PathCase: pathways database system
PathCase: pathways database system
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DOI：
10.1093/bioinformatics/btn459
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发表时间：
2008-11-01
期刊：
影响因子：
5.8
通讯作者：
Ozsoyoglu, Zehra Meral
中科院分区：
文献类型：
--
作者：
Elliott, Brendan;Kirac, Mustafa;Ozsoyoglu, Zehra Meral
动机：作为细胞活动的蓝图，生物学途径表征了基因组实体在各种细胞机制中的作用，因此，它们在网络上的可用性、操纵性和可查询性对于促进正在进行的生物学研究非常重要。在这篇文章中，我们介绍了PathCase的新功能，PathCase是一个在遗传，分子，生物化学和有机体的细节。新功能包括：（i）具有新架构的基于网络的系统，包括服务器端和客户端，并促进可扩展性，以及不同途径数据库的灵活和容易的适应，（ii）用于代谢途径的交互式客户端可视化工具，具有强大的可视化能力，并具有集成的基因和生物体查看器，（iii）两种不同的查询能力：一个先进的查询界面，为计算机精明的用户，和内置的查询，易于使用，可以直接发出从途径可视化和（iv）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。
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.