Tags

Type your tag names separated by a space and hit enter

A Python library for FAIRer access and deposition to the Metabolomics Workbench Data Repository.
Metabolomics. 2018; 14(5):64.M

Abstract

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.

Authors+Show Affiliations

Center for Environmental and Systems Biochemistry, University of Kentucky, Lexington, KY, 40356, USA. andrey.smelter@uky.edu.Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, 40356, USA. hunter.moseley@uky.edu. Markey Cancer Center, University of Kentucky, Lexington, KY, 40356, USA. hunter.moseley@uky.edu. Center for Environmental and Systems Biochemistry, University of Kentucky, Lexington, KY, 40356, USA. hunter.moseley@uky.edu. Institute for Biomedical Informatics, University of Kentucky, Lexington, KY, 40356, USA. hunter.moseley@uky.edu.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

29706851

Citation

Smelter, Andrey, and Hunter N B. Moseley. "A Python Library for FAIRer Access and Deposition to the Metabolomics Workbench Data Repository." Metabolomics : Official Journal of the Metabolomic Society, vol. 14, no. 5, 2018, p. 64.
Smelter A, Moseley HNB. A Python library for FAIRer access and deposition to the Metabolomics Workbench Data Repository. Metabolomics. 2018;14(5):64.
Smelter, A., & Moseley, H. N. B. (2018). A Python library for FAIRer access and deposition to the Metabolomics Workbench Data Repository. Metabolomics : Official Journal of the Metabolomic Society, 14(5), 64. https://doi.org/10.1007/s11306-018-1356-6
Smelter A, Moseley HNB. A Python Library for FAIRer Access and Deposition to the Metabolomics Workbench Data Repository. Metabolomics. 2018;14(5):64. PubMed PMID: 29706851.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - A Python library for FAIRer access and deposition to the Metabolomics Workbench Data Repository. AU - Smelter,Andrey, AU - Moseley,Hunter N B, Y1 - 2018/04/20/ PY - 2017/10/19/received PY - 2018/03/26/accepted PY - 2018/5/1/entrez PY - 2018/5/1/pubmed PY - 2018/5/1/medline KW - Data validation KW - FAIR KW - Metabolomics Workbench KW - mwTab KW - mwtab Python package SP - 64 EP - 64 JF - Metabolomics : Official journal of the Metabolomic Society JO - Metabolomics VL - 14 IS - 5 N2 - 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. SN - 1573-3882 UR - https://www.unboundmedicine.com/medline/citation/29706851/A_Python_library_for_FAIRer_access_and_deposition_to_the_Metabolomics_Workbench_Data_Repository_ L2 - https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/29706851/ DB - PRIME DP - Unbound Medicine ER -
Try the Free App:
Prime PubMed app for iOS iPhone iPad
Prime PubMed app for Android
Prime PubMed is provided
free to individuals by:
Unbound Medicine.