A collection of molecular formula databases for HERMES

A compilation of different molecule databases ready to be used in HERMES. We have compiled different open-access DBs and adapted their format to the HERMES requisite columns. Since all databases share the "Name" and "MolecularFormula" columns, merges between databases can be easily generated.

More databases and merges will be added in the future. If you have any suggestions or want to contribute, feel free to contact us!

All rights reserved to the original authors of the databases.

Description of the files:

• ECMDB.csv: Entries from E. coli Metabolome Database. 3760 compounds.
• Merge_KEGG_ECMDB.csv: a merge between all metabolites from KEGG pathways associated to E.coli K12 with the ECMDB.csv from above. 6107 compounds.
• Merge_LipidMaps_LipidBlast.csv: a merge between lipid entities from LipidMaps LMSD and the metadata (just Name and Molecular Formula) of LipidBlast entries. 163453 compounds.
• norman.xls: Entries from NORMAN SusDat, containing common and emerging drugs, pollutants, etc. 52019 compounds.
• PubChemLite_31Oct2020.csv Adapted column names from https://zenodo.org/record/4183801. 371,663 compounds related to exposomics.
• MS1_2ID.csv. Merge of HMDB, ChEBI and NORMAN compounds. 183911 compounds related to Human Metabolism, drugs, etc..
• COCONUT_NP.csv: parsed collection of entries from the COlleCtion of Open Natural ProdUcTs (COCONUT).406752 compounds.
• DiTriPeptides.csv: a list of all theoretically possible dipeptides (400) and tripeptides (8000) and their associated molecular formulas. 8400 compounds.