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

Introduction The Metabolomics Workbench Data Repository is a public repository of mass spectrometry and nuclear magnetic resonance data and metadata derived from a wide variety of metabolomics studies. The data and metadata for each study is deposited, stored, and accessed via files in the domain-sp...

Ausführliche Beschreibung

Gespeichert in:
Bibliographische Detailangaben
Veröffentlicht in:Metabolomics Jg. 14; H. 5; S. 64 - 8
Hauptverfasser: Smelter, Andrey, Moseley, Hunter N. B.
Format: Journal Article
Sprache:Englisch
Veröffentlicht: New York Springer US 01.05.2018
Springer Nature B.V
Schlagworte:
Biochemistry
Biomedical and Life Sciences
Biomedicine
Cell Biology
Developmental Biology
Documentation
Integration
Interfaces
Libraries
Life Sciences
Mass spectroscopy
Metabolomics
Metadata
Molecular Medicine
NMR
Nuclear magnetic resonance
Software reviews
Software/Database
Data validation
mwtab Python package
Metabolomics Workbench
FAIR
mwTab
ISSN:1573-3882, 1573-3890
Online-Zugang:Volltext
Tags: Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
Beschreibung
Zusammenfassung:Introduction The Metabolomics Workbench Data Repository is a public repository of mass spectrometry and nuclear magnetic resonance data and metadata derived from a wide variety of metabolomics studies. The data and metadata for each study is deposited, stored, and accessed via files in the domain-specific ‘mwTab’ flat file format. Objectives In order to improve the accessibility, reusability, and interoperability of the data and metadata stored in ‘mwTab’ formatted files, we implemented a Python library and package. This Python package, named ‘mwtab’, is a parser for the domain-specific ‘mwTab’ flat file format, which provides facilities for reading, accessing, and writing ‘mwTab’ formatted files. Furthermore, the package provides facilities to validate both the format and required metadata elements of a given ‘mwTab’ formatted file. Methods In order to develop the ‘mwtab’ package we used the official ‘mwTab’ format specification. We used Git version control along with Python unit-testing framework as well as continuous integration service to run those tests on multiple versions of Python. Package documentation was developed using sphinx documentation generator. Results The ‘mwtab’ package provides both Python programmatic library interfaces and command-line interfaces for reading, writing, and validating ‘mwTab’ formatted files. Data and associated metadata are stored within Python dictionary- and list-based data structures, enabling straightforward, ‘pythonic’ access and manipulation of data and metadata. Also, the package provides facilities to convert ‘mwTab’ files into a JSON formatted equivalent, enabling easy reusability of the data by all modern programming languages that implement JSON parsers. The ‘mwtab’ package implements its metadata validation functionality based on a pre-defined JSON schema that can be easily specialized for specific types of metabolomics studies. The library also provides a command-line interface for interconversion between ‘mwTab’ and JSONized formats in raw text and a variety of compressed binary file formats. Conclusions The ‘mwtab’ package is an easy-to-use Python package that provides FAIRer utilization of the Metabolomics Workbench Data Repository. The source code is freely available on GitHub and via the Python Package Index. Documentation includes a ‘User Guide’, ‘Tutorial’, and ‘API Reference’. The GitHub repository also provides ‘mwtab’ package unit-tests via a continuous integration service.
Bibliographie:ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
content type line 14
content type line 23
ISSN:1573-3882
1573-3890
DOI:10.1007/s11306-018-1356-6