Using Biological Pathway Data with Paxtools

A rapidly growing corpus of formal, computable pathway information can be used to answer important biological questions including finding non-trivial connections between cellular processes, identifying significantly altered portions of the cellular network in a disease state and building predictive models that can be used for precision medicine. Due to its complexity and fragmented nature, however, working with pathway data is still difficult. We present Paxtools, a Java library that contains algorithms, software components and converters for biological pathways represented in the standard BioPAX language. Paxtools allows scientists to focus on their scientific problem by removing technical barriers to access and analyse pathway information. Paxtools can run on any platform that has a Java Runtime Environment and was tested on most modern operating systems. Paxtools is open source and is available under the Lesser GNU public license (LGPL), which allows users to freely use the code in their software systems with a requirement for attribution. Source code for the current release (4.2.0) can be found in Software S1. A detailed manual for obtaining and using Paxtools can be found in Protocol S1. The latest sources and release bundles can be obtained from biopax.org/paxtools.

快速增长的形式化可计算通路信息语料库，可用于解答诸多重要生物学问题：包括挖掘细胞过程间的非平凡关联、识别疾病状态下细胞网络中显著失调的区域，以及构建可应用于精准医学的预测模型。然而，由于通路数据本身兼具复杂性与碎片化特性，其实际应用仍存在诸多障碍。本文介绍Paxtools：一款针对标准BioPAX语言所描述的生物通路，集成了算法、软件组件与格式转换器的Java库。Paxtools可消除通路信息获取与分析的技术壁垒，使科研人员能够专注于核心科学问题的研究。Paxtools可在搭载Java运行时环境（Java Runtime Environment）的任意平台上运行，且已在多数现代操作系统上完成测试验证。Paxtools为开源软件，采用宽通用公共许可证（Lesser GNU Public License, LGPL）进行授权，允许用户在其软件系统中自由使用该代码，但需注明原作者。当前版本（4.2.0）的源代码可在Software S1中获取。关于Paxtools的获取与使用的详细指南，可参见Protocol S1。最新的源代码与发布包可从biopax.org/paxtools获取。