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National Metabolomics Data Repository
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StudiesAs of 11/28/20 the National Metabolomics Data Repository (NMDR) contains 1263 publicly available studies. A total of 1532 studies have been processed by the NMDR and the remainder (269) will be made available subject to their embargo dates.
Recently released studies on NMDR
ST001378 - Global metabolomics of COPD2020; Homo sapiens; Seoul National University Hospital
ST001512 - Diel investments in phytoplankton metabolite production influenced by associated heterotrophic bacteria; Thalassiosira pseudonana; University of Georgia
ST001498 - Interday validation of of developed quantatation method; Fecal Bacteria; Helmholtz Centre for Environmental Research - UFZ
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Highlights
November 25, 2020
MetENPWeb: Try MetENPWeb for metabolite class enrichment and species-specific KEGG pathways.
The workflow is also available as an R package from GitHub . Read more on biorxivRefMet Correspondence:
Please read our new RefMet correspondence in Nature Methods
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Lipid Notation in RefMet and lipid m/z calculation tools
View table of over 170 revised lipid abbreviations covered by RefMet, including structure examples and m/z calculation tools for a variety of adducts.
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Convert your metabolite name to standardized nomenclature via RefMet
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Exemplary Studies
A list of exemplary studies are listed here which adhere to the submission guidelines of Metabolomics Workbench. Specifically, publically available studies having all or most of the features below were identified as exemplary studies.
- Well-written study summary
- Detailed metadata for collection/treatment/chromatography/MS/NMR, etc.
- Post-processing details
- Presence of control samples
- Raw data availability for samples and controls
- One-to-one mapping of sample names to raw data file name
- Internal standards (with measurements)
- Clear and organized metabolite annotations
These include different analysis (GC-MS, LC-MS, NMR) and species type. We recommend looking at these studies as a model example before submitting to Metabolomics Workbench.
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Metabolomics News
30-01-2020- Jupyter Notebooks has been released to analyze studies
Analysis of all the studies in Metabolomics workbench can now be done by launching Jupyter Notebooks The notebooks can be launched at Binder. Alternatively, you may download notebooks from Github repository.
- Individual mwTab file for all studies can now be viewed and downloaded as JSON format.
- Jupyter Notebooks has been released to analyze studies
