massDatabase：用于公共化合物和途径数据库操作的实用程序。
massDatabase: utilities for the operation of the public compound and pathway database.
机构信息
Department of Genetics, Stanford University School of Medicine, Stanford, CA 94304, USA.
Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA.
出版信息
Bioinformatics. 2022 Sep 30;38(19):4650-4651. doi: 10.1093/bioinformatics/btac546.
SUMMARY
One of the major challenges in liquid chromatography coupled to mass spectrometry data is converting many metabolic feature entries to biological function information, such as metabolite annotation and pathway enrichment, which are based on the compound and pathway databases. Multiple online databases have been developed. However, no tool has been developed for operating all these databases for biological analysis. Therefore, we developed massDatabase, an R package that operates the online public databases and combines with other tools for streamlined compound annotation and pathway enrichment. massDatabase is a flexible, simple and powerful tool that can be installed on all platforms, allowing the users to leverage all the online public databases for biological function mining. A detailed tutorial and a case study are provided in the Supplementary Material.
AVAILABILITY AND IMPLEMENTATION
https://massdatabase.tidymass.org/.
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
摘要
在液相色谱-质谱联用数据中，将许多代谢特征条目转换为基于化合物和途径数据库的生物功能信息（如代谢物注释和途径富集）是主要挑战之一。已经开发了多个在线数据库。但是，没有开发用于对所有这些数据库进行生物分析的工具。因此，我们开发了 massDatabase，这是一个 R 包，可用于操作在线公共数据库，并与其他工具结合使用，用于简化化合物注释和途径富集。massDatabase 是一个灵活、简单且功能强大的工具，可以在所有平台上安装，允许用户利用所有在线公共数据库进行生物功能挖掘。在补充材料中提供了详细的教程和案例研究。
可用性和实现
https://massdatabase.tidymass.org/。
补充信息
补充数据可在“Bioinformatics”在线获取。
Zotero 插件