To conduct the chemoinformatic characterization of the 11 epigenetic-focused data sets, we calculated properties of pharmaceutical interest; molecular scaffolds using the classic and most common method by Bemis-Murcko, and a novel approach to identify core structures and analog series automatically. We also quantify the chemical diversity and synthetic accessibility using whole-molecule structural fingerprints. To explore the distribution of the chemical libraries in chemical space, we generated two complementary and recently introduced visual representations of the chemical space, namely, Constellation Plots and eCSNs. The details of the data sets, their preparation, calculation of the properties, scaffolds, and fingerprints are described in the following sections.