LCSB Environmental Cheminformatics Group
Published April 1, 2020 | Version ECMDB2.0_11112019
Dataset Open

ECMDB2.0 MetFrag Local CSV

Authors/Creators

  • 1. LCSB, Uni Luxembourg

Description

This is a local CSV file of ECMDB 2.0 (http://ecmdb.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.

This file is for users wanting to integrate the latest ECMDB 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.

The ECMDB is an expertly curated database containing extensive metabolomic data and metabolic pathway diagrams about Escherichia coli (strain K12, MG1655). This database includes significant quantities of “original” data compiled by members of the Wishart laboratory as well as additional material derived from hundreds of textbooks, scientific journals, metabolic reconstructions and other electronic databases.

Notes

Anyone using this resource should also cite the original publications from the Wishart Lab: (1) Sajed, T., Marcu, A., Ramirez, M., Pon, A., Guo, A., Knox, C., Wilson, M., Grant, J., Djoumbou, Y. and Wishart, D. (2015). ECMDB 2.0: A richer resource for understanding the biochemistry of E. coli. Nucleic Acids Res, p.gkv1060. PMID: 26481353. (2) ECMDB: The E. coli Metabolome Database. Guo AC, Jewison T, Wilson M, Liu Y, Knox C, Djoumbou Y, Lo P, Mandal R, Krishnamurthy R, Wishart DS. Nucleic Acids Res. 2012 Jan;41(Database issue):D625-30. PMID: 23109553

Files

EColiMDB_11Nov2019.csv

Files (1.6 MB)

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md5:0c8e0dfd5b5b2c91510a86fca384abfc
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Additional details

Related works

Is supplement to
http://ecmdb.ca/ (URL)
https://msbi.ipb-halle.de/MetFrag/ (URL)
10.1093/nar/gkv1060 (DOI)
10.1093/nar/gks992 (DOI)