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
. 2012 Jan;40(Database issue):D400-12.
doi: 10.1093/nar/gkr1132. Epub 2011 Dec 2.

PubChem's BioAssay Database

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

PubChem's BioAssay Database

Yanli Wang et al. Nucleic Acids Res. 2012 Jan.

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.

PubMed Disclaimer

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.
See this image and copyright information in PMC

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