CloMet: A Novel Open-Source and Modular Software Platform That Connects Established Metabolomics Repositories and Data Analysis Resources

The field of metabolomics has witnessed the development
of hundreds
of computational tools, but only a few have become cornerstones of
this field. While MetaboLights and Metabolomics Workbench are two
well-established data repositories for metabolomics data sets, Workflows4Metabolomics
and MetaboAnalyst are two well-established web-based data analysis
platforms for metabolomics. Yet, the raw data stored in the aforementioned
repositories lack standardization in terms of the file system format
used to store the associated acquisition files. Consequently, it is
not straightforward to reuse available data sets as input data in
the above-mentioned data analysis resources, especially for non-expert
users. This paper presents CloMet, a novel open-source modular software
platform that contributes to standardization, reusability, and reproducibility
in the metabolomics field. CloMet, which is available through a Docker
file, converts raw and NMR-based metabolomics data from MetaboLights
and Metabolomics Workbench to a file format that can be used directly
either in MetaboAnalyst or in Workflows4Metabolomics. We validated
both CloMet and the output data using data sets from these repositories.
Overall, CloMet fills the gap between well-established data repositories
and web-based statistical platforms and contributes to the consolidation
of a data-driven perspective of the metabolomics field by leveraging
and connecting existing data and resources.