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

Area of Science:

• Metabolomics
• Bioinformatics
• Data Science

Background:

• The Metabolomics Workbench Data Repository stores diverse metabolomics data using the 'mwTab' flat file format.
• Accessibility and interoperability of this data are crucial for scientific advancement.

Purpose of the Study:

• To develop a Python package, 'mwtab', for improved accessibility, reusability, and interoperability of 'mwTab' formatted data.
• To provide tools for reading, writing, and validating 'mwTab' files and their associated metadata.

Main Methods:

• Development of the 'mwtab' package based on the official 'mwTab' format specification.
• Utilized Git for version control, Python's unit-testing framework, and continuous integration for testing.
• Package documentation generated using the Sphinx documentation generator.

Main Results:

• The 'mwtab' package offers Python library and command-line interfaces for data manipulation and validation.
• Data and metadata are stored in accessible Python data structures, facilitating easy programmatic access.
• Conversion to JSON format enables interoperability with other programming languages; validation is schema-based.

Conclusions:

• The 'mwtab' package promotes FAIRer data utilization from the Metabolomics Workbench.
• The package is open-source, freely available on GitHub and PyPI, with comprehensive documentation and unit tests.