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massDatabase: utilities for the operation of the public compound and pathway database

View ORCID ProfileXiaotao Shen, Chuchu Wang, Michael P. Snyder
doi: https://doi.org/10.1101/2022.06.02.494457
Xiaotao Shen
1Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94304, USA
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  • For correspondence: mpsnyder@stanford.edu
Chuchu Wang
2Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
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Michael P. Snyder
1Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94304, USA
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  • For correspondence: mpsnyder@stanford.edu
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Abstract

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.edu

Supplementary information Supplementary data are available at Bioinformatics online.

Competing Interest Statement

M.S. is a co-founder and member of the scientific advisory boards of the following: Personalis, SensOmics, Filtricine, Qbio, January, Mirvie, and Oralome.

Footnotes

  • https://massdatabase.tidymass.org/

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted June 03, 2022.
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massDatabase: utilities for the operation of the public compound and pathway database
Xiaotao Shen, Chuchu Wang, Michael P. Snyder
bioRxiv 2022.06.02.494457; doi: https://doi.org/10.1101/2022.06.02.494457
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massDatabase: utilities for the operation of the public compound and pathway database
Xiaotao Shen, Chuchu Wang, Michael P. Snyder
bioRxiv 2022.06.02.494457; doi: https://doi.org/10.1101/2022.06.02.494457

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