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There are two main contributions of this study: first, it provides a comprehensive analysis of the existing sources of links between two biological databases and the literature, including three sources of curated links and one source of automatically extracted links.
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We interviewed biocurators to obtain workflows from eight biological databases.
GSEA20 was used to analyze whether a previously defined gene sets show statistically significant, concordant differences between two biological states.
Correlation of RPKM distribution between two biological replicates.
The error bars represent standard error between three biological replicates.
Error bars show the standard deviation between three biological replicate cultivations.
Two biological pathway databases were considered, KEGG (http://www.genome.ad.jp/kegg/pathway.html) and BioCarta (http://www.biocarta.com/).
In addition, the index uses synonym databases [2] to cross-reference between various biological databases and the entities on the pathways.
Durinck, S. et al. BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis.
Reproducibility between the two biological replicates was assessed using Pearson correlation and correlation significance (t conversion).
To our knowledge, this is the first study to compare the curation of links between biological databases and literature databases.
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