Bioinformatics Research Group, SRI International, Menlo Park, CA 94025, USA.
BMC Bioinformatics. 2011 May 19;12:176. doi: 10.1186/1471-2105-12-176.
Displaying complex metabolic-map diagrams, for Web browsers, and allowing users to interact with them for querying and overlaying expression data over them is challenging.
We present a Web-based metabolic-map diagram, which can be interactively explored by the user, called the Cellular Overview. The main characteristic of this application is the zooming user interface enabling the user to focus on appropriate granularities of the network at will. Various searching commands are available to visually highlight sets of reactions, pathways, enzymes, metabolites, and so on. Expression data from single or multiple experiments can be overlaid on the diagram, which we call the Omics Viewer capability. The application provides Web services to highlight the diagram and to invoke the Omics Viewer. This application is entirely written in JavaScript for the client browsers and connect to a Pathway Tools Web server to retrieve data and diagrams. It uses the OpenLayers library to display tiled diagrams.
This new online tool is capable of displaying large and complex metabolic-map diagrams in a very interactive manner. This application is available as part of the Pathway Tools software that powers multiple metabolic databases including Biocyc.org: The Cellular Overview is accessible under the Tools menu.
为 Web 浏览器显示复杂的代谢图谱，并允许用户与之交互以查询和覆盖表达数据，这是具有挑战性的。
我们提出了一个基于 Web 的代谢图谱，称为“细胞概览”，用户可以通过它进行交互。该应用程序的主要特点是具有缩放用户界面，使用户能够随意关注网络的适当粒度。各种搜索命令可用于直观地突出显示反应、途径、酶、代谢物等的集合。来自单个或多个实验的表达数据可以覆盖在图谱上，我们称之为“组学查看器”功能。该应用程序完全用 JavaScript 编写，用于客户端浏览器，并连接到 Pathway Tools Web 服务器以检索数据和图谱。它使用 OpenLayers 库来显示平铺的图谱。
这个新的在线工具能够以非常交互的方式显示大型和复杂的代谢图谱。该应用程序是 Pathway Tools 软件的一部分，为包括 Biocyc.org 在内的多个代谢数据库提供支持：“细胞概览”可在“工具”菜单下访问。
