NutriEpiDB: a database for dietary compounds with epigenetic targets

Abstract

Understanding the relationship between dietary compounds and epigenetic mechanisms is central to research in nutrigenomics and human health. Structured datasets that systematically integrate dietary, molecular, and epigenetic information are essential for reproducible and data-driven investigation in this domain. This dataset compiles curated associations between 653 unique dietary compounds, 585 food sources, and 80 epigenetic targets, extracted from 1,963 primary research articles identified through systematic searches in PubMed and Web of Science. Compound identification was performed via large language model-assisted extraction and subsequently standardized using PubChem, RDKit, and semantic clustering procedures. Binding affinity data were incorporated for human proteins with validated epigenetic function, prioritizing records with quantitative measures. Variables are harmonized and annotated using recognized chemical and biological ontologies. This resource supports research on nutriepigenomics, compound–mechanism associations, and food-derived bioactives, enabling hypothesis generation, validation studies, and data mining in nutritional, biomedical, and computational research contexts.