PubChem 2023 Update

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2022 Oct 28

PMID 36305812

Authors

Sunghwan Kim

Jie Chen

Tiejun Cheng

Asta Gindulyte

Jia He

Siqian He

Qingliang Li

Benjamin A Shoemaker

Paul A Thiessen

Bo Yu

Leonid Zaslavsky

Jian Zhang

Evan E Bolton

Affiliations

Soon will be listed here.

Abstract

PubChem (https://pubchem.ncbi.nlm.nih.gov) is a popular chemical information resource that serves a wide range of use cases. In the past two years, a number of changes were made to PubChem. Data from more than 120 data sources was added to PubChem. Some major highlights include: the integration of Google Patents data into PubChem, which greatly expanded the coverage of the PubChem Patent data collection; the creation of the Cell Line and Taxonomy data collections, which provide quick and easy access to chemical information for a given cell line and taxon, respectively; and the update of the bioassay data model. In addition, new functionalities were added to the PubChem programmatic access protocols, PUG-REST and PUG-View, including support for target-centric data download for a given protein, gene, pathway, cell line, and taxon and the addition of the 'standardize' option to PUG-REST, which returns the standardized form of an input chemical structure. A significant update was also made to PubChemRDF. The present paper provides an overview of these changes.

Citing Articles

Foundation models in bioinformatics.

Guo F, Guan R, Li Y, Liu Q, Wang X, Yang C Natl Sci Rev. 2025; 12(4):nwaf028.

PMID: 40078374 PMC: 11900445. DOI: 10.1093/nsr/nwaf028.

Identification of Systemic Drug Targets for Anti-cavernous Fibrosis in the Treatment of Erectile Dysfunction, Guided by Genome-Wide Mendelian Randomization.

Chen Z, Wang Q, Zhang L, Qiu J, Zeng Y, Kuang H Am J Mens Health. 2025; 19(2):15579883251323187.

PMID: 40077914 PMC: 11905014. DOI: 10.1177/15579883251323187.

Drug-Checking and Monitoring New Psychoactive Substances: Identification of the U-48800 Synthetic Opioid Using Mass Spectrometry, Nuclear Magnetic Resonance Spectroscopy, and Bioinformatic Tools.

Pereira M, Familia C, Martins D, Cunha M, Dias M, Neng N Int J Mol Sci. 2025; 26(5).

PMID: 40076839 PMC: 11900529. DOI: 10.3390/ijms26052219.

Targeting Glucosylceramide Synthase: Innovative Drug Repurposing Strategies for Lysosomal Diseases.

Canini G, Mazzinelli E, Nocca G, Lattanzi W, Arcovito A Int J Mol Sci. 2025; 26(5).

PMID: 40076817 PMC: 11900012. DOI: 10.3390/ijms26052195.

Predictions of the Biological Effects of the Main Components of Tarragon Essential Oil.

Pujicic A, Popescu I, Dascalu D, Petreus D, Isvoran A Int J Mol Sci. 2025; 26(5).

PMID: 40076487 PMC: 11899843. DOI: 10.3390/ijms26051860.

References

Schoch C, Ciufo S, Domrachev M, Hotton C, Kannan S, Khovanskaya R . NCBI Taxonomy: a comprehensive update on curation, resources and tools. Database (Oxford). 2020; 2020. PMC: 7408187. DOI: 10.1093/database/baaa062. View

Wang Y, Bryant S, Cheng T, Wang J, Gindulyte A, Shoemaker B . PubChem BioAssay: 2017 update. Nucleic Acids Res. 2016; 45(D1):D955-D963. PMC: 5210581. DOI: 10.1093/nar/gkw1118. View

Wen M, Blau S, Spotte-Smith E, Dwaraknath S, Persson K . BonDNet: a graph neural network for the prediction of bond dissociation energies for charged molecules. Chem Sci. 2021; 12(5):1858-1868. PMC: 8179073. DOI: 10.1039/d0sc05251e. View

Yamada I, Shiota M, Shinmachi D, Ono T, Tsuchiya S, Hosoda M . The GlyCosmos Portal: a unified and comprehensive web resource for the glycosciences. Nat Methods. 2020; 17(7):649-650. DOI: 10.1038/s41592-020-0879-8. View

