Abstract
Background: An 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. Results: The 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. Conclusions: The 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.
| Original language | English |
|---|---|
| Article number | 299 |
| Journal | BMC Bioinformatics |
| Volume | 24 |
| Issue number | 1 |
| DOIs | |
| State | Published - Dec 2023 |
Bibliographical note
Funding Information:This work has been supported by the National Science Foundation [NSF 1419282 and NSF 2020026 to H.N.B.M.], the NIH National Institute of Environmental Health and Safety [NIH NIEHS P42 ES007380 to University of Kentucky Superfund Research Center], and the National Institute of Health [NIH CF R03OD030603 to H.N.B.M.]. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health nor the National Science Foundation.
Funding Information:
The authors would like to acknowledge the amazing degree of care and effort that Shankar Subramaniam, Eoin Fahy, and the whole MW/UC San Diego team have put into provisioning FAIR access to metabolite studies and their incredible effort in expanding and maintaining the repository. The authors would also like to acknowledge Nicholas Santini for his assistance in designing the HTML and CSS of the Metabolomics Workbench File Status website.
Publisher Copyright:
© 2023, The Author(s).
Keywords
- FAIR
- Metabolomics Workbench
- Metadata repository
- Validation
- Website
- mwtab
ASJC Scopus subject areas
- Structural Biology
- Biochemistry
- Molecular Biology
- Computer Science Applications
- Applied Mathematics