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The mwtab Python Library for RESTful Access and Enhanced Quality Control, Deposition, and Curation of the Metabolomics Workbench Data Repository

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, a...

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Detalles Bibliográficos
Autores principales: Powell, Christian D., Moseley, Hunter N.B.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8000456/
https://www.ncbi.nlm.nih.gov/pubmed/33808985
http://dx.doi.org/10.3390/metabo11030163
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author Powell, Christian D.
Moseley, Hunter N.B.
author_facet Powell, Christian D.
Moseley, Hunter N.B.
author_sort Powell, Christian D.
collection PubMed
description 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.
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spelling pubmed-80004562021-03-28 The mwtab Python Library for RESTful Access and Enhanced Quality Control, Deposition, and Curation of the Metabolomics Workbench Data Repository Powell, Christian D. Moseley, Hunter N.B. Metabolites Article 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. MDPI 2021-03-12 /pmc/articles/PMC8000456/ /pubmed/33808985 http://dx.doi.org/10.3390/metabo11030163 Text en © 2021 by the authors. https://creativecommons.org/licenses/by/4.0/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 (http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) ).
spellingShingle Article
Powell, Christian D.
Moseley, Hunter N.B.
The mwtab Python Library for RESTful Access and Enhanced Quality Control, Deposition, and Curation of the Metabolomics Workbench Data Repository
title The mwtab Python Library for RESTful Access and Enhanced Quality Control, Deposition, and Curation of the Metabolomics Workbench Data Repository
title_full The mwtab Python Library for RESTful Access and Enhanced Quality Control, Deposition, and Curation of the Metabolomics Workbench Data Repository
title_fullStr The mwtab Python Library for RESTful Access and Enhanced Quality Control, Deposition, and Curation of the Metabolomics Workbench Data Repository
title_full_unstemmed The mwtab Python Library for RESTful Access and Enhanced Quality Control, Deposition, and Curation of the Metabolomics Workbench Data Repository
title_short The mwtab Python Library for RESTful Access and Enhanced Quality Control, Deposition, and Curation of the Metabolomics Workbench Data Repository
title_sort mwtab python library for restful access and enhanced quality control, deposition, and curation of the metabolomics workbench data repository
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8000456/
https://www.ncbi.nlm.nih.gov/pubmed/33808985
http://dx.doi.org/10.3390/metabo11030163
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