A Major Update and Improved Validation Functionality in the mwtab Python Library and the Metabolomics Workbench File Status Website

P. Travis Thompson; Hunter N.B. Moseley

doi:10.3390/metabo16010076

A Major Update and Improved Validation Functionality in the mwtab Python Library and the Metabolomics Workbench File Status Website

P. Travis Thompson
, Hunter N.B. Moseley

Research output: Contribution to journal › Article › peer-review

1 Scopus citations

Abstract

Background: The Metabolomics Workbench (MW) is a public scientific data repository consisting of experimental data and metadata from metabolomics studies collected with mass spectroscopy (MS) and nuclear magnetic resonance (NMR) analyses. Although not as rapidly as in the past, MW has steadily evolved, updating its mwTab and JSON deposition text file formats and its web-based infrastructure. However, the growth of MW has been exponential since its inception in 2013 and continues to be exponential, with the number of datasets hosted on the repository increasing by 50% since April 2024. As part of regular maintenance to keep up with changes to the mwTab file format and an earnest effort to use MW datasets in meta-analyses, the mwtab Python package has been updated. Methods: Updates include better error handling for batch processing, better parsing to read more files without error, and extensive improvements to the validation capabilities of the package. These updates also required our mwFileStatusWebsite to be updated and improved. Results: We used the enhanced validation features of the mwtab package to evaluate all available datasets in MW to facilitate improved curation, FAIRness of the repository, and reuse for meta-analyses. Conclusions: Version 2.0.0 of the mwtab Python package is now officially released and freely available on GitHub and the Python Package Index (PyPI) under a Clear Berkeley Software Distribution (BSD) license, with documentation available on GitHub. The updated mwFileStatusWebsite is also officially in its 2.0.0 version.

Original language	English
Article number	76
Number of pages	22
Journal	Metabolites
Volume	16
Issue number	1
DOIs	https://doi.org/10.3390/metabo16010076
State	Published - Jan 2026

Bibliographical note

Publisher Copyright:
© 2026 by the authors.

Funding

The National Institutes of Health (NIH) Reform Act of 2006 established the NIH Common Fund to support cross-cutting, trans-NIH programs. The Common Fund’s Metabolomics Program, started in 2012 and supported until 2022, established the Metabolomics Common Fund’s National Metabolomics Data Repository, known as the Metabolomics Workbench (MW), as a longstanding, public repository for national and international metabolomics data and metadata []. This repository consists of experimental data and related metadata for metabolomics studies collected with mass spectroscopy (MS) and nuclear magnetic resonance (NMR) analytical platforms. MW is organized into specific projects, studies, and analyses (experiments). Each analysis can be accessed and downloaded in the mwTab tabular format [] or as JavaScript Object Notation (JSON) formatted files [,], both of which are text-based. MW offers a web interface to search, access, deposit, or download organized metabolomics data and metadata. Additionally, MW offers a REpresentational State Transfer (REST) interface to download and view (meta)data []. Since MW’s establishment in 2013, the repository has grown exponentially, roughly doubling every two to three years. As of 22 October 2025, MW contained a total of 2466 projects, 3795 studies, and 6125 analyses. The authors would like to acknowledge the diligence that Shankar Subramaniam, Eoin Fahy, and the whole MW/UC San Diego team have put into provisioning FAIR access to metabolite studies and their incredible effort in keeping up with the exponential growth of the repository. Metabolomics Workench is funded by NIH (U24-DK141185). This research was funded by NIH/NIEHS, grant number P42ES007380 (UK Superfund Research Center); NSF, grant number 2020026 (PI Moseley); and NIH, grant number 1R03LM014928-01 (PI Moseley).

Funders	Funder number
National Institutes of Health (NIH)
NIH	U24-DK141185
National Institutes of Health/National Institute of Environmental Health Sciences	P42ES007380
National Science Foundation Arctic Social Science Program	1R03LM014928-01, 2020026

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

SDG 3 Good Health and Well-being

Keywords

Python package
data deposition
data validation
metabolomics workbench

ASJC Scopus subject areas

Endocrinology, Diabetes and Metabolism
Biochemistry
Molecular Biology

Access to Document

10.3390/metabo16010076

Cite this

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title = "A Major Update and Improved Validation Functionality in the mwtab Python Library and the Metabolomics Workbench File Status Website",

abstract = "Background: The Metabolomics Workbench (MW) is a public scientific data repository consisting of experimental data and metadata from metabolomics studies collected with mass spectroscopy (MS) and nuclear magnetic resonance (NMR) analyses. Although not as rapidly as in the past, MW has steadily evolved, updating its mwTab and JSON deposition text file formats and its web-based infrastructure. However, the growth of MW has been exponential since its inception in 2013 and continues to be exponential, with the number of datasets hosted on the repository increasing by 50\% since April 2024. As part of regular maintenance to keep up with changes to the mwTab file format and an earnest effort to use MW datasets in meta-analyses, the mwtab Python package has been updated. Methods: Updates include better error handling for batch processing, better parsing to read more files without error, and extensive improvements to the validation capabilities of the package. These updates also required our mwFileStatusWebsite to be updated and improved. Results: We used the enhanced validation features of the mwtab package to evaluate all available datasets in MW to facilitate improved curation, FAIRness of the repository, and reuse for meta-analyses. Conclusions: Version 2.0.0 of the mwtab Python package is now officially released and freely available on GitHub and the Python Package Index (PyPI) under a Clear Berkeley Software Distribution (BSD) license, with documentation available on GitHub. The updated mwFileStatusWebsite is also officially in its 2.0.0 version.",

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author = "Thompson, \{P. Travis\} and Moseley, \{Hunter N.B.\}",

note = "Publisher Copyright: {\textcopyright} 2026 by the authors.",

year = "2026",

month = jan,

doi = "10.3390/metabo16010076",

language = "English",

volume = "16",

number = "1",

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AB - Background: The Metabolomics Workbench (MW) is a public scientific data repository consisting of experimental data and metadata from metabolomics studies collected with mass spectroscopy (MS) and nuclear magnetic resonance (NMR) analyses. Although not as rapidly as in the past, MW has steadily evolved, updating its mwTab and JSON deposition text file formats and its web-based infrastructure. However, the growth of MW has been exponential since its inception in 2013 and continues to be exponential, with the number of datasets hosted on the repository increasing by 50% since April 2024. As part of regular maintenance to keep up with changes to the mwTab file format and an earnest effort to use MW datasets in meta-analyses, the mwtab Python package has been updated. Methods: Updates include better error handling for batch processing, better parsing to read more files without error, and extensive improvements to the validation capabilities of the package. These updates also required our mwFileStatusWebsite to be updated and improved. Results: We used the enhanced validation features of the mwtab package to evaluate all available datasets in MW to facilitate improved curation, FAIRness of the repository, and reuse for meta-analyses. Conclusions: Version 2.0.0 of the mwtab Python package is now officially released and freely available on GitHub and the Python Package Index (PyPI) under a Clear Berkeley Software Distribution (BSD) license, with documentation available on GitHub. The updated mwFileStatusWebsite is also officially in its 2.0.0 version.

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A Major Update and Improved Validation Functionality in the mwtab Python Library and the Metabolomics Workbench File Status Website

Abstract

Bibliographical note

Funding

UN SDGs

Keywords

ASJC Scopus subject areas

Access to Document

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