A Python library for FAIRer access and deposition to the Metabolomics Workbench Data Repository

• DOI: 10.1007/s11306-018-1356-6
• Publication Date: 2018-04-20T11:26:26Z
• Authors: Andrey Smelter; Hunter N. B. Moseley
• Keywords: Python; JSON; Workbench; File format

The Metabolomics Workbench Data Repository is a public repository of mass spectrometry and nuclear magnetic resonance data metadata derived from wide variety metabolomics studies. for each study deposited, stored, accessed via files in the domain-specific 'mwTab' flat file format. In order to improve accessibility, reusability, interoperability stored formatted files, we implemented Python library package. This package, named 'mwtab', parser format, which provides facilities reading, accessing, writing files. Furthermore, package validate both format required elements given file. develop 'mwtab' used official specification. We Git version control along with unit-testing framework as well continuous integration service run those tests on multiple versions Python. Package documentation was developed using sphinx generator. programmatic interfaces command-line writing, validating associated are within dictionary- list-based structures, enabling straightforward, 'pythonic' access manipulation metadata. Also, convert into JSON equivalent, easy reusability by all modern programming languages that implement parsers. implements its validation functionality based pre-defined schema can be easily specialized specific types also interface interconversion between JSONized formats raw text compressed binary formats. an easy-to-use FAIRer utilization Repository. source code freely available GitHub Index. Documentation includes 'User Guide', 'Tutorial', 'API Reference'. unit-tests service.