As for secondary databases, we outline some data sources below that enable researchers to collect information on deal characteristics, acquirer-target relations, outcomes, and integration.
The integration with genome databases such as JGI [ 24], PlantGDB [ 25] and Genbank, as well as cross-links to secondary databases and annotation tools like PlntTFDB [ 26], ProMEX [ 27], Quantprime [ 28], MapMan [ 10] further increases the utility of the ChlamyCyc web-portal.
The InterPro database was chosen for these searches, as it unites secondary databases that contain overlapping information on protein families, domains and functional sites [ 37].
Moreover, as this practice is not documented, it is misleading for the construction of secondary databases such as Bgee based on the primary transcriptome data.
MImerge removes such redundancies by merging interactions from secondary databases such as iRefIndex (16).
The misannotations and errors may perpetuate throughout each new genome, ultimately propagating into secondary databases such as UniProt [ 17] and KEGG [ 46], and domain-specific databases such as PATRIC [ 47].
Moreover, our group has been developing a procedure to enrich secondary databases such as COG [ 12] and KEGG Orthology (to be published) with UniRef50 clusters [ 16] available from UniProt, therefore allowing the inclusion of data from incompletely sequenced genomes.
These tasks are facilitated by large secondary databases such as Genevestigator (Hruz et al., 2008), BioGPS (Wu et al., 2013), the Gene Expression Atlas Kapusheskyy et al., 2010) or Bgee (Bastian et al., 2008) that allow mining of many microarray experiments at the same time.
Hence, secondary databases such as Swiss-Prot (http://www.expasy.ch/sprot/), PFAM (http://pfam.sanger.ac.uk) or KEGG (http://www.genome.ad.jp/kegg), to mention only a few, have been implemented to analyze specific functional aspects and to improve the annotation procedures and results.
