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tidysbml:R/用于将SBML提取到数据框架中的生物导体包

Veronica Paparozzi¹, Christine Nardini¹

¹Institute for Applied Mathematics (IAC) "Mauro Picone", National Research Council (CNR), Rome 00185, Italy.

Bioinformatics advances

|October 16, 2024

概括

tidysbml R包简化了从系统生物学标记语言 (SBML) 文件中提取生物数据,如分区,物种和反应. 这便于使用流行的R包进行网络构建和分析.

科学领域:

系统生物学系统生物学
生物信息学是一种生物信息学.
计算生物学计算生物学

背景情况:

系统生物学标记语言 (SBML) 是一种代表生物化学模型的标准.
从SBML文件中提取数据并将其转换为可用的格式,对于分析来说可能是非常具有挑战性的.
生物网络的构建和分析需要高效的数据处理.

研究的目的:

介绍tidysbml,一个用于从SBML文件中提取数据的R包.
提供一个用户友好的方法来访问分区,物种和反应.
促进定制生物网络的构建和分析.

主要方法:

开发了一个R包,名为tidysbml.ml.
实现了用于解析SBML文档的功能 (高达3级).
在表格结构 (R数据框架) 中输出数据,以方便操作.

主要成果:

成功地从SBML文件中提取分区,物种和反应数据.
生成的表格式数据结构与R的数据处理工具兼容.
从Reactome SBML文件中进行示范数据提取.

结论:

tidysbml简化了从SBML中提取数据,提高了生物信息的可访问性.
该软件包通过与graph和RCy3.3等R软件包的集成支持下游网络分析.
tidysbml为系统生物学研究和定制网络构建提供了有价值的工具.

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