set of information. The Semantic Web community has made great strides in proposing solutions to these problems, and many efforts are underway to apply Semantic Web techniques to the problem of information retrieval in the life sciences space. This article gives an overview of the principles underlying a Semantic Web-enabled information retrieval system: creating a unified abstraction for knowledge using the RDF semantic network model; designing semantic lenses that extract contextually relevant subsets of information; and assembling semantic lenses into powerful information displays. Furthermore, concrete examples of how these principles can be applied to life science problems including a scenario involving a drug discovery dashboard prototype called BioDash are provided.

Keywords: Semantic Web, RDF, visualization, BioDash, Haystack, Semantic Web Browser, ontology, information retrieval

Submitted: February 5, 2007. Accepted: April 5, 2007.


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