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The human protein database was downloaded as FASTA-formatted sequences from UniProt protein database (released in October, 2016).
Databases The DrugBank database was downloaded in SDF format from http://www.drugbank.ca/.
The database was downloaded on November 20th , 2012and sampling and analyses are conducted on the interventions that were included in the database at that time.
Oxytricha trifallax mitochondrial genomic peptides and bacterial genomes database were downloaded from GenBank as a mapping reference to remove reads which were probably contaminated by mitochondria or bacteria.
The FAERS database was downloaded entirely into an.xml file, then an R script (Additional file 5) was developed to extract the adverse effects data of all approved drugs.
The June 2015 version of the CHEMBL database was downloaded and filtered to retain all compounds containing a benzene ring and with MW < 800 Dalton leading to a dataset with 1,098,971 compounds.
All screening examinations from the PPMI database were downloaded (209 healthy controls, (HC), 448 with Parkinson's disease (PD)), including data acquired from multiple different centres, using the same acquisition settings (see Table 1).
The mouse EST and ncRNA database were downloaded from GenBank.
The human SNP database was downloaded from the NCBI dbSNP database (build 130, released June 2009) [7].
Arabidopsis thaliana RefSeq database was downloaded from the FTP site of The Arabidopsis Information Resources (ftp.arabidopsis.org).org
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com