Metabolomics Workbench: An international repository for metabolomics data and metadata, metabolite standards, protocols, tutorials and training, and analysis tools
By Manish Sud, E. Fahy, Dawn Cotter, K. Azam, Ilango Vadivelu, C. Burant, A. Edison, Oliver Fiehn, R. Higashi, K. S. Nair and 2 more. Nucleic Acids Res., 2015
849 citations recorded by the source corpus.
The Metabolomics Workbench, available at www.metabolomicsworkbench.org, is a public repository for metabolomics metadata and experimental data spanning various species and experimental platforms, metabolite standards, metabolite structures, protocols, tutorials, and training material and other educational resources. It provides a computational platform to integrate, analyze, track, deposit and disseminate large volumes of heterogeneous data from a wide variety of metabolomics studies including mass spectrometry (MS) and nuclear magnetic resonance spectrometry (NMR) data spanning over 20 different species covering all the major taxonomic categories including humans and other mammals, plants, insects, invertebrates and microorganisms. Additionally, a number of protocols are provided for a range of metabolite classes, sample types, and both MS and NMR-based studies, along with a metabolite structure database. The metabolites characterized in the studies available on the Metabolomics Workbench are linked to chemical structures in the metabolite structure database to facilitate comparative analysis across studies. The Metabolomics Workbench, part of the data coordinating effort of the National Institute of Health (NIH) Common Fund's Metabolomics Program, provides data from the Common Fund's Metabolomics Resource Cores, metabolite standards, and analysis tools to the wider metabolomics community and seeks data depositions from metabolomics researchers across the world.
Subfields: Molecular Biology
View Paper: https://www.semanticscholar.org/paper/66af3c4ae4674549790a6b82bbc72464ce2b285c
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Citations in the corpus
- Metabolomics and Multi-Omics Integration: A Survey of Computational Methods and Resources (2020, methodology): “Single-omic repositories include MetaboLights [36] and Metabolomics Workbench [37] for metabolome data, the PRoteomics IDEntifications Database [38] for proteome data, Gene Expression Omnibus [39] and Sequence Read Archive [40] for genomic data, the Encyclopedia of DNA Elements [41] for functional e”
- HMDB 4.0: the human metabolome database for 2018 (2017, background): “(8), MetaboLights (9), the Metabolomics Workbench (10), Lipid Maps (11) and the HMDB (12).”
- Software Tools and Approaches for Compound Identification of LC-MS/MS Data in Metabolomics (2018, methodology): “In fact, very few reports in published research have more than 20% identified compounds in untargeted analysis, as can be seen at the Metabolomics Workbench [30], or the European metabolomics repository MetaboLights [31].”
- MetaboAnalyst 5.0: narrowing the gap between raw spectra and functional insights (2021, methodology): “We have added support to allow users to easily perform analyses on published datasets deposited in the Metabolomics Workbench.”
- NOREVA: normalization and evaluation of MS-based metabolomics data (2017, methodology): “These online pipelines include XCMS (41), MetaboAnalyst (42), Normalyzer (37), MetaDB (43), MetDAT (44), MSPrep (45), Metabolomics Workbench (46) and Workflow4Metabolomics (47).”