The mwtab python library for restful access and enhanced quality control, deposition, and curation of the metabolomics workbench data repository

Christian D. Powell; Hunter N.B. Moseley

doi:10.3390/metabo11030163

The mwtab python library for restful access and enhanced quality control, deposition, and curation of the metabolomics workbench data repository

Christian D. Powell, Hunter N.B. Moseley

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

3 Scopus citations

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.

Original language	English
Article number	163
Journal	Metabolites
Volume	11
Issue number	3
DOIs	https://doi.org/10.3390/metabo11030163
State	Published - Mar 2021

Bibliographical note

Funding Information:
Funding: 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).

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).The authors would like to acknowledge the amazing degree of care and effort 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 expanding and maintaining the repository. We have been in regular contact with the MW staff members, and when we have raised issues with errors in specific data files or had questions, they have always promptly responded to resolve the issue, in some instances replying and resolving the issue in less than 12 h.

Publisher Copyright:
© 2021 by the authors. Licensee MDPI, Basel, Switzerland.

Keywords

Data deposition
Data validation
Metabolomics workbench
Python package

ASJC Scopus subject areas

Endocrinology, Diabetes and Metabolism
Biochemistry
Molecular Biology

UN SDGs

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

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10.3390/metabo11030163

Cite this

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title = "The mwtab python library for restful access and enhanced quality control, deposition, and curation of the metabolomics workbench data repository",

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 {\textquoteleft}mwTab{\textquoteright} 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 {\textquoteleft}mwtab{\textquoteright} Python library and package have been continuously updated to mirror the changes in the {\textquoteleft}mwTab{\textquoteright} 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 {\textquoteleft}mwtab{\textquoteright} 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.",

keywords = "Data deposition, Data validation, Metabolomics workbench, Python package",

author = "Powell, {Christian D.} and Moseley, {Hunter N.B.}",

note = "Funding Information: Funding: 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). 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).The authors would like to acknowledge the amazing degree of care and effort 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 expanding and maintaining the repository. We have been in regular contact with the MW staff members, and when we have raised issues with errors in specific data files or had questions, they have always promptly responded to resolve the issue, in some instances replying and resolving the issue in less than 12 h. Publisher Copyright: {\textcopyright} 2021 by the authors. Licensee MDPI, Basel, Switzerland.",

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The mwtab python library for restful access and enhanced quality control, deposition, and curation of the metabolomics workbench data repository

Abstract

Bibliographical note

Keywords

ASJC Scopus subject areas

UN SDGs

Access to Document

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