PathCase: pathways database system

Bioinformatics
Brendan ElliottZehra Meral Ozsoyoglu

Abstract

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. 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. Available o...Continue Reading

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Citations

Dec 17, 2009·Bioinformatics·Ozgun BaburChris Sander
Jun 10, 2010·Bioinformatics·Brian KemperJun'ichi Tsujii
May 13, 2010·Nucleic Acids Research·Alptug DilekUgur Dogrusoz
Apr 20, 2010·Journal of Bioinformatics and Computational Biology·Ali CakmakRichard W Hanson
Sep 8, 2010·BMC Bioinformatics·Donny SohLimsoon Wong
Mar 8, 2008·BMC Bioinformatics·Ali Cakmak, Gultekin Ozsoyoglu
Nov 11, 2011·BMC Systems Biology·Ali CakmakZ Meral Ozsoyoglu
Jun 16, 2012·BMC Systems Biology·Sarp A CoskunZehra Meral Ozsoyoglu
Sep 7, 2013·BMC Systems Biology·Sarp A CoskunGultekin Ozsoyoglu
Jan 1, 2013·Health Information Science and Systems·Stephen R JohnsonGultekin Ozsoyoglu
Jun 24, 2010·Trends in Biotechnology·Sophia AnaniadouDouglas B Kell
May 3, 2015·Nucleic Acids Research·Allison PonDavid S Wishart
Apr 24, 2018·Critical Reviews in Biotechnology·Junhua WangJianping Wen

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