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BSIS: An Experiment in Automating Bioinformatics Tasks Through Intelligent Workflow Construction

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Semantic e-Science

Part of the book series: Annals of Information Systems ((AOIS,volume 11))

Abstract

Existing bioinformatics tools are extremely difficult to integrate and inter-operate, because of the diversity of service deployment techniques and the representational heterogeneity of biological data they are interacting with. This chapter presents the BioService Integration System (BSIS), a general framework which provides a graphic-based workflow language. The language enables the description of workflows composed of abstract semantic Web services and references to biologically relevant data. The workflows constructed in BSIS can be instantiated through automated planning techniques and automatically executed by adapting the Web Service Integration Framework (WSIF). A prototype implementation of the system is presented to demonstrate the effectiveness and efficiency of the approach.

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Notes

  1. 1.

    This distinction will be explained in detail later in the chapter, when we discuss the workflow language.

  2. 2.

    Project home: http://www.jgraph.org.

  3. 3.

    A fluent is a proposition whose truth value can change over time.

  4. 4.

    Indeed, this is the internal representation of a workflow used in our system.

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Acknowledgments

The authors would like to thank the anonymous reviewers for their insightful comments. The authors wish to thank the following researchers for helping in different stages of this project: Gopal Gupta, Arlin Stoltzfus, Julie Thompson, Francisco Prosdocimi, Brook Milligan, Tu Phan, and Samat Jain.

The research has been partially supported by NSF grants IIS-0812267, HRD-0420407, and CNS-0220590.

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Authors and Affiliations

  1. Department of Computer Science, New Mexico State University, Las Cruces, NM, USA

    Yu Pan, Enrico Pontelli & Son Cao Tran

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  1. Yu Pan
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  2. Enrico Pontelli
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  3. Son Cao Tran
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Correspondence to Yu Pan .

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Editors and Affiliations

  1. College of Computer Science, Zhejiang University, Zheda Road 38, Hangzhou, 310058, China, People's Republic

    Huajun Chen

  2. Drug Discovery Pte Ltd., Lilly Singapore Centre for, Biomedical Grove 8A, Singapore, 138648, Singapore

    Yimin Wang

  3. Center for Medical Informatics, Yale University School of Medicine, Cedar St. 333, New Haven, 06520-8009, Connecticut, USA

    Kei-Hoi Cheung

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Pan, Y., Pontelli, E., Tran, S.C. (2010). BSIS: An Experiment in Automating Bioinformatics Tasks Through Intelligent Workflow Construction. In: Chen, H., Wang, Y., Cheung, KH. (eds) Semantic e-Science. Annals of Information Systems, vol 11. Springer, Boston, MA. https://doi.org/10.1007/978-1-4419-5908-9_6

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