PathCase: Pathways database system

  • Elliott B
  • Kirac M
  • Cakmak A
 et al. 
  • 50


    Mendeley users who have this article in their library.
  • 32


    Citations of this article.


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

Get free article suggestions today

Mendeley saves you time finding and organizing research

Sign up here
Already have an account ?Sign in

Find this document


  • Ali CakmakIstanbul Sehir Universitesi

  • Brendan Elliott

  • Mustafa Kirac

  • Gokhan Yavas

  • Stephen Mayes

  • En Cheng

Cite this document

Choose a citation style from the tabs below

Save time finding and organizing research with Mendeley

Sign up for free