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