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.
Highlights
The Metabolomics Workbench (MW) is a public scientific data repository of metabolomics experimental datasets that was established in 2013 [1]
The 1.0.1 release of the ‘mwtab’ package includes a number of new features and changes for both Application Programming Interface (API) and Command-Line Interface (CLI) usage
The 1.0.1 release is available for import via pip from the Python Package Index (PyPI) or can be manually installed from the GitHub repository [9,10]
Summary
The Metabolomics Workbench (MW) is a public scientific data repository of metabolomics experimental datasets that was established in 2013 [1]. The repository consists of experimental data and metadata from metabolomics studies collected with mass spectroscopy (MS) and nuclear magnetic resonance (NMR) technologies. Studies, and experiments (analyses) can be accessed via MW in ‘mwTab’ (text-based files) or JavaScript Object Notation (JSON) formatted files [2,3]. MW offers a web-based interface to analyze, track, deposit, or download data. MW offers a REpresentational State Transfer (REST) interface to download and view data [4]. Over the last three years, the MW repository has continued to quickly grow and contains more than 1000 projects as of November 2020, which can be subdivided into more than 1500 studies and more than 2500 individual analyses. The MW has maintained its ‘mwTab’ file format, consisting of text-based blocks, which use tabs to organize data, and published an updated specification guide at the beginning of 2019
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