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Cited by 1,625

The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.

PubChem 2025 update

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·2025·Nucleic Acids Research
DOI 10.1093/nar/gkae1059
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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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Research works printed but not linked: 49

  1. Kim, 2021, Exploring chemical information in PubChem, Current Protocols, 1, e217, 10.1002/cpz1.217 · DOI
  2. Kim, 2016, PubChem substance and compound databases, Nucleic Acids Res., 44, D1202, 10.1093/nar/gkv951 · DOI · Paper page
  3. Kim, 2022, PubChem protein, gene, pathway, and taxonomy data collections: bridging biology and chemistry through target-centric views of PubChem data, J. Mol. Biol., 434, 167514, 10.1016/j.jmb.2022.167514 · DOI
  4. Hähnke, 2018, PubChem chemical structure standardization, J. Cheminformatics, 10, 36, 10.1186/s13321-018-0293-8 · DOI
  5. Kim, 2019, PubChem 2019 update: improved access to chemical data, Nucleic Acids Res., 47, D1102, 10.1093/nar/gky1033 · DOI · Paper page
  6. Kim, 2021, PubChem in 2021: new data content and improved web interfaces, Nucleic Acids Res., 49, D1388, 10.1093/nar/gkaa971 · DOI · Paper page
  7. Kim, 2018, An update on PUG-REST: RESTful interface for programmatic access to PubChem, Nucleic Acids Res., 46, W563, 10.1093/nar/gky294 · DOI
  8. Kim, 2015, PUG-SOAP and PUG-REST: web services for programmatic access to chemical information in PubChem, Nucleic Acids Res., 43, W605, 10.1093/nar/gkv396 · DOI
  9. Zhao, 2023, NPASS database update 2023: quantitative natural product activity and species source database for biomedical research, Nucleic Acids Res., 51, D621, 10.1093/nar/gkac1069 · DOI
  10. Wishart, 2021, MarkerDB: an online database of molecular biomarkers, Nucleic Acids Res., 49, D1259, 10.1093/nar/gkaa1067 · DOI
  11. International Union of Pure and Applied Chemistry, 1979, Ionisation Constants of Organic Acids in Aqueous Solution
  12. International Union of Pure and Applied Chemistry, 1965, Dissociation Constants of Organic Bases in Aqueous Solution
  13. International Union of Pure and Applied Chemistry, 1972, Dissociation Constants of Organic Bases in Aqueous Solution, Supplement
  14. Wishart, 2015, T3DB: the toxic exposome database, Nucleic Acids Res., 43, D928, 10.1093/nar/gku1004 · DOI
  15. Yang, 2013, Genomics of Drug Sensitivity in Cancer (GDSC): a resource for therapeutic biomarker discovery in cancer cells, Nucleic Acids Res., 41, D955, 10.1093/nar/gks1111 · DOI · Paper page
  16. Shinbo, 2006, KNApSAcK:AComprehensive Species-Metabolite Relationship Database, 165, 10.1007/3-540-29782-0_13 · DOI
  17. Ramirez-Gaona, 2017, YMDB 2.0: A significantly expanded version of the yeast metabolome database, Nucleic Acids Res., 45, D440, 10.1093/nar/gkw1058 · DOI
  18. Kirkwood, 2022, Development and application of multidimensional lipid libraries to investigate lipidomic dysregulation related to smoke inhalation injury severity, J. Proteome Res., 21, 232, 10.1021/acs.jproteome.1c00820 · DOI
  19. Foster, 2022, Uncovering PFAS and other xenobiotics in the dark metabolome using ion mobility spectrometry, mass defect analysis, and machine learning, Environ. Sci. Technol., 56, 9133, 10.1021/acs.est.2c00201 · DOI
  20. Oughtred, 2021, The BioGRID database: a comprehensive biomedical resource of curated protein, genetic, and chemical interactions, Protein Sci., 30, 187, 10.1002/pro.3978 · DOI · Paper page
  21. Salwinski, 2004, The Database of Interacting Proteins: 2004 update, Nucleic Acids Res., 32, D449, 10.1093/nar/gkh086 · DOI · Paper page
  22. Tsherniak, 2017, Defining a cancer dependency map, Cell, 170, 564, 10.1016/j.cell.2017.06.010 · DOI · Paper page
  23. Pontén, 2008, The Human Protein Atlas - a tool for pathology, J. Pathol., 216, 387, 10.1002/path.2440 · DOI
  24. Zahn-Zabal, 2020, The neXtProt knowledgebase in 2020: data, tools and usability improvements, Nucleic Acids Res., 48, D328
  25. del Toro, 2022, The IntAct database: efficient access to fine-grained molecular interaction data, Nucleic Acids Res., 50, D648, 10.1093/nar/gkab1006 · DOI · Paper page
  26. DiStefano, 2022, The gene curation coalition: a global effort to harmonize gene–disease evidence resources, Genet. Med., 24, 1732, 10.1016/j.gim.2022.04.017 · DOI
  27. Bastian, 2021, The Bgee suite: integrated curated expression atlas and comparative transcriptomics in animals, Nucleic Acids Res., 49, D831, 10.1093/nar/gkaa793 · DOI
