Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2010 Jan;38(Database issue):D255-66.
doi: 10.1093/nar/gkp965. Epub 2009 Nov 19.

An overview of the PubChem BioAssay resource

Yanli Wang  1 , Evan Bolton, Svetlana Dracheva, Karen Karapetyan, Benjamin A Shoemaker, Tugba O Suzek, Jiyao Wang, Jewen Xiao, Jian Zhang, Stephen H Bryant
Affiliations

An overview of the PubChem BioAssay resource

Yanli Wang et al. Nucleic Acids Res. 2010 Jan.

Abstract

The PubChem BioAssay database (http://pubchem.ncbi.nlm.nih.gov) is a public repository for biological activities of small molecules and small interfering RNAs (siRNAs) hosted by the US National Institutes of Health (NIH). It archives experimental descriptions of assays and biological test results and makes the information freely accessible to the public. A PubChem BioAssay data entry includes an assay description, a summary and detailed test results. Each assay record is linked to the molecular target, whenever possible, and is cross-referenced to other National Center for Biotechnology Information (NCBI) database records. 'Related BioAssays' are identified by examining the assay target relationship and activity profile of commonly tested compounds. A key goal of PubChem BioAssay is to make the biological activity information easily accessible through the NCBI information retrieval system-Entrez, and various web-based PubChem services. An integrated suite of data analysis tools are available to optimize the utility of the chemical structure and biological activity information within PubChem, enabling researchers to aggregate, compare and analyze biological test results contributed by multiple organizations. In this work, we describe the PubChem BioAssay database, including data model, bioassay deposition and utilities that PubChem provides for searching, downloading and analyzing the biological activity information contained therein.

PubMed Disclaimer

Figures

Figure 1.
Figure 1.
PubChem home page. One can search PubChem Substance, Compound and BioAssay by entering the search term into the input box or access the summary, chemical structure search and bioactivity analysis service using the respective links.
Figure 2.
Figure 2.
(a and b) Tool for visualizing related bioassay relationships. One can examine the four types of derived bioassay neighboring relationships for AID 1751 targeting human muscle isoform 2 pyruvate kinase using the provided ‘Target Similarity’, ‘Activity Overlap’, ‘Depositor’ and ‘Common BioSystems’ tabs.
Figure 2.
Figure 2.
(a and b) Tool for visualizing related bioassay relationships. One can examine the four types of derived bioassay neighboring relationships for AID 1751 targeting human muscle isoform 2 pyruvate kinase using the provided ‘Target Similarity’, ‘Activity Overlap’, ‘Depositor’ and ‘Common BioSystems’ tabs.
Figure 3.
Figure 3.
Search of the PubChem BioAssay database using the keywords ‘Parkinson’s disease’ returns, among others, a series of related assays screening for the various targets associated with the disease process. Cross-links with other database records such as active compounds and protein targets are available via the links pop-up menus at the top of the DocSum page for the entire search result list and are available via link menus on the right side of each entry in the DocSum for the individual bioassay record.
Figure 4.
Figure 4.
A screenshot for the BioAssay ‘Limits’ page. One can use this facility to retrieve bioassay records for a particular target using the ‘Target’ menu, to collect a list of bioassays records that have IC50 reported using the ‘Active Concentration|Specified’ option, to identify siRNA screening experiments using the ‘BioAssay Type|Substance Type|RNAi’ feature, or to find out assays targeting a specific protein by selecting one from the ‘Target’ menu.
Figure 5.
Figure 5.
A summary view of PubChem BioAssay AID 1844 contributed by one of the screening centers of the NIH Molecular Libraries Program. This assay summarizes the process for identifying inhibitors of the nuclear receptor Steroidogenic Factor 1 (SF-1) and reports four chemical probes identified by this assay project. Multiple links are provided to allow one to retrieve and analyze testing results using available tools.
See this image and copyright information in PMC

Similar articles

  • Database resources of the National Center for Biotechnology Information.
    Sayers EW, Beck J, Bolton EE, Bourexis D, Brister JR, Canese K, Comeau DC, Funk K, Kim S, Klimke W, Marchler-Bauer A, Landrum M, Lathrop S, Lu Z, Madden TL, O'Leary N, Phan L, Rangwala SH, Schneider VA, Skripchenko Y, Wang J, Ye J, Trawick BW, Pruitt KD, Sherry ST. Sayers EW, et al. Nucleic Acids Res. 2021 Jan 8;49(D1):D10-D17. doi: 10.1093/nar/gkaa892. Nucleic Acids Res. 2021. PMID: 33095870 Free PMC article. Review.
  • PubChem's BioAssay Database.
    Wang Y, Xiao J, Suzek TO, Zhang J, Wang J, Zhou Z, Han L, Karapetyan K, Dracheva S, Shoemaker BA, Bolton E, Gindulyte A, Bryant SH. Wang Y, et al. Nucleic Acids Res. 2012 Jan;40(Database issue):D400-12. doi: 10.1093/nar/gkr1132. Epub 2011 Dec 2. Nucleic Acids Res. 2012. PMID: 22140110 Free PMC article.
  • 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.
  • Database resources of the National Center for Biotechnology Information.
    Sayers EW, Barrett T, Benson DA, Bolton E, Bryant SH, Canese K, Chetvernin V, Church DM, Dicuccio M, Federhen S, Feolo M, Geer LY, Helmberg W, Kapustin Y, Landsman D, Lipman DJ, Lu Z, Madden TL, Madej T, Maglott DR, Marchler-Bauer A, Miller V, Mizrachi I, Ostell J, Panchenko A, Pruitt KD, Schuler GD, Sequeira E, Sherry ST, Shumway M, Sirotkin K, Slotta D, Souvorov A, Starchenko G, Tatusova TA, Wagner L, Wang Y, John Wilbur W, Yaschenko E, Ye J. Sayers EW, et al. Nucleic Acids Res. 2010 Jan;38(Database issue):D5-16. doi: 10.1093/nar/gkp967. Epub 2009 Nov 12. Nucleic Acids Res. 2010. PMID: 19910364 Free PMC article.
  • PubChem: a public information system for analyzing bioactivities of small molecules.
    Wang Y, Xiao J, Suzek TO, Zhang J, Wang J, Bryant SH. Wang Y, et al. Nucleic Acids Res. 2009 Jul;37(Web Server issue):W623-33. doi: 10.1093/nar/gkp456. Epub 2009 Jun 4. Nucleic Acids Res. 2009. PMID: 19498078 Free PMC article.
See all similar articles

Cited by

See all "Cited by" articles

References

    1. Bolton EE, Wang Y, Thiessen PA, Bryant SH. PubChem: integrated platform of small molecules and biological activities. Annu. Rep. Comput. Chem. 2008;4 Chapter 12, 217–241.
    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. Sayers EW, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V, Church DM, DiCuccio M, Edgar R, Federhen S, et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2009;37:D5–D15. - PMC - PubMed
    1. Zerhouni E. Medicine. The NIH Roadmap. Science. 2003;302:63–72. - PubMed
    1. Zerhouni EA. Clinical research at a crossroads: the NIH roadmap. J. Invest. Med. 2006;54:171–173. - PubMed

Publication types

Substances

-