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This article is part of the supplement: Proceedings of the 11th Annual Bioinformatics Open Source Conference (BOSC) 2010

Open Access Proceedings

SADI, SHARE, and the in silico scientific method

Mark D Wilkinson*, Luke McCarthy, Benjamin Vandervalk, David Withers, Edward Kawas and Soroush Samadian

Author Affiliations

Heart + Lung Institute at St. Paul’s Hospital, University of British Columbia, Vancouver, BC, Canada, V6Z 1Y6

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BMC Bioinformatics 2010, 11(Suppl 12):S7  doi:10.1186/1471-2105-11-S12-S7

Published: 21 December 2010

Abstract

Background

The emergence and uptake of Semantic Web technologies by the Life Sciences provides exciting opportunities for exploring novel ways to conduct in silico science. Web Service Workflows are already becoming first-class objects in “the new way”, and serve as explicit, shareable, referenceable representations of how an experiment was done. In turn, Semantic Web Service projects aim to facilitate workflow construction by biological domain-experts such that workflows can be edited, re-purposed, and re-published by non-informaticians. However the aspects of the scientific method relating to explicit discourse, disagreement, and hypothesis generation have remained relatively impervious to new technologies.

Results

Here we present SADI and SHARE - a novel Semantic Web Service framework, and a reference implementation of its client libraries. Together, SADI and SHARE allow the semi- or fully-automatic discovery and pipelining of Semantic Web Services in response to ad hoc user queries.

Conclusions

The semantic behaviours exhibited by SADI and SHARE extend the functionalities provided by Description Logic Reasoners such that novel assertions can be automatically added to a data-set without logical reasoning, but rather by analytical or annotative services. This behaviour might be applied to achieve the “semantification” of those aspects of the in silico scientific method that are not yet supported by Semantic Web technologies. We support this suggestion using an example in the clinical research space.