  28. Ochoa, 2023, The next-generation Open Targets Platform: reimagined, redesigned, rebuilt, Nucleic Acids Res., 51, D1353, 10.1093/nar/gkac1046 · DOI · Paper page
  29. Parr, 2014, The Encyclopedia of Life v2: providing global access to knowledge about life on Earth, Biodiversity Data Journal, 2, e1079, 10.3897/BDJ.2.e1079 · DOI
  30. Baldarelli, 2024, Mouse Genome Informatics: an integrated knowledgebase system for the laboratory mouse, Genetics, 227, iyae031, 10.1093/genetics/iyae031 · DOI
  31. Vedi, 2023, 2022 updates to the Rat Genome Database: A Findable, Accessible, Interoperable, and Reusable (FAIR) resource, Genetics, 224, iyad042, 10.1093/genetics/iyad042 · DOI
  32. Bradford, 2022, Zebrafish information network, the knowledgebase for Danio rerio research, Genetics, 220, iyac016, 10.1093/genetics/iyac016 · DOI · Paper page
  33. Öztürk-Çolak, 2024, FlyBase: updates to the Drosophila genes and genomes database, Genetics, 227, iyad211, 10.1093/genetics/iyad211 · DOI
  34. Wong, 2023, Saccharomyces genome database update: server architecture, pan-genome nomenclature, and external resources, Genetics, 224, iyac191, 10.1093/genetics/iyac191 · DOI
  35. Rutherford, 2024, PomBase: a global core biodata resource—growth, collaboration, and sustainability, Genetics, 227, iyae007, 10.1093/genetics/iyae007 · DOI
  36. Sternberg, 2024, WormBase 2024: status and transitioning to alliance infrastructure, Genetics, 227, iyae050, 10.1093/genetics/iyae050 · DOI
  37. Fisher, 2023, Xenbase: key features and resources of the Xenopus model organism knowledgebase, Genetics, 224, iyad018, 10.1093/genetics/iyad018 · DOI
  38. Kim, 2024, Glycoscience data content in the NCBI Glycans and PubChem, Anal. Bioanal. Chem., 10.1007/s00216-024-05459-7 · DOI
  39. Varki, 2015, Symbol nomenclature for graphical representations of glycans, Glycobiology, 25, 1323, 10.1093/glycob/cwv091 · DOI
  40. Neelamegham, 2019, Updates to the symbol nomenclature for glycans guidelines, Glycobiology, 29, 620, 10.1093/glycob/cwz045 · DOI
  41. Lewis, 2023, Cataloging natural sialic acids and other nonulosonic acids (NulOs), and their representation using the symbol nomenclature for glycans, Glycobiology, 33, 99, 10.1093/glycob/cwac072 · DOI
  42. Alocci, 2019, GlyConnect: glycoproteomics goes visual, interactive, and analytical, J. Proteome Res., 18, 664, 10.1021/acs.jproteome.8b00766 · DOI
  43. Kim, 2016, Literature information in PubChem: associations between PubChem records and scientific articles, J. Cheminformatics, 8, 32, 10.1186/s13321-016-0142-6 · DOI
  44. Knox, 2024, DrugBank 6.0: the DrugBank Knowledgebase for 2024, Nucleic Acids Res., 52, D1265, 10.1093/nar/gkad976 · DOI
  45. Wishart, 2022, HMDB 5.0: the Human Metabolome Database for 2022, Nucleic Acids Res., 50, D622, 10.1093/nar/gkab1062 · DOI
  46. Zaslavsky, 2021, Discovering and summarizing relationships between chemicals, genes, proteins, and diseases in PubChem, Front. Res. Metrics Analyt., 6, 689059, 10.3389/frma.2021.689059 · DOI
  47. Fu, 2015, PubChemRDF: towards the semantic annotation of PubChem compound and substance databases, J. Cheminformatics, 7, 34, 10.1186/s13321-015-0084-4 · DOI
  48. Dumontier, 2014, The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery, J. Biomed. Semantics, 5, 14, 10.1186/2041-1480-5-14 · DOI
  49. Ison, 2013, EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats, Bioinformatics, 29, 1325, 10.1093/bioinformatics/btt113 · DOI

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Metadata

Authors
Kim, S., Chen, J., Cheng, T., Gindulyte, A., He, J., He, S., Li, Q., Shoemaker, B. A., Thiessen, P. A., Yu, B., Zaslavsky, L., Zhang, J., & Bolton, E. E.
Venue
Nucleic Acids Research
Publisher
Oxford University Press (OUP)
Published
2024-11-18
Volume
53
Issue
D1
Pages
D1516-D1525
ISSN
  • 0305-1048
  • 1362-4962
DOI
10.1093/nar/gkae1059
Cited by
1,625
References
2
Language
en
Funders
  • National Center for Biotechnology
  • National Institutes of Health

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CoChat. (2026). Citation check: PubChem 2025 update. https://app.cochat.ai/papers/10.1093/nar/gkae1059
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Kim, S., Chen, J., Cheng, T., Gindulyte, A., He, J., He, S., Li, Q., Shoemaker, B. A., Thiessen, P. A., Yu, B., Zaslavsky, L., Zhang, J., & Bolton, E. E. (2025). PubChem 2025 update. Nucleic Acids Research. https://doi.org/10.1093/nar/gkae1059

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Bibliographic data: Semantic Scholar, OpenAlex, Crossref.

Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).

Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.