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The Bioverse API and Web Application

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Computational Systems Biology

Part of the book series: Methods in Molecular Biology ((MIMB,volume 541))

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Abstract

The Bioverse is a framework for creating, warehousing and presenting biological information based on hierarchical levels of organisation. The framework is guided by a deeper philosophy of desiring to represent all relationships between all components of biological systems towards the goal of a wholistic picture of organismal biology. Data from various sources are combined into a single repository and a uniform interface is exposed to access it. The power of the approach of the Bioverse is that, due to its inclusive nature, patterns emerge from the acquired data and new predictions are made. The implementation of this repository (beginning with acquisition of source data, processing in a pipeline, and concluding with storage in a relational database) and interfaces to the data contained in it, from a programmatic application interface to a user friendly web application, are discussed.

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Acknowledgements

We acknowledge the invaluable help in the form of comments, contributions, and critiques of the Bioverse from all members of the Samudrala group and the Department of Microbiology at the University of Washington.

Many researchers have helped in the creation of the Bioverse and Protinfo web servers. We thank the scientific community (more properly attributed in Section 3.2) for making available data and techniques we have used and relied on.

This work was and is currently supported in part by the University of Washington’s Advanced Technology Initiative in Infectious Diseases, Puget Sound Partners in Global Health, NSF CAREER Grant, NSF Grant DBI-0217241, NIH Grant GM068152 and a Searle Scholar Award to Ram Samudrala.

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Authors and Affiliations

  1. Department of Microbiology, University of Washington, Seattle, WA, USA

    Michal Guerquin, Zach Frazier & Ram Samudrala

  2. Computational Biology and Bioinformatics, Pacific Northwest National Laboratory, Richland, WA, USA

    Jason McDermott

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  1. Michal Guerquin
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  3. Zach Frazier
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  4. Ram Samudrala
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    © 2009 Humana Press, a part of Springer Science+Business Media, LLC

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    Guerquin, M., McDermott, J., Frazier, Z., Samudrala, R. (2009). The Bioverse API and Web Application. In: Ireton, R., Montgomery, K., Bumgarner, R., Samudrala, R., McDermott, J. (eds) Computational Systems Biology. Methods in Molecular Biology, vol 541. Humana Press. https://doi.org/10.1007/978-1-59745-243-4_22

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    • DOI: https://doi.org/10.1007/978-1-59745-243-4_22

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    • Publisher Name: Humana Press

    • Print ISBN: 978-1-58829-905-5

    • Online ISBN: 978-1-59745-243-4

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