The mwtab Python Library for RESTful Access and Enhanced Quality Control, Deposition, and Curation of the Metabolomics Workbench Data Repository

Powell, Christian D.; Moseley, Hunter N. B.

doi:10.3390/metabo11030163

Cited by 13 publications

(20 citation statements)

References 16 publications

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“…Typically, a distinction is made between required, recommended and optional information that data curators of such a file must, should or may include. All of the following formats have in common that they are based on a tabular, human readable and easily inspectable data model, consisting of linked tables that report study and sample metadata, quantities, features, identification details and supporting evidence, either in a single file (mwTab [ 35 ], mzTab and mzTab-M) or as separate files (ISA-Tab [ 36 ]). The generation of report files following these formats is supported by specifications, supplied validation tools and libraries in different programming languages to simplify implementation [ 35 , 37 , 38 , 39 ].…”

Section: Data Standards and Formatsmentioning

confidence: 99%

“…All of the following formats have in common that they are based on a tabular, human readable and easily inspectable data model, consisting of linked tables that report study and sample metadata, quantities, features, identification details and supporting evidence, either in a single file (mwTab [ 35 ], mzTab and mzTab-M) or as separate files (ISA-Tab [ 36 ]). The generation of report files following these formats is supported by specifications, supplied validation tools and libraries in different programming languages to simplify implementation [ 35 , 37 , 38 , 39 ]. First, recommendations for minimum reporting standards for lipidomics mass spectrometry have been published [ 40 ], which align well with the supported metadata in the above-mentioned data formats.…”

Section: Data Standards and Formatsmentioning

confidence: 99%

“…Metabolomics Workbench [ 14 , 35 ] is another repository for metabolomics study metadata and raw MS and NMR data. It uses a single, text-based, tab-separated format (mwTab) and requires MS and NMR data to be provided preferably in mzML, mzXML or CDF formats.…”

Section: Databases Repositories and Other Resourcesmentioning

confidence: 99%

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A Current Encyclopedia of Bioinformatics Tools, Data Formats and Resources for Mass Spectrometry Lipidomics

et al. 2022

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Mass spectrometry is a widely used technology to identify and quantify biomolecules such as lipids, metabolites and proteins necessary for biomedical research. In this study, we catalogued freely available software tools, libraries, databases, repositories and resources that support lipidomics data analysis and determined the scope of currently used analytical technologies. Because of the tremendous importance of data interoperability, we assessed the support of standardized data formats in mass spectrometric (MS)-based lipidomics workflows. We included tools in our comparison that support targeted as well as untargeted analysis using direct infusion/shotgun (DI-MS), liquid chromatography−mass spectrometry, ion mobility or MS imaging approaches on MS1 and potentially higher MS levels. As a result, we determined that the Human Proteome Organization-Proteomics Standards Initiative standard data formats, mzML and mzTab-M, are already supported by a substantial number of recent software tools. We further discuss how mzTab-M can serve as a bridge between data acquisition and lipid bioinformatics tools for interpretation, capturing their output and transmitting rich annotated data for downstream processing. However, we identified several challenges of currently available tools and standards. Potential areas for improvement were: adaptation of common nomenclature and standardized reporting to enable high throughput lipidomics and improve its data handling. Finally, we suggest specific areas where tools and repositories need to improve to become FAIRer.

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Section: Data Standards and Formatsmentioning

confidence: 99%

Section: Data Standards and Formatsmentioning

confidence: 99%

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A Current Encyclopedia of Bioinformatics Tools, Data Formats and Resources for Mass Spectrometry Lipidomics

et al. 2022

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“…Even with minimum standards, deposition quality is a constant issue that hinders FAIRness [41][42][43]. For research data types that have no procedures or minimum standards, these problems are far worse.…”

Section: Background and Summarymentioning

confidence: 99%

A FAIR approach for detecting and sharing PFAS hot-spot areas and water systems

Ojha

Thompson

Powell

et al. 2022

Preprint

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Per- and polyfluoroalkyl substances (PFAS) contamination in water sources near potential PFAS users is well known. Therefore, it is useful for PFAS stakeholders to visualize hot-spot areas and bring attention to the water systems that are near to those areas. Towards this end, we extracted information about PFAS sources, drinking water information, sewer water information, and Source Water Assessment Protection Program (SWAPP) information from publicly available sources to create five different maps in ArcGIS Online that highlight PFAS contamination in relation to potential PFAS users. Following the FAIR (Findable, Accessible, Interoperable and Reusable) principles, we created a Figshare repository that includes all data and associated metadata with these five ArcGIS maps. Moreover, the Figshare repository includes a metadata description of the maps in JSON format that adheres to a draft Minimum Information about Geospatial Information System (MIAGIS) standard we have developed. We hope this MIAGIS draft will assist in establishing a GIS standards group that will develop the draft into a full standard for the wider GIS community. We have also developed a miagis Python package that facilitates the generation of a MIAGIS-compliant JSON metadata file.

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“…With the release of the 1.1.0 version of the mwtab Python package (Powell and Moseley, 2021), the MetabolomicsWB file validation functionality of the package was greatly improved and updated to follow the latest mwTab file format specification. The mwtab package was again used to find formatting errors in mwTab files, undercovering that a majority of the datafiles hosted on MetabolomicsWB have some degree of inconsistency to their file format specification.…”

Section: Introductionmentioning

confidence: 99%

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

Powell

Moseley

2022

Preprint

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Motivation: 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 and to enhance the package's 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. Results: The 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 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. Availability: Metabolomics 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.

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The mwtab Python Library for RESTful Access and Enhanced Quality Control, Deposition, and Curation of the Metabolomics Workbench Data Repository

Cited by 13 publications

References 16 publications

A Current Encyclopedia of Bioinformatics Tools, Data Formats and Resources for Mass Spectrometry Lipidomics

A Current Encyclopedia of Bioinformatics Tools, Data Formats and Resources for Mass Spectrometry Lipidomics

A FAIR approach for detecting and sharing PFAS hot-spot areas and water systems

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

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