Introduction to PubChem BioAssay Yanli Wang MCBIOS Little Rock, Arkansas March 24, 2017
Access, search, data retrieval, use Outline Overview of PubChem Access, search, data retrieval, use Hand-on practice *at PubChem we have several goals *public depo system *various sources
Access, search, data retrieval, use…
PubChem Access & Search … Entrez PubChem Home PubChem FTP Structure Search Public search engine Google etc. Bioactivity analysis tools, data view PUG-REST E-utils
PubChem Data Access – text/numeric search – fielded/range search Interfaces – text/numeric search – fielded/range search – precomputed relationship • 2-D, 3-D, identity groups • related bioassays • hierarchical classification – inter-database links • biomedical literature, MeSH • protein, gene, 3D structure • pathways, taxonomy, OMIM – external resource links • Tools – bioactivity analysis • SAR analysis • across assay/target comparison • mine related datasets – chemical structure analysis • structure normalization • 2D, 3D similarity search • structure clustering – data download – FTP site – programmatic Utilities
PubChem Data Access – text/numeric search – fielded/range search Interfaces – text/numeric search – fielded/range search – precomputed relationship • 2-D, 3-D, identity groups • related bioassays • hierarchical classification – inter-database links • biomedical literature, MeSH • protein, gene, 3D structure • pathways, taxonomy, OMIM – external resource links • Tools – bioactivity analysis • SAR analysis • across assay/target comparison • mine related datasets – chemical structure analysis • structure normalization • 2D, 3D similarity search • structure clustering – data download – FTP site – programmatic Utilities
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 acetylcholine receptor … https://pubchem.ncbi.nlm.nih.gov/assay/bioactivity.html?geneid=11438 How to get here???
PubChem Access & Search … Entrez BioAssay Classification Browser PubChem FTP
Entrez Substance & Compound … Chemical name Synonym Chemical Property Links: Tools Cross-reference Related data
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 … https://pubchem.ncbi.nlm.nih.gov/compound/5995 Goal #1 Androgen page … 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 research data OMIM Protein BioSystems a pathway db assay target Gene assay target drug annotation MeSH assay target Nucleotide Depositor links *to this end *hosted by NCBI *providing additional annotation Nucleotide: AID 1637 GEO Taxonomy Structure a mirror of Protein Data Bank (PDB) CDD conserved protein family domain
BioAssay links to many other databases PubMed research data OMIM Protein assay target BioSystems a pathway db Gene assay target drug annotation MeSH Nucleotide assay target Depositor links *to this end *hosted by NCBI *providing additional annotation Nucleotