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Briefings in Bioinformatics Advance Access published online on December 6, 2008
Briefings in Bioinformatics, doi:10.1093/bib/bbn052
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© The Author 2008. Published by Oxford University Press. For Permissions, please email: journals.permissions@oxfordjournals.org

Building biomedical web communities using a semantically aware content management system

Sudeshna Das, Lisa Girard, Tom Green, Louis Weitzman, Alister Lewis-Bowen and Tim Clark

Corresponding author. Sudeshna Das, Initiative in Innovative Computing, Harvard University, 60 Oxford Street, Cambridge, MA, USA. Tel: +(617) 384-5668; Fax: +(617) 496-0482; E-mail: sudeshna_das{at}harvard.edu

Web-based biomedical communities are becoming an increasingly popular vehicle for sharing information amongst researchers and are fast gaining an online presence. However, information organization and exchange in such communities is usually unstructured, rendering interoperability between communities difficult. Furthermore, specialized software to create such communities at low cost—targeted at the specific common information requirements of biomedical researchers—has been largely lacking. At the same time, a growing number of biological knowledge bases and biomedical resources are being structured for the Semantic Web. Several groups are creating reference ontologies for the biomedical domain, actively publishing controlled vocabularies and making data available in Resource Description Framework (RDF) language. We have developed the Science Collaboration Framework (SCF) as a reusable platform for advanced structured online collaboration in biomedical research that leverages these ontologies and RDF resources. SCF supports structured ‘Web 2.0’ style community discourse amongst researchers, makes heterogeneous data resources available to the collaborating scientist, captures the semantics of the relationship among the resources and structures discourse around the resources. The first instance of the SCF framework is being used to create an open-access online community for stem cell research—StemBook (http://www.stembook.org). We believe that such a framework is required to achieve optimal productivity and leveraging of resources in interdisciplinary scientific research. We expect it to be particularly beneficial in highly interdisciplinary areas, such as neurodegenerative disease and neurorepair research, as well as having broad utility across the natural sciences.

Keywords: Semantic Web, scientific communities, ontology, content management system

Submitted: August 8, 2008. Received (in revised form): October 23, 2008.


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