PubChem's BioAssay Database

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.

[1]  G F Pinto,et al.  Pocket computer program for fitting the Hill equation. , 1984, Computers in biology and medicine.

[2]  Gregory D. Schuler,et al.  Database resources of the National Center for Biotechnology Information: update , 2004, Nucleic acids research.

[3]  Norbert Perrimon,et al.  FlyRNAi: the Drosophila RNAi screening center database , 2005, Nucleic Acids Res..

[4]  P. Schultz,et al.  A chemical biology approach reveals period shortening of the mammalian circadian clock by specific inhibition of GSK-3β , 2008, Proceedings of the National Academy of Sciences.

[5]  Yanli Wang,et al.  PubChem: Integrated Platform of Small Molecules and Biological Activities , 2008 .

[6]  T. Hirota,et al.  High-throughput screening and chemical biology: new approaches for understanding circadian clock mechanisms. , 2009, Chemistry & biology.

[7]  Yanli Wang,et al.  PubChem: a public information system for analyzing bioactivities of small molecules , 2009, Nucleic Acids Res..

[8]  R. Damoiseaux,et al.  Integrated Chemical Genomics Reveals Modifiers of Survival in Human Embryonic Stem Cells , 2009, Stem cells.

[9]  Min Jae Lee,et al.  Enhancement of Proteasome Activity by a Small-Molecule Inhibitor of Usp14 , 2010, Nature.

[10]  James R. Brown,et al.  Thousands of chemical starting points for antimalarial lead identification , 2010, Nature.

[11]  Evan Bolton,et al.  An overview of the PubChem BioAssay resource , 2009, Nucleic Acids Res..

[12]  P. Hajduk,et al.  Navigating the kinome. , 2011, Nature chemical biology.

[13]  John P. Overington,et al.  ChEMBL: a large-scale bioactivity database for drug discovery , 2011, Nucleic Acids Res..