LCSB Environmental Cheminformatics Group
Published September 17, 2019 | Version YMDB2.0_17092019
Dataset Open

YMDB2.0 MetFrag Local CSV

Authors/Creators

  • 1. LCSB, Uni Luxembourg

Contributors

Related person:

  • 1. LCSB, Uni Luxembourg

Description

This is a local CSV file of YMDB 2.0 (http://www.ymdb.ca/) for MetFrag (https://msbi.ipb-halle.de/MetFrag/).

Data was extracted to CSV from the SDF, with column headers for compulsory fields adjusted to fit the MetFrag format. One entry with no SMILES was filled in using the InChI in OpenBabel; entries with no monoisotopic mass or formula were filled in using functions in RChemMass (https://github.com/schymane/RChemMass/), finally one generic formula (row 746) was replaced with the formula from the InChI. 

This file is for users wanting to integrate the latest YMDB into MetFrag CL workflows (offline), this file will be integrated into MetFrag online; please use the file in the dropdown menu rather than uploading this one.

Notes

Anyone using this resource should also cite the original publications from the Wishart Lab: YMDB 2.0: A Significantly Expanded Version of the Yeast Metabolome Database. Ramirez-Guana M, Marcu A, Pon A, Guo AC, Sajed T, Wishart NA, Karu N, Djoumbou Y, Arndt D and Wishart DS. Nucleic Acids Res. 2017 Jan 4;45(D1):D440-D445. PubMed: 27899612 YMDB: The Yeast Metabolome Database. Jewison T, Neveu V, Lee J, Knox C, Liu P, Mandal R, Murthy RK, Sinelnikov I, Guo AC, Wilson M, Djoumbou Y and Wishart DS. Nucleic Acids Res. 2012 Jan;40(Database ussue):D815-20. PubMed: 22064855

Files

YMDB2_17Sept2019.csv

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Additional details

Related works

Is supplement to
http://www.ymdb.ca/ (URL)
https://msbi.ipb-halle.de/MetFrag/ (URL)
10.1093/nar/gkw1058 (DOI)
10.1093/nar/gkr916 (DOI)