PT  - JOURNAL ARTICLE
AU  - Xiaotao Shen
AU  - Chuchu Wang
AU  - Michael P. Snyder
TI  - <em>massDatabase</em>: utilities for the operation of the public compound and pathway database
AID  - 10.1101/2022.06.02.494457
DP  - 2022 Jan 01
TA  - bioRxiv
PG  - 2022.06.02.494457
4099  - http://biorxiv.org/content/early/2022/06/03/2022.06.02.494457.short
4100  - http://biorxiv.org/content/early/2022/06/03/2022.06.02.494457.full
AB  - Summary One of the major challenges in LC-MS data (metabolome, lipidome, and exposome) 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, containing lots of information about compounds and pathways. However, there is still no tool 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 analysis. 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 Materials.Availability and implementation https://massdatabase.tidymass.org/.Contact shenxt{at}stanford.edu and mpsnyder{at}stanford.eduSupplementary information Supplementary data are available at Bioinformatics online.Competing Interest StatementM.S. is a co-founder and member of the scientific advisory boards of the following: Personalis, SensOmics, Filtricine, Qbio, January, Mirvie, and Oralome.