Jacobs A, Williams D, Hickey K, Patrick N, Williams A, Chalk S . CAS Common Chemistry in 2021: Expanding Access to Trusted Chemical Information for the Scientific Community. J Chem Inf Model. 2022; 62(11):2737-2743. PMC: 9199008. DOI: 10.1021/acs.jcim.2c00268. View

Stork C, Wagner J, Friedrich N, de Bruyn Kops C, Sicho M, Kirchmair J . Hit Dexter: A Machine-Learning Model for the Prediction of Frequent Hitters. ChemMedChem. 2017; 13(6):564-571. DOI: 10.1002/cmdc.201700673. View

Ludwig M, Duhrkop K, Bocker S . Bayesian networks for mass spectrometric metabolite identification via molecular fingerprints. Bioinformatics. 2018; 34(13):i333-i340. PMC: 6022630. DOI: 10.1093/bioinformatics/bty245. View

. UniProt: the universal protein knowledgebase in 2021. Nucleic Acids Res. 2020; 49(D1):D480-D489. PMC: 7778908. DOI: 10.1093/nar/gkaa1100. View

Clark K, Karsch-Mizrachi I, Lipman D, Ostell J, Sayers E . GenBank. Nucleic Acids Res. 2015; 44(D1):D67-72. PMC: 4702903. DOI: 10.1093/nar/gkv1276. View

10.

Kim S, Thiessen P, Bolton E, Chen J, Fu G, Gindulyte A . PubChem Substance and Compound databases. Nucleic Acids Res. 2015; 44(D1):D1202-13. PMC: 4702940. DOI: 10.1093/nar/gkv951. View

11.

Himmetoglu B . Tree based machine learning framework for predicting ground state energies of molecules. J Chem Phys. 2016; 145(13):134101. DOI: 10.1063/1.4964093. View

12.

Kim S, Chen J, Cheng T, Gindulyte A, He J, He S . PubChem 2019 update: improved access to chemical data. Nucleic Acids Res. 2018; 47(D1):D1102-D1109. PMC: 6324075. DOI: 10.1093/nar/gky1033. View

13.

Stathias V, Turner J, Koleti A, Vidovic D, Cooper D, Fazel-Najafabadi M . LINCS Data Portal 2.0: next generation access point for perturbation-response signatures. Nucleic Acids Res. 2019; 48(D1):D431-D439. PMC: 7145650. DOI: 10.1093/nar/gkz1023. View

14.

Kim S, Chen J, Cheng T, Gindulyte A, He J, He S . PubChem in 2021: new data content and improved web interfaces. Nucleic Acids Res. 2020; 49(D1):D1388-D1395. PMC: 7778930. DOI: 10.1093/nar/gkaa971. View

15.

Dey V, Machiraju R, Ning X . Improving Compound Activity Classification via Deep Transfer and Representation Learning. ACS Omega. 2022; 7(11):9465-9483. PMC: 8945064. DOI: 10.1021/acsomega.1c06805. View

16.

Hastings J, Owen G, Dekker A, Ennis M, Kale N, Muthukrishnan V . ChEBI in 2016: Improved services and an expanding collection of metabolites. Nucleic Acids Res. 2015; 44(D1):D1214-9. PMC: 4702775. DOI: 10.1093/nar/gkv1031. View

17.

Falaguera M, Mestres J . Identification of the Core Chemical Structure in SureChEMBL Patents. J Chem Inf Model. 2021; 61(5):2241-2247. DOI: 10.1021/acs.jcim.1c00151. View

18.

Benson D, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman D, Ostell J . GenBank. Nucleic Acids Res. 2016; 45(D1):D37-D42. PMC: 5210553. DOI: 10.1093/nar/gkw1070. View

19.

Bairoch A . The Cellosaurus, a Cell-Line Knowledge Resource. J Biomol Tech. 2018; 29(2):25-38. PMC: 5945021. DOI: 10.7171/jbt.18-2902-002. View

20.

Ashburner M, Ball C, Blake J, Botstein D, Butler H, Cherry J . Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000; 25(1):25-9. PMC: 3037419. DOI: 10.1038/75556. View