Protocol

Computational Systems Biology

Volume 541 of the series Methods in Molecular Biology pp 535-549

Date:

Computational Representation of Biological Systems

  • Zach FrazierAffiliated withDepartment of Microbiology, University of Washington
  • , Jason McDermottAffiliated withComputational Biology and Bioinformatics, Pacific Northwest National Laboratory
  • , Michal GuerquinAffiliated withDepartment of Microbiology, University of Washington
  • , Ram SamudralaAffiliated withDepartment of Microbiology, University of Washington

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Abstract

Integration of large and diverse biological data sets is a daunting problem facing systems biology researchers. Exploring the complex issues of data validation, integration, and representation, we present a systematic approach for the management and analysis of large biological data sets based on data warehouses. Our system has been implemented in the Bioverse, a framework combining diverse protein information from a variety of knowledge areas such as molecular interactions, pathway localization, protein structure, and protein function.

Key words

Bioverse data integration molecular interactions protein structure protein function data warehouse database bioinformatics