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Bioinformatics Advance Access originally published online on January 18, 2007
Bioinformatics 2007 23(6):780-782; doi:10.1093/bioinformatics/btl648
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© The Author 2007. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

DataBiNS: a BioMoby-based data-mining workflow for biological pathways and non-synonymous SNPs

Young C. Song {dagger}, Edward Kawas {dagger}, Ben M. Good , Mark D. Wilkinson and Scott J. Tebbutt *

James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research, St. Paul's Hospital, University of British Columbia, Vancouver, V6Z 1Y6, Canada

*To whom correspondence should be addressed.


  Abstract

Summary: DataBiNS is a custom-designed BioMoby Web Service workflow that integrates non-synonymous coding single nucleotide polymorphisms (nsSNPs) data with structure/function and pathway data for the relevant protein. A KEGG Pathway Identifier representing a specific human biological pathway initializes the DataBiNS workflow. The workflow retrieves a list of publications, gene ontology annotations and nsSNP information for each gene involved in the biological pathway. Manual inspection of output data from several trial runs confirms that all expected information is appropriately retrieved by the workflow services. The use of an automated BioMoby workflow, rather than manual ‘surfing’, to retrieve the necessary data, significantly reduces the effort required for functional interpretation of SNP data, and thus encourages more speculative investigation. Moreover, the modular nature of the individual BioMoby Services enables fine-grained reusing of each service in other workflows, thus reducing the effort required to achieve similar investigations in the future.

Availability: The workflow is freely available as a Taverna SCUFL XML document at the iCAPTURE Centre web site, http://www.mrl.ubc.ca/who/who_bios_scott_tebbutt.shtml.

Contact: stebbutt{at}mrl.ubc.ca

Supplementary information: Additional information, including test result data, is available from the iCAPTURE Centre web site (see above).

{dagger}The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.

Associate Editor: Alfonso Valcencia

Received on September 18, 2006; revised on November 16, 2006; accepted on December 18, 2006

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