Pathway Tools软件与Reactome软件的比较
A Comparison of the Pathway Tools Software with the Reactome Software
摘要：
本文档比较了SRI的Pathway Tools（PTools）软件与Reactome软件。这两个软件系统服务于途径生物信息学领域，包括代谢途径和信号通路的表示和分析。该比较涵盖了途径生物信息学功能，但不涵盖Reactome软件中完全不存在的Pathway Tools的其他主要方面：Pathway Tools基因组信息学功能，监管信息学功能和基于表格的分析工具（SmartTables）。我们的总体调查结果如下。(1)PTools在基本信息页面上明显领先于Reactome。例如，PTools通路布局算法已经发展到了几十年的高级状态，而Reactome通路布局难以辨认，忽略了重要信息，并且是手动创建的，因此无法扩展到数千个基因组。(2)PTools在组学分析方面远远领先于Reactome。PTools包含Reactome提供的所有omics分析方法，并包含Reactome缺乏的多个方法。(3)PTools包含一个代谢路径搜索工具（搜索通过代谢网络的路径），这是Reactome所缺乏的。(4)PTools在从基因组信息推断代谢途径以创建新的代谢数据库方面明显领先于Reactome。(5)PTools有大量的代谢建模工具，而Reactome没有。(6)PTools比Reactome更具可扩展性，处理18，000个基因组，而Reactome处理90个基因组。(7)PTools拥有比Reactome更大的用户群。PTools为17个网站提供支持，而Reactome只有两个。PTools已获得10，800名用户的许可（Reactome许可用户数未知）。
英文摘要：
This document compares SRI's Pathway Tools (PTools) software with the Reactome software. Both software systems serve the pathway bioinformatics area, including representation and analysis of metabolic pathways and signaling pathways. The comparison covers pathway bioinformatics capabilities, but does not cover other major facets of Pathway Tools that are completely absent from the Reactome software: Pathway Tools genome-informatics capabilities, regulatory informatics capabilities, and table-based analysis tools (SmartTables). Our overall findings are as follows. (1) PTools is significantly ahead of Reactome in its basic information pages. For example, PTools pathway layout algorithms have been developed to an advanced state over several decades, whereas Reactome pathway layouts are illegible, omit important information, and are created manually and therefore cannot scale to thousands of genomes. (2) PTools is far ahead of Reactome in omics analysis. PTools includes all of the omics-analysis methods that Reactome provides, and includes multiple methods that Reactome lacks. (3) PTools contains a metabolic route search tool (searching for paths through the metabolic network), which Reactome lacks. (4) PTools is significantly ahead of Reactome in inference of metabolic pathways from genome information to create new metabolic databases. (5) PTools has an extensive complement of metabolic-modeling tools whereas Reactome has none. (6) PTools is more scalable than Reactome, handling 18,000 genomes versus 90 genomes for Reactome. (7) PTools has a larger user base than Reactome. PTools powers 17 websites versus two for Reactome. PTools has been licensed by 10,800 users (Reactome licensed user count is unknown).
机构、总结、中文摘要均由AI分析而来，可能存在错误，请以论文正文为准。
