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The majority of Gemma's datasets is downloaded from the Gene Expression Omnibus (GEO), which provides primarily free text descriptions of data and limited use of controlled vocabularies (Barrett et al., 2007).
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Original structural datasets were downloaded from the File Transfer Protocol (FTP) archive (version: December 2012) of the PDB using the script "rsyncPDB.sh".
Sequence datasets were downloaded and processed as described below.
Normalized data from the Giordano and Jarzab datasets were downloaded from the authors' websites.
All 19 loggers were recovered and full datasets were downloaded successfully from all devices.
Full text datasets were downloaded from PubMed Central (http://www.ncbi.nlm.nih.gov/pmc/about/ftp.html).nih.gov/pmc/about/ftp.html
The first two datasets were downloaded from the researcher's website (http://scsie.uv.es/chipsdna/chipsdna-e.html datos).html datos
The two other datasets were downloaded from the authors' websites: the Giordano dataset (http://dot.ped.med.umich.edu 2000/pub/PPARG/index.html) and the Jarzab dataset (http://www.genomika.pl/thyroidcancer/PTCCancerRes.html).html
Two public microarray datasets were downloaded from the GEO database for comparative studies, the Kim (GSE3438) and the Takeno (GSE15081) datasets.
Large-scale microarray profiling of disease and norm as well as smaller scale datasets were downloaded from Global Expression Omnibus (GEO) platform at NCBI [34].
The Treated and the Untreated datasets were downloaded from Stanford database (http://hivdb.stanford.edu/) [53], selecting only subtype B sequences.
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