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Bioinformatics Advance Access published online on August 26, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn459
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© The Author (2008). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

PathCase: Pathways Database System

B. Elliott , M. Kirac , A. Cakmak , G. Yavas , S. Mayes , E. Cheng , Y. Wang , C. Gupta , G. Ozsoyoglu and Z.M. Ozsoyoglu

Department of Electrical Engineering and Computer Science Case Western Reserve University, Cleveland, OH 44106, USA

*To whom correspondence should be addressed. Mustafa Kirac, E-mail: kirac{at}case.edu, muskirac{at}gmail.com


  Abstract

Motivation: As the blueprints of cellular actions, biological pathways characterize the roles of genomic entities in various cellular mechanisms, and as such, their availability, manipulation, and queriability over the web is important to facilitate ongoing biological research.

Results: In this paper, we present the new features of PathCase, a system to store, query, visualize and analyze metabolic pathways at different levels of genetic, molecular, biochemical and organismal detail. The new features include: (a) a web-based system with a new architecture, containing a server-side and a client-side, and promoting scalability, and flexible and easy adaptation of different pathway databases, (b) an interactive client-side visualization tool for metabolic pathways, with powerful visualization capabilities, and with integrated gene and organism viewers, (c) two distinct querying capabilities: an advanced querying interface for computer savvy-users, and built-in queries for ease of use, that can be issued directly from pathway visualizations, and (d) a pathway functionality analysis tool. PathCase is now available for three different data sets, namely, KEGG pathways data, sample pathways from the literature, and BioCyc pathways for humans.

Availability: Available online at http://nashua.case.edu/pathways

Contact: pathcase{at}case.edu

Associate Editor: Prof. Dmitrij Frishman

Received on March 6, 2008; revised on July 16, 2008; accepted on August 21, 2008

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