Distilled chemical databases derived from publicly available compound databases for use with ChemDistiller (part of Metaspace).

To use, place HDF5 files to the folder with the chemical databases to be used for ChemDistiller (unpack multivolume zip archives for large databases). ChemDistiller will load them when started - just supply it with the path to the folder with the databases as one of the command line options or place them in the default ChemDistiller DBs folder.

These are not the original compound databases from the Internet, but the re-processed ones. Only the original SMILES and compound IDs were used from the source databases.Fingerprints, Fragprints, InChi strings etc. were generated using either OpenBabel/Pybel or our scripts (see ChemDistiller documentation for details). 

For detailed information about licensing of the source databases please see corresponding websites:

Database	Description	Compound Count	Source URL
BMDB 	 	Bovine metabolome	7,834	http://www.cowmetdb.ca/cgi-bin/browse.cgiChEBI 	 	Chemical Entities of Biological Interest	81,753	https://www.ebi.ac.uk/chebi/DrugBank 	 	Drugs	7,013	https://www.drugbank.ca/ECMDB 	 	E. coli metabolome	3,730	http://ecmdb.ca/EMolecules 	 	Purchasable screening compounds	7,938,551	https://www.emolecules.com/FooDB 	 	Food constituents	22,763	http://foodb.ca/HMDB 	 	Human metabolome	41,758	http://www.hmdb.ca/LipidMaps	 	Lipids	40,228	http://www.lipidmaps.org/MassBank 	 	HQ Mass spectra	11,865	http://www.massbank.jp/?lang=enMINE	\EcoCycMINE	Metabolic in silico network expansion databases	52,864	http://minedatabase.mcs.anl.gov/#/home 	\KEGGMINE		556,666	 
 	\YMDBMINE		98,539	 
PhenolExplorer	\Compounds	Polyphenol contents in food	489	http://phenol-explorer.eu/ 	\Metabolites		366	 
PlantCyc	 	Plant metabolome	50,931	http://www.plantcyc.org/PubChem	 	Compound database	86,963,867	https://pubchem.ncbi.nlm.nih.gov/SMPDB	 	Small molecule pathway database	4,297	http://smpdb.ca/T3DB 	 	Toxins	3,339	http://www.t3db.ca/UNPD	 	Universal natural products database	228,789	http://pkuxxj.pku.edu.cn/UNPD/download.phpYMDB 	 	Yeast metabolome	1,997	http://www.ymdb.ca/Zinc	 	Commercially-available compounds for virtual screening	42,241,167	http://zinc.docking.org/
Currently these databases are for internal use by the Metaspace consortium only before we clear out any possible licensing issues (although there should not be any as the databases used are publicly available).