A collection of molecular formula databases for HERMES

<p>A compilation of different molecule databases ready to be used in <a href="https://www.biorxiv.org/content/10.1101/2021.03.08.434466v1">HERMES</a>. We have compiled different open-access&nbsp;DBs and adapted their format to the HERMES requisite columns. Since all databases share the &quot;Name&quot; and &quot;MolecularFormula&quot; columns, merges between databases can be easily generated.</p> <p>More databases and merges will be added in the future. If you have any suggestions or want to contribute, feel free to contact&nbsp;us!</p> <p>All rights reserved to the original authors of the databases.</p> <p>Description of the files:</p> <ul> <li>ECMDB.csv: Entries from&nbsp;<a href="https://ecmdb.ca/"><em>E. coli</em> Metabolome Database</a>. 3760 compounds.</li> <li>Merge_KEGG_ECMDB.csv: a merge between all metabolites from <a href="https://www.genome.jp/kegg/pathway.html">KEGG pathways</a> associated to E.coli K12 with the ECMDB.csv from above. 6107 compounds.</li> <li>Merge_LipidMaps_LipidBlast.csv: a merge between lipid entities from <a href="https://www.lipidmaps.org/resources/databases/index.php">LipidMaps</a>&nbsp;LMSD and the metadata (just Name and Molecular Formula) of <a href="https://fiehnlab.ucdavis.edu/projects/LipidBlast">LipidBlast</a>&nbsp;entries. 163453 compounds.</li> <li>norman.xls: Entries from <a href="https://www.norman-network.com/nds/susdat/susdatSearchShow.php">NORMAN SusDat</a>, containing common and emerging drugs, pollutants, etc. 52019 compounds.</li> <li>PubChemLite_31Oct2020.csv Adapted column names from&nbsp;<a href="https://zenodo.org/record/4183801">https://zenodo.org/record/4183801</a>.&nbsp;371,663 compounds related to exposomics.</li> <li>MS1_2ID.csv. Merge of HMDB, ChEBI and NORMAN compounds. 183911 compounds related to Human Metabolism, drugs, etc..</li> <li>COCONUT_NP.csv: parsed collection of entries from the COlleCtion of Open Natural ProdUcTs (<a href="https://coconut.naturalproducts.net/">COCONUT</a>).406752&nbsp;compounds.</li> <li>DiTriPeptides.csv: a list of all theoretically possible dipeptides&nbsp;(400) and tripeptides (8000) and their associated molecular formulas. 8400 compounds.</li> </ul>