PathCase: pathways database system.
BACKGROUND
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.


BACKGROUND
Available online at http://nashua.case.edu/pathways
Elliott
Brendan
B
Department of Electrical Engineering and Computer Science, Case Western Reserve University, Cleveland, OH 44106, USA.
Kirac
Mustafa
M
Cakmak
Ali
A
Yavas
Gokhan
G
Mayes
Stephen
S
Cheng
En
E
Wang
Yuan
Y
Gupta
Chirag
C
Ozsoyoglu
Gultekin
G
Meral Ozsoyoglu
Zehra
Z
D003198:Computer Simulation; D016208:Databases, Factual; D053858:Metabolic Networks and Pathways; D012984:Software; D014584:User-Computer Interface