This study aimed to analyze the recent progress of research on food chemicals and food components acting with epigenetic targets, building a compound database that integrates the information on the chemical structure of food chemicals and other natural products with the epigenetic activity profile. The scientific papers and compound database were analyzed using chemoinformatics, data mining, and visualization approaches to identify the most frequent epigenetic targets and related therapeutic areas associated with food chemicals reported so far, the food chemicals and other natural products most studied, and their epigenetic activity profile. The chemical structure contents, diversity, and coverage in the chemical space of the compounds in the molecular database were evaluated using quantitative methods and data visualization techniques. Since a compound data set's chemical diversity and chemical space depend on the structure representation, we explored the chemical multiverse, e.g., chemical space generated with multiple structure representations. As part of the analysis, we explored the relationships between the chemical structures and the epigenetic activity profile using the structure-property landscapes concept.