Elliott Brendan, Kirac Mustafa, Cakmak Ali, Yavas Gokhan, Mayes Stephen, Cheng En, Wang Yuan, Gupta Chirag, Ozsoyoglu Gultekin, Meral Ozsoyoglu Zehra
Department of Electrical Engineering and Computer Science, Case Western Reserve University, Cleveland, OH 44106, USA.
Bioinformatics. 2008 Nov 1;24(21):2526-33. doi: 10.1093/bioinformatics/btn459. Epub 2008 Aug 26.
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 online at http://nashua.case.edu/pathways
作为细胞活动的蓝图，生物途径表征了基因组实体在各种细胞机制中的作用，因此，其在网络上的可用性、可操作性和可查询性对于促进正在进行的生物学研究非常重要。
在本文中，我们展示了PathCase的新特性，PathCase是一个用于存储、查询、可视化和分析不同遗传、分子、生化和生物体细节水平的代谢途径的系统。新特性包括：（i）一个具有新架构的基于网络的系统，包含服务器端和客户端，可促进可扩展性，并能灵活轻松地适配不同的途径数据库；（ii）一个用于代谢途径的交互式客户端可视化工具，具有强大的可视化功能，并集成了基因和生物体查看器；（iii）两种不同的查询功能：一个供精通计算机的用户使用的高级查询界面，以及便于使用的内置查询，可直接从途径可视化中发出；（iv）一个途径功能分析工具。PathCase现在可用于三种不同的数据集，即KEGG途径数据、文献中的样本途径和人类的BioCyc途径。
