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Introduction to PubChem BioAssay Yanli Wang MCBIOS Little Rock, Arkansas March 24, 2017 Outline • Overview of PubChem •Access, search, data retrieval, use • Hand-on practice 2 Access, search, data retrieval, use… PubChem Access & Search … PubChem Home Entrez PubChem FTP E-utils PUG-REST Entrez Bioactivity analysis tools, data view Structure Search Public search engine Google etc. PubChem Data Access • Interfaces • Tools – bioactivity analysis – text/numeric search – fielded/range search – precomputed relationship • SAR analysis • across assay/target comparison • mine related datasets • 2-D, 3-D, identity groups • related bioassays • hierarchical classification – chemical structure analysis • structure normalization • 2D, 3D similarity search • structure clustering – inter-database links • biomedical literature, MeSH • protein, gene, 3D structure • pathways, taxonomy, OMIM – data download – FTP site – programmatic Utilities – external resource links • PubChem Data Access • Interfaces • Tools – bioactivity analysis – text/numeric search – fielded/range search – precomputed relationship • SAR analysis • across assay/target comparison • mine related datasets • 2-D, 3-D, identity groups • related bioassays • hierarchical classification – chemical structure analysis • structure normalization • 2D, 3D similarity search • structure clustering – inter-database links • biomedical literature, MeSH • protein, gene, 3D structure • pathways, taxonomy, OMIM – data download – FTP site – programmatic Utilities – external resource links • PubChem Access & Search … Entrez BioAssay Classification Browser PubChem FTP Search PubChem with Entrez … Three PubChem databases Free text search Search by indexed field Advanced search for complex query Refine/combine search Entrez links (Related Data) Access from Gene, PubMed etc. Goal #1 Collect bioactivity data for a compound … How to get here??? Bioactivity data for androgen … https://pubchem.ncbi.nlm.nih.gov/assay/bioactivity.html?cid=5995 Goal 2 Collect bioactivity data for a gene … Bioactivity data for alpha4 nicotinic How to get here??? acetylcholine receptor … https://pubchem.ncbi.nlm.nih.gov/assay/bioactivity.html?geneid=11438 PubChem Access & Search … Entrez BioAssay Classification Browser PubChem FTP Entrez Substance & Compound … Chemical name Synonym Chemical Property Links: • • Cross-reference Related data Tools Search Androgen … Search result … Access tools … Subset of rule 5 & bioactivity data … Subset with annotations … Links, related data, cross-references … Specific search using index field … Specific search using index field … follow up Androgen page … Goal #1 https://pubchem.ncbi.nlm.nih.gov/compound/5995 Entrez PubChem BioAssay … Assay name, description, protocol Target information (protein name, gene symbol Annotations, comments Depositor information Chemical name of tested substance Links: • • Cross-reference Related data Search “nicotinic acetylcholine receptors” … Search rattus … Access search history … Search history … Combine search query … Advanced search … Complex query … Index fields … BioAssay links to many other databases PubMed OMIM Protein BioSystems a pathway db drug annotation Gene Nucleotide MeSH Depositor links GEO Taxonomy CDD conserved protein family domain Structure a mirror of Protein Data Bank (PDB) 33 Access BioAssay from Entrez Gene … Search “nicotinic acetylcholine receptors” in Gene … Retrieve genes associated with BioAssay … Search history … Retrieve assays targeting nicotinic acetylcholine receptors … Gene page for … Links of BioAssay data targeting CHRNA4 … Bioactivity data for CHRNA4 … Goal #2 Entrez search summary … General free text search Specific search by indexed field Advanced search for complex query via Limits page Refine/combine search with Boolean operation Entrez links (Related Data) Access from Gene, PubMed etc. PubChem Access & Search … Entrez BioAssay Classification Browser PubChem FTP BioAssay Tools … PubChem Access & Search … Entrez BioAssay Classification Browser PubChem FTP PubChem BioAssay FTP … ftp://ftp.ncbi.nlm.nih.gov/pubchem/Bioassay/ PubChem references • Bolton E, Wang Y, et al. PubChem: Integrated Platform of Small Molecules and Biological Activities. Chapter 12 IN Annual Reports in Computational Chemistry, Volume 4, Elsevier: Oxford, UK; 2008, pp. 217-240. • Wang Y, et al. PubChem BioAssay: 2017 update. Nucleic Acids Res. 2017, 45(D1):D1075-1082. • Li Q, Cheng T, Wang Y*, Bryant SH*. PubChem as a public resource for drug discovery. Drug Discov Today. 2010, 15(23-24):1052-1057. • Pan Y, Cheng, T, Wang Y*, Bryant SH*. Pathway Analysis for Drug Repositioning Based on Public Database Mining. J Chem Inf Model. 2014, 54, 407−418 • Cheng T, Pan Y, Hao M, Wang Y*, Bryant SH*. PubChem Applications in Drug Discovery – a Bibliometric Analysis, Drug Discovery Today, 2014, 19(11), 1751-6