The Bioverse API and Web Application

  • Michal Guerquin
  • Jason McDermott
  • Zach Frazier
  • Ram Samudrala
Part of the Methods in Molecular Biology book series (MIMB, volume 541)


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.

Key words

Bioverse framework systems biology proteomics interaction protein structure functional annotation prediction visualization server programming interface data warehouse 



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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Copyright information

© Humana Press, a part of Springer Science+Business Media, LLC 2009

Authors and Affiliations

  • Michal Guerquin
    • 1
  • Jason McDermott
    • 2
  • Zach Frazier
    • 1
  • Ram Samudrala
    • 1
  1. 1.Department of MicrobiologyUniversity of WashingtonSeattleUSA
  2. 2.Computational Biology and BioinformaticsPacific Northwest National LaboratoryRichlandUSA

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