Powell Christian D, Moseley Hunter N B
Department of Computer Science (Data Science Program), University of Kentucky, Lexington, KY 40506, USA.
Markey Cancer Center, University of Kentucky, Lexington, KY 40506, USA.
Metabolites. 2021 Mar 12;11(3):163. doi: 10.3390/metabo11030163.
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.
代谢组学工作台（MW）是一个公共科学数据存储库，由通过质谱（MS）和核磁共振（NMR）分析收集的代谢组学研究的实验数据和元数据组成。MW一直在不断发展；更新其“mwTab”文本文件格式，添加JavaScript对象表示法（JSON）文件格式，实现代表性状态转移（REST）接口，并且在过去三年中存储库中托管的数据集数量几乎增加了两倍。为了跟上MW存储库快速发展的状态，“mwtab”Python库和包不断更新，以反映“mwTab”和JSON化格式的变化，并包含许多新增强功能，包括与MW REST接口交互的方法、增强的格式验证功能以及用于解析和搜索特定代谢物数据和元数据的高级功能。我们使用增强的格式验证功能来评估MW中所有可用的数据集，以促进存储库更好的管理和实现“可查找、可访问、互操作和可重用（FAIR）”原则。“mwtab”Python包现已正式发布为1.0.1版本，可在GitHub和Python包索引（PyPI）上免费获取，遵循宽松的伯克利软件发布（BSD）许可，文档可在ReadTheDocs上获取。
