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Bioinformatics Advance Access originally published online on August 26, 2008
Bioinformatics 2008 24(21):2526-2533; 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

Brendan Elliott , Mustafa Kirac *, Ali Cakmak , Gokhan Yavas , Stephen Mayes , En Cheng , Yuan Wang , Chirag Gupta , Gultekin Ozsoyoglu and Zehra Meral Ozsoyoglu

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

*To whom correspondence should be addressed.


  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 article, 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: (i) 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, (ii) an interactive client-side visualization tool for metabolic pathways, with powerful visualization capabilities, and with integrated gene and organism viewers, (iii) 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 (iv) a pathway functionality analysis tool. PathCase is now available for three different datasets, 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: Dmitrij Frishman

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

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