Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.
Bioinformatics. 2011 Dec 15;27(24):3437-8. doi: 10.1093/bioinformatics/btr586. Epub 2011 Oct 21.
BioPAX is a standard language for representing and exchanging models of biological processes at the molecular and cellular levels. It is widely used by different pathway databases and genomics data analysis software. Currently, the primary source of BioPAX data is direct exports from the curated pathway databases. It is still uncommon for wet-lab biologists to share and exchange pathway knowledge using BioPAX. Instead, pathways are usually represented as informal diagrams in the literature. In order to encourage formal representation of pathways, we describe a software package that allows users to create pathway diagrams using CellDesigner, a user-friendly graphical pathway-editing tool and save the pathway data in BioPAX Level 3 format.
The plug-in is freely available and can be downloaded at ftp://ftp.pantherdb.org/CellDesigner/plugins/BioPAX/ CONTACT: huaiyumi@usc.edu
Supplementary data are available at Bioinformatics online.
BioPAX 是一种用于表示和交换分子和细胞水平生物过程模型的标准语言。它被不同的通路数据库和基因组数据分析软件广泛使用。目前，BioPAX 数据的主要来源是经过编目的通路数据库的直接导出。湿实验生物学家仍然不常用 BioPAX 来共享和交换通路知识。相反，通路通常在文献中以非正式的图表表示。为了鼓励对通路进行正式表示，我们描述了一个软件包，允许用户使用 CellDesigner 创建通路图表，CellDesigner 是一个用户友好的图形通路编辑工具，并以 BioPAX Level 3 格式保存通路数据。
该插件是免费提供的，可以从 ftp://ftp.pantherdb.org/CellDesigner/plugins/BioPAX/ 下载。
补充数据可在 Bioinformatics 在线获得。
