PathCase: pathways database system

被引：30

作者：

Elliott, Brendan ^{[1
]}

Kirac, Mustafa ^{[1
]}

Cakmak, Ali ^{[1
]}

Yavas, Gokhan ^{[1
]}

Mayes, Stephen ^{[1
]}

Cheng, En ^{[1
]}

Wang, Yuan ^{[1
]}

Gupta, Chirag ^{[1
]}

Ozsoyoglu, Gultekin ^{[1
]}

Ozsoyoglu, Zehra Meral ^{[1
]}

机构：

[1] Case Western Reserve Univ, Dept Elect Engn & Comp Sci, Cleveland, OH 44106 USA

来源：

BIOINFORMATICS | 2008年 / 24卷 / 21期

基金：

美国国家科学基金会;

关键词：

D O I：

10.1093/bioinformatics/btn459

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页码：2526 / 2533

页数：8

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