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Updated: Sep 2, 2025

A Web Tool for Generating High Quality Machine-readable Biological Pathways
Published on: February 8, 2017
massDatabase: utilities for the operation of the public compound and pathway database
Xiaotao Shen1, Chuchu Wang2, Michael P Snyder1
1Department of Genetics, Stanford University School of Medicine, Stanford, CA 94304, USA.
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.
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