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. 2025 Jan 6;53(D1):D1516-D1525.
doi: 10.1093/nar/gkae1059.

PubChem 2025 update

Sunghwan Kim  1 , Jie Chen  1 , Tiejun Cheng  1 , Asta Gindulyte  1 , Jia He  1 , Siqian He  1 , Qingliang Li  1 , Benjamin A Shoemaker  1 , Paul A Thiessen  1 , Bo Yu  1 , Leonid Zaslavsky  1 , Jian Zhang  1 , Evan E Bolton  1
Affiliations

PubChem 2025 update

Sunghwan Kim et al. Nucleic Acids Res. .

Abstract

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.

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Figures

Graphical Abstract
Graphical Abstract
Figure 1.
Figure 1.
Number of monthly unique users who visited PubChem. The statistics in this Figure include both interactive and programmatic users.
Figure 2.
Figure 2.
Consolidated References section of the Compound Summary page for dextromethorphan (CID 5360696), accessible at https://pubchem.ncbi.nlm.nih.gov/compound/5360696#section=Consolidated-References.
Figure 3.
Figure 3.
Comparison of the top-3 chemicals listed in the patent and literature knowledge panels (https://pubchem.ncbi.nlm.nih.gov/compound/9875401#section=Chemical-Co-Occurrences-in-Patents) and literature knowledge panel (https://pubchem.ncbi.nlm.nih.gov/compound/9875401#section=Chemical-Co-Occurrences-in-Literature) for rivaroxaban (CID 9875401). The data were retrieved on 1 September 2024.
Figure 4.
Figure 4.
Partial screenshot of the summary page for naphtha, available at https://pubchem.ncbi.nlm.nih.gov/compound/Naphtha (accessed on 1 September 2024).
See this image and copyright information in PMC

References

    1. Kim S., Chen J., Cheng T., Gindulyte A., He J., He S., Li Q., Shoemaker B.A., Thiessen P.A., Yu B.et al.. PubChem 2023 update. Nucleic Acids Res. 2023; 51:D1373–D1380. - PMC - PubMed
    1. Kim S. Exploring chemical information in PubChem. Current Protocols. 2021; 1:e217. - PMC - PubMed
    1. Kim S., Thiessen P.A., Bolton E.E., Chen J., Fu G., Gindulyte A., Han L.Y., He J.E., He S.Q., Shoemaker B.A.et al.. PubChem substance and compound databases. Nucleic Acids Res. 2016; 44:D1202–D1213. - PMC - PubMed
    1. Kim S., Cheng T.J., He S.Q., Thiessen P.A., Li Q.L., Gindulyte A., Bolton E.E.. PubChem protein, gene, pathway, and taxonomy data collections: bridging biology and chemistry through target-centric views of PubChem data. J. Mol. Biol. 2022; 434:167514. - PMC - PubMed
    1. Hähnke V.D., Kim S., Bolton E.E.. PubChem chemical structure standardization. J. Cheminformatics. 2018; 10:36. - PMC - PubMed

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