NPBS Atlas: a comprehensive data resource for exploring the biological sources of natural products
Tingjun Xu, Jinfang Dai, Yingyong Li, Junhong Zhou, Yingli Zhao, Wei‐Ming Chen, Xiao‐Song Xue · Journal of Cheminformatics · 2025
Natural products continue to play a pioneering role in drug discovery due to their extraordinary chemical and biological diversity. However, their full therapeutic potential remains largely underutilized, hindered by the fragmented documentation of biological origins in existing data resources. Here, we present natural product and biological source atlas (NPBS Atlas), a data resource covers over 218,000 natural products fully annotated with comprehensive biological sources, bioactivities, and references. The database established through systematic text mining and expert manual curation, places special emphasis on curating source organism data through the information of scientific nomenclature, taxonomic classification, source parts, and the source of Traditional Chinese Medicines. NPBS Atlas represents significant advancement in natural product data resources through its unique content, specialized annotations, and featured data, thereby enabling unprecedented exploration of nature-derived chemical diversity through biological context. The web interface of NPBS Atlas is freely available at https://biochemai.cstspace.cn/npbs/ . Records all major biological sources of natural products, including plants, animals, fungi, and bacteria, with dedicated annotation for marine-derived organisms. Unique documentation of source organisms' parts (e.g., roots, stems, leaves, fruits, etc.) and Traditional Chinese Medicine (TCM) applications—featured data absent in similar resources. More than 14,000 natural products annotated with bioactivities (e.g., cytotoxic, antioxidative, antibacterial, antitumor activities, etc.)—curated therapeutic profiles unavailable in comparable repositories.