An overview of the PubChem BioAssay resource

By Yanli Wang, Evan E. Bolton, S. Dracheva, Karen Karapetyan, Benjamin A. Shoemaker, Tugba Onal Suzek, Jiyao Wang, Jewen Xiao, Jian Zhang, Stephen H. Bryant. 2009

301 citations recorded by the source corpus.

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.

Subfields: Computational Theory and Mathematics, Pharmacology, Physical and Theoretical Chemistry

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Citations in the corpus

ChEMBL: a large-scale bioactivity database for drug discovery (2011, background): “The PubChem BioAssay database accepts deposited results from many laboratories and screening centres and contains a large quantity of data, primarily from high-throughput screening experiments, measuring inhibition of a target by large numbers of compounds, often at a single compound concentration.”
PubChem's BioAssay Database (2011, background): “Contributions from some other organizations were described previously (1).”
PubChem3D: Shape compatibility filtering using molecular shape quadrupoles (2011, background): “Background PubChem is an open and free resource of the biological activities of small molecules [1-4].”
New Perspectives on How to Discover Drugs from Herbal Medicines: CAM's Outstanding Contribution to Modern Therapeutics (2013, background): “network analysis, and other high-throughput studies, as well as structural and biochemical studies, have provided a wealth of information for integrated systems-level analysis of drug action and molecular targets, including the beneficial and adverse effects for humans [130, 131].”
PubChem as a public resource for drug discovery (2010, background): “Many bioassay targets in PubChem are biologically related as revealed by sequence homology analysis [1].”
Structure and dynamics of molecular networks: A novel paradigm of drug discovery: A comprehensive review (2012, background): “…2009 miRGen http://diana.cslab.ece.ntua.gr/mirgen Alexiou et al., 2010 TransMir Regulatory information of microRNAs http://202.38.126.151/hmdd/mirna/tf Wang et al., 2010a PutMir http://www.isical.ac.in/~bioinfo_miu/TF-miRNA.php Bandyopadhyay & Bhattacharyya, 2010 MiRandola Extracellular microRNA…”
PubChem3D: Biologically relevant 3-D similarity (2011, background): “gov) [18-21] as a part of its Molecular Libraries Roadmap Initiative.”
Effects of multiple conformers per compound upon 3-D similarity search and bioassay data analysis (2012, background): “Background PubChem [1-4] is a public repository for biological activities of small molecules, consisting of three primary databases: PubChem Substance, PubChem Compound, and PubChem BioAssay.”
PubChem3D: Similar conformers (2011, background): “…with links to: Medical Subject Heading (MeSH) [18], through which one can locate scientific literature about a similar chemical structure in PubMed [19]; PubChem BioAssay database [3], where one can find biological and experimental data, including protein binding inhibition values; and protein 3-”
PubChem3D: conformer ensemble accuracy (2013, background): “An example of such a repository is PubChem [1-4] (http:// pubchem.”
PubChem3D: a new resource for scientists (2011, unknown): “PubChem [1-4](http://pubchem.”
PubChem3D: Conformer generation (2011, background): “PubChem [1-4] is an open archive for the biological activities of small molecules.”
PubChem3D: Diversity of shape (2011, methodology): “Conformers were generated for chemical structures in the PubChem Compound database[15-18] as described in the Materials and Methods section.”