Creating interactive, web-based and data-enriched maps with the Systems Biology Graphical Notation
Creating interactive, web-based and data-enriched maps with the Systems Biology Graphical Notation
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DOI：
10.1038/nprot.2012.002
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发表时间：
2012-03-01
期刊：
影响因子：
14.8
通讯作者：
Schreiber, Falk
中科院分区：
文献类型：
--
作者：
Junker, Astrid;Rohn, Hendrik;Schreiber, Falk
系统生物学图形符号（SBGN）是一种用于统一表示生物过程和网络的新兴标准。本文以基因调控和代谢为例，通过手工绘制或使用SBGN- ed工具自动翻译来构建SBGN图谱。此外，本文还讨论了利用不同类型的组学数据来丰富SBGN图谱，以便将数值数据纳入这些网络的背景下，以促进实验数据的解释。最后，将这些地图输出到公共网站，包括可点击的图像，支持科学界的结果交流。关于所描述的功能，其他工具部分与SBGN-ED重叠。然而，目前，SBGN- ed是唯一一个结合了所有这些功能的工具，包括在SBGN中表示、数据映射和网站导出。该协议旨在帮助科学家一步一步地完成整个过程，整个过程大约需要90分钟。
The Systems Biology Graphical Notation (SBGN) is an emerging standard for the uniform representation of biological processes and networks. By using examples from gene regulation and metabolism, this protocol shows the construction of SBGN maps by either manual drawing or automatic translation using the tool SBGN-ED. In addition, it discusses the enrichment of SBGN maps with different kinds of -omics data to bring numerical data into the context of these networks in order to facilitate the interpretation of experimental data. Finally, the export of such maps to public websites, including clickable images, supports the communication of results within the scientific community. With regard to the described functionalities, other tools partially overlap with SBGN-ED. However, currently, SBGN-ED is the only tool that combines all of these functions, including the representation in SBGN, data mapping and website export. This protocol aims to assist scientists with the step-by-step procedure, which altogether takes similar to 90 min.