Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2012 Jan;40(Database issue):D400-12.
doi: 10.1093/nar/gkr1132. Epub 2011 Dec 2.

PubChem's BioAssay Database

Affiliations
Free PMC article

PubChem's BioAssay Database

Yanli Wang et al. Nucleic Acids Res. .
Free PMC article

Abstract

PubChem (http://pubchem.ncbi.nlm.nih.gov) is a public repository for biological activity data of small molecules and RNAi reagents. The mission of PubChem is to deliver free and easy access to all deposited data, and to provide intuitive data analysis tools. The PubChem BioAssay database currently contains 500,000 descriptions of assay protocols, covering 5000 protein targets, 30,000 gene targets and providing over 130 million bioactivity outcomes. PubChem's bioassay data are integrated into the NCBI Entrez information retrieval system, thus making PubChem data searchable and accessible by Entrez queries. Also, as a repository, PubChem constantly optimizes and develops its deposition system answering many demands of both high- and low-volume depositors. The PubChem information platform allows users to search, review and download bioassay description and data. The PubChem platform also enables researchers to collect, compare and analyze biological test results through web-based and programmatic tools. In this work, we provide an update for the PubChem BioAssay resource, including information content growth, data model extension and new developments of data submission, retrieval, analysis and download tools.

Figures

Figure 1.
Figure 1.
The summary view of a PubChem bioassay record. Assay results can be retrieved through the Show Data | Active and Show Data | All links.
Figure 2.
Figure 2.
Entrez DocSum report for bioassay search results.
Figure 3.
Figure 3.
PubChem BioActivity Summary service. (A) assay-centric view for multiple compounds; (B) compound-centric view; (C) target-centric view; (D) assay centric view for a single compound.
Figure 3.
Figure 3.
PubChem BioActivity Summary service. (A) assay-centric view for multiple compounds; (B) compound-centric view; (C) target-centric view; (D) assay centric view for a single compound.
Figure 4.
Figure 4.
A new service for drawing dose–response curves.
Figure 5.
Figure 5.
PubChem BioAssay FTP directory structure.
Figure 6.
Figure 6.
Web-based assay download service.

Similar articles

  • PubChem BioAssay: 2014 update.
    Wang Y, Suzek T, Zhang J, Wang J, He S, Cheng T, Shoemaker BA, Gindulyte A, Bryant SH. Wang Y, et al. Nucleic Acids Res. 2014 Jan;42(Database issue):D1075-82. doi: 10.1093/nar/gkt978. Epub 2013 Nov 5. Nucleic Acids Res. 2014. PMID: 24198245 Free PMC article.
  • PubChem BioAssay: 2017 update.
    Wang Y, Bryant SH, Cheng T, Wang J, Gindulyte A, Shoemaker BA, Thiessen PA, He S, Zhang J. Wang Y, et al. Nucleic Acids Res. 2017 Jan 4;45(D1):D955-D963. doi: 10.1093/nar/gkw1118. Epub 2016 Nov 29. Nucleic Acids Res. 2017. PMID: 27899599 Free PMC article.
  • An overview of the PubChem BioAssay resource.
    Wang Y, Bolton E, Dracheva S, Karapetyan K, Shoemaker BA, Suzek TO, Wang J, Xiao J, Zhang J, Bryant SH. Wang Y, et al. Nucleic Acids Res. 2010 Jan;38(Database issue):D255-66. doi: 10.1093/nar/gkp965. Epub 2009 Nov 19. Nucleic Acids Res. 2010. PMID: 19933261 Free PMC article.
  • Getting the most out of PubChem for virtual screening.
    Kim S. Kim S. Expert Opin Drug Discov. 2016 Sep;11(9):843-55. doi: 10.1080/17460441.2016.1216967. Epub 2016 Aug 5. Expert Opin Drug Discov. 2016. PMID: 27454129 Free PMC article. Review.
  • PubChem as a public resource for drug discovery.
    Li Q, Cheng T, Wang Y, Bryant SH. Li Q, et al. Drug Discov Today. 2010 Dec;15(23-24):1052-7. doi: 10.1016/j.drudis.2010.10.003. Epub 2010 Oct 21. Drug Discov Today. 2010. PMID: 20970519 Free PMC article. Review.
See all similar articles

Cited by 134 articles

See all "Cited by" articles

References

    1. Wang Y, Bolton E, Dracheva S, Karapetyan K, Shoemaker BA, Suzek TO, Wang J, Xiao J, Zhang J, Bryant SH. An overview of the PubChem BioAssay resource. Nucleic Acids Res. 2010;38:D255–D266. - PMC - PubMed
    1. Wang Y, Xiao J, Suzek TO, Zhang J, Wang J, Bryant SH. PubChem: a public information system for analyzing bioactivities of small molecules. Nucleic Acids Res. 2009;37:W623–W633. - PMC - PubMed
    1. Bolton EE, Wang Y, Thiessen PA, Bryant SH. PubChem: integrated platform of small molecules and biological activities. Annu. Rep. Comput. Chem. 2008;4:217–241.
    1. Sayers EW, Barrett T, Benson DA, Bolton E, Bryant SH, Canese K, Chetvernin V, Church DM, DiCuccio M, Federhen S, et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2011;39:D38–D51. - PMC - PubMed
    1. Damoiseaux R, Sherman SP, Alva JA, Peterson C, Pyle AD. Integrated chemical genomics reveals modifiers of survival in human embryonic stem cells. Stem Cells. 2009;27:533–542. - PMC - PubMed

Publication types

Substances

Feedback