PubChem 2025 update

• Published in: Nucleic acids research Vol. 53; no. D1; pp. D1516 - D1525
• Main Authors: Kim, Sunghwan, Chen, Jie, Cheng, Tiejun, Gindulyte, Asta, He, Jia, He, Siqian, Li, Qingliang, Shoemaker, Benjamin A, Thiessen, Paul A, Yu, Bo, Zaslavsky, Leonid, Zhang, Jian, Bolton, Evan E
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 06.01.2025
• Subjects: Database Issue; Databases, Chemical; Humans; Internet; Patents as Topic; United States; User-Computer Interface; United States
• ISSN: 0305-1048; 1362-4962; 1362-4962
• DOI: 10.1093/nar/gkae1059

PubChem (https://pubchem.ncbi.nlm.nih.gov) is a large and highly-integrated public chemical database resource at NIH. In the past two years, significant updates were made to PubChem. With additions from over 130 new sources, PubChem contains >1000 data sources, 119 million compounds, 322 million substances and 295 million bioactivities. New interfaces, such as the consolidated literature panel and the patent knowledge panel, were developed. The consolidated literature panel combines all references about a compound into a single list, allowing users to easily find, sort, and export all relevant articles for a chemical in one place. The patent knowledge panels for a given query chemical or gene display chemicals, genes, and diseases co-mentioned with the query in patent documents, helping users to explore relationships between co-occurring entities within patent documents. PubChemRDF was expanded to include the co-occurrence data underlying the literature knowledge panel, enabling users to exploit semantic web technologies to explore entity relationships based on the co-occurrences in the scientific literature. The usability and accessibility of information on chemicals with non-discrete structures (e.g. biologics, minerals, polymers, UVCBs and glycans) were greatly improved with dedicated web pages that provide a comprehensive view of all available information in PubChem for these chemicals.