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To assess if an annotation value annotates a distinct cluster of conditions or not, we compute the Silhouette value (SV, [ 24]).
In those cases where a given compound-target pair had multiple bioactivity values annotated, the mean value was used.
The standard deviations for the bioactivity values annotated on the same compound-target combination are in less than 2% of the cases higher than two pIC50 units (Additional file 3: Figure S2A), whereas more than 90% of the repeated bioactivities exhibit a standard deviation close to zero (Additional file 3: Figure S2B).
Windows with a coefficient higher than 75% of the maximal value are annotated with a significant period.
During modeling, each UML class, attribute and enumeration value was annotated with a human readable definition of the semantic meaning of that class or attribute.
The average pIC50 value was calculated when multiple IC50 values were annotated on the same compound-target combination.
Reads per kilobase of exon model per million mapped reads (RPKM), as defined by Mortazavi et al. (2008) expression values for annotated genes have been computed by aligning reads against annotated Ensembl 57 transcripts with RazerS (Weese et al., 2009), (see Supplementary Material).
The dataset was extracted from ChEMBL 2. Only compounds tested on rat or human receptors by radio-ligand binding assays and for which p K i bioactivity values were annotated with a '=' relationship were included in the final dataset.
Log 2 transformed expression values were annotated with HUGO symbols.
All missing values were annotated 'NaN'.
Expression values for annotated genes were calculated as RPKM [ 137].
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