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bioRxiv · 10.1101/2022.03.04.483070

The Metabolomics Workbench File Status Website: A Metadata Repository Promoting FAIR Principles of Metabolomics Data

Powell, C. D.·Moseley, H. N. B.
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Abstract

MotivationAn updated version of the mwtab Python package for programmatic access to the Metabolomics Workbench (MetabolomicsWB) data repository was released at the beginning of 2021. Along with updating the package to match the changes to MetabolomicsWBs mwTab file format and to enhance the packages functionality, the package included format validation facilities which were used to detect and catalog file inconsistencies and errors across all publically available datasets in MetabolomicsWB. ResultsThe Metabolomics Workbench File Status website was developed to provide continuous validation of MetabolomicsWB data files and a useful interface to find all inconsistencies and errors that are found. This list of detectable issues/errors include format parsing errors, format compliance issues, access problems via MetabolomicsWBs REST interface, and other small inconsistencies that can hinder reusability. The website uses the mwtab Python package to pull down and validate each available analysis file and then generates an html report. The website is updated on a weekly basis. Moreover, the Python website design utilizes GitHub and GitHub.io, providing an easy to replicate template for implementing other metadata, virtual, and meta-repositories. AvailabilityMetabolomics Workbench file status website can be accessed at: https://moseleybioinformaticslab.github.io/mwFileStatusWebsite/. The mwtab Python library is available on GitHub: https://github.com/MoseleyBioinformaticsLab/mwtab, PyPI: https://pypi.org/project/mwtab/, and documentation is available on ReadTheDocs: https://mwtab.readthedocs.io/. Metabolomics Workbench analysis data files used for analysis presented here along with the generated HTML files of the website are available on FigShare: https://doi.org/10.6084/m9.figshare.19221159. Contacthunter.moseley@uky.edu Supplementary informationSupplementary data are available at FigShare online.

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Powell, C. D., Moseley, H. N. B.. 2022-03-07. The Metabolomics Workbench File Status Website: A Metadata Repository Promoting FAIR Principles of Metabolomics Data. https://doi.org/10.1101/2022.03.04.483070

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