The nodes and links used to construct this network database were imported from nine public databases, namely, EntrezGene interaction [16], MINT [17], DIP [18], CTD [19], TTD [20], ChemBank [21], PharmGKB [22], OMIM [23], and GAD [24] (Table 1).
Results from BLAST searches against the UniProt database were imported from EST2uni, and GO annotation in Blast2GO was performed with default parameters (E-value threshold of e-6).
The custom legume database contains protein sequences imported from the NCBInr protein database for a range of legumes, including Medicago sativa, M. truncatula, Lotus japonicus, Glycine max, Pisum sativum, Phaseolus vulguris, Lupinus albus and L. luteus (Lei et al. unpublished).
It may be imported from databases using web services such as the Pathway Commons Web Service Client or the WikiPathways Web Service Client [ 31, 32] as a 'simplified binary model' (see Fig. Five in [ 33]) or it may be downloaded directly from the web.
Gene information other than that found in the TAIR database (http://www.arabidopsis.org/) was imported from the SGD (www.yeastgenome.org/) and NCBI (www.ncbi.nlm.nih.gov/) databases.
Resources include raw sequencing chromatograms, contig alignments, text files of both raw and trimmed sequence, BLAST searching of the database, a GO Browser, and annotations imported from BLAST searches against the databases listed in Table 3.
The functional subsets from the molecular signature database or MSigDB GSEA, including modules representing metabolic and signaling pathways imported from online pathway databases such as BioCarta [ 19], signalling pathway database [ 20] and the Kyoto Encyclopedia of Genes and Genomes (KEGG) [ 21].
But all this was trumped when, in making up the page that was to carry the Saturday prize puzzle for 20 August, the wrong puzzle was imported from the database and, instead of No. 25,406 by Brummie, the previous day's No. 25,405 by Araucaria was reprinted in the paper, while the correct puzzle was published on the website.
During method development, these MRM transitions were imported from the database to the MassHunter Data Acquisition program where these transitions were used for screening and confirmation purpose.
The content data are imported from each database.
