Abstract
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. MW has been constantly evolving; updating its ‘mwTab’ text file format, adding a JavaScript Object Notation (JSON) file format, implementing a REpresentational State Transfer (REST) interface, and nearly quadrupling the number of datasets hosted on the repository within the last three years. In order to keep up with the quickly evolving state of the MW repository, the ‘mwtab’ Python library and package have been continuously updated to mirror the changes in the ‘mwTab’ and JSONized formats and contain many new enhancements including methods for interacting with the MW REST interface, enhanced format validation features, and advanced features for parsing and searching for specific metabolite data and metadata. We used the enhanced format validation features to evaluate all available datasets in MW to facilitate improved curation and FAIRness of the repository. The ‘mwtab’ Python package is now officially released as version 1.0.1 and is freely available on GitHub and the Python Package Index (PyPI) under a Clear Berkeley Software Distribution (BSD) license with documentation available on ReadTheDocs.
Document Type
Article
Publication Date
3-12-2021
Digital Object Identifier (DOI)
https://doi.org/10.3390/metabo11030163
Funding Information
This research was funded by NIH/NIEHS, grant number P42ES007380 (UK Superfund Research Center); NSF, grant number 1419282 (Moseley); NSF, grant number 2020026 (Moseley); and NIH, grant number R03OD030603 (Moseley).
Related Content
The data presented in this study, supplemental materials, scripts used, and version of the updated mwtab Python package used are openly available in FigShare at https://doi.org/10.6084/m9.figshare.12094104.
Repository Citation
Powell, Christian D. and Moseley, Hunter N. B., "The mwtab Python Library for RESTful Access and Enhanced Quality Control, Deposition, and Curation of the Metabolomics Workbench Data Repository" (2021). Markey Cancer Center Faculty Publications. 160.
https://uknowledge.uky.edu/markey_facpub/160
Notes/Citation Information
Published in Metabolites, v. 11, issue 3, 163.
© 2021 by the authors. Licensee MDPI, Basel, Switzerland.
This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).