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Metabolomics Workbench

Infrastructure for Metabolomics data, tools and interfaces

Description

The Metabolomics Workbench (MW), supported by the National Institutes of Health, serves as the national and international repository for metabolomics data and metadata and provides analysis tools and access to metabolite standards, protocols, tutorials, training and more. As of August 2022, the National Metabolomics Data Repository (NMDR) contains approximately 2200 MS and NMR studies, the RefMet data resource containing over 163,000 annotated metabolite species (serving as the metabolite standard reference), a curated metabolite database with over 164,000 structures, and a large suite of enhanced and web-interactive tools for analysis. In addition to options for data deposition, user access and tool interfaces and a suite of tools, the MW provides a set of minimal metadata standards. MW also provides a suite of cloud computing tools. MyBinder a free service hosts Jupyter python notebooks to retrieve and analyze data for studies on the Workbench. A total of 17 Notebooks are available.

Technical Information

Download / Web-service link:
Source code repository:
NA
Programming languages:
R,
Javascript,
PHP,
PostGreSQL,
Python,
RShinyApp
Platforms:
Web browser - all,
Cloud-based,
Portable
Output formats:
mwTab,
JSON,
TSV,
CSV,
Molfile,
PDF,
Compressed files
Input formats:
Web forms,
mwTab,
Text tables,
Text files,
PDF,
Excel,
Word,
Compressed files
Web platform:
Yes
CLI:
Yes
GUI:
Yes
License:
GPL
Desktop client:
No

Tasks

2) Lipidomics data repositories
Provide project doi:
Yes
Number of datasets:
1730
Processed data:
Yes
Raw data:
Yes
Experimental metadata:
Yes
Dataset curation:
Yes
Analyses types:
MS,
NMR