The metabolomics workbench file status website: a metadata repository promoting FAIR principles of metabolomics data

BMC Bioinformatics

Software

Christian D. Powell¹  Hunter N. B. Moseley² 

[1] Department of Computer Science (Data Science Program), University of Kentucky, 40506, Lexington, KY, USA;Markey Cancer Center, University of Kentucky, 40506, Lexington, KY, USA;Superfund Research Center, University of Kentucky, 40506, Lexington, KY, USA;Markey Cancer Center, University of Kentucky, 40506, Lexington, KY, USA;Superfund Research Center, University of Kentucky, 40506, Lexington, KY, USA;Department of Molecular and Cellular Biochemistry, University of Kentucky, 40506, Lexington, KY, USA;Institute for Biomedical Informatics, University of Kentucky, 40506, Lexington, KY, USA;

关键词: Metabolomics Workbench;    Validation;    mwtab;    FAIR;    Metadata repository;    Website;   

DOI  :  10.1186/s12859-023-05423-9

 received in 2022-05-19, accepted in 2023-07-18,  发布年份 2023

来源: Springer

【 摘 要 】

BackgroundAn 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 MetabolomicsWB’s ‘mwTab’ file format specification and enhancing the package’s functionality, the included validation facilities were used to detect and catalog file inconsistencies and errors across all publicly available datasets in MetabolomicsWB.ResultsThe MetabolomicsWB File Status website was developed to provide continuous validation of MetabolomicsWB data files and a useful interface to all found inconsistencies and errors. This list of detectable issues/errors include format parsing errors, format compliance issues, access problems via MetabolomicsWB’s 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.ConclusionsThe MetabolomicsWB File Status website provides a metadata repository of validation metadata to promote the FAIR use of existing metabolomics datasets from the MetabolomicsWB data repository.

【 授权许可】

CC BY   
© The Author(s) 2023

【 图 表 】

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