Introduction: The Metabolomics Workbench Data Repository is a public repository of mass spectrometry and nuclear magnetic resonance data and metadata derived from a wide variety of metabolomics studies. The data and metadata for each study is deposited, stored, and accessed via files in the domain-specific ‘mwTab’ flat file format. Objectives: In order to improve the accessibility, reusability, and interoperability of the data and metadata stored in ‘mwTab’ formatted files, we implemented a Python library and package. This Python package, named ‘mwtab’, is a parser for the domain-specific ‘mwTab’ flat file format, which provides facilities for reading, accessing, and writing ‘mwTab’ formatted files. Furthermore, the package provides facilities to validate both the format and required metadata elements of a given ‘mwTab’ formatted file. Methods: In order to develop the ‘mwtab’ package we used the official ‘mwTab’ format specification. We used Git version control along with Python unit-testing framework as well as continuous integration service to run those tests on multiple versions of Python. Package documentation was developed using sphinx documentation generator. Results: The ‘mwtab’ package provides both Python programmatic library interfaces and command-line interfaces for reading, writing, and validating ‘mwTab’ formatted files. Data and associated metadata are stored within Python dictionary- and list-based data structures, enabling straightforward, ‘pythonic’ access and manipulation of data and metadata. Also, the package provides facilities to convert ‘mwTab’ files into a JSON formatted equivalent, enabling easy reusability of the data by all modern programming languages that implement JSON parsers. The ‘mwtab’ package implements its metadata validation functionality based on a pre-defined JSON schema that can be easily specialized for specific types of metabolomics studies. The library also provides a command-line interface for interconversion between ‘mwTab’ and JSONized formats in raw text and a variety of compressed binary file formats. Conclusions: The ‘mwtab’ package is an easy-to-use Python package that provides FAIRer utilization of the Metabolomics Workbench Data Repository. The source code is freely available on GitHub and via the Python Package Index. Documentation includes a ‘User Guide’, ‘Tutorial’, and ‘API Reference’. The GitHub repository also provides ‘mwtab’ package unit-tests via a continuous integration service.
|State||Published - May 1 2018|
Bibliographical noteFunding Information:
Funding This work was supported in part by the National Science Foundation grant NSF 1252893 (Hunter N.B. Moseley) and the National Institutes of Health grant NIH 1U24DK097215-01A1 (Richard M. Higashi, Teresa W.-M. Fan, Andrew N. Lane, and Hunter N.B. Moseley).
The authors wish to thank Eoin Fahy, Dawn Cotter, and other Metabolomics Workbench staff for providing the official ‘mwTab’ format files specification as well as for the opportunity to provide feedback on ‘mwTab’ files via the MW usability meeting and helpful discussions. Software available at: http://software.cesb.uky.edu , https://github.com/MoseleyBioinformaticsLab/mwtab , https://pypi.org/project/mwtab , http://mwtab.readthedocs.io.
© 2018, The Author(s).
- Data validation
- Metabolomics Workbench
- mwtab Python package
ASJC Scopus subject areas
- Endocrinology, Diabetes and Metabolism
- Clinical Biochemistry