使用 OmniPath 将来自已编辑通路资源的数据导入 Cytoscape。
Bringing data from curated pathway resources to Cytoscape with OmniPath.
机构信息
Faculty of Medicine, Joint Research Centre for Computational Biomedicine (JRC-COMBINE), RWTH Aachen University, Aachen 52074, Germany.
Computer Laboratory, University of Cambridge, CB3 0FD, Cambridge, UK.
出版信息
Bioinformatics. 2020 Apr 15;36(8):2632-2633. doi: 10.1093/bioinformatics/btz968.
SUMMARY
Multiple databases provide valuable information about curated pathways and other resources that can be used to build and analyze networks. OmniPath combines 61 (and continuously growing) network resources into a comprehensive collection, with over 120 000 interactions. We present here the OmniPath App, a Cytoscape plugin to flexibly import data from OmniPath via a simple and intuitive interface. Thus, it makes possible to directly access the large body of high-quality knowledge provided by OmniPath within Cytoscape for inspection and further use with other tools.
AVAILABILITY AND IMPLEMENTATION
The OmniPath App has been developed for Cytoscape 3 in the Java programing language. The latest source code and the plugin can be found at: https://github.com/saezlab/Omnipath_Cytoscape and http://apps.cytoscape.org/apps/omnipath, respectively.
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
摘要
多个数据库提供了有关已整理途径和其他资源的有价值信息，这些信息可用于构建和分析网络。OmniPath 将 61 个（并且在不断增加）网络资源组合成一个全面的集合，其中包含超过 120000 个相互作用。我们在此介绍 OmniPath App，这是 Cytoscape 的一个插件，可通过简单直观的界面从 OmniPath 灵活地导入数据。因此，可以直接在 Cytoscape 中访问 OmniPath 提供的大量高质量知识，并可与其他工具一起进一步使用。
可用性和实现
OmniPath App 是使用 Java 编程语言为 Cytoscape 3 开发的。最新的源代码和插件可分别在以下网址找到：https://github.com/saezlab/Omnipath_Cytoscape 和 http://apps.cytoscape.org/apps/omnipath。
补充信息
补充数据可在 Bioinformatics 在线获取。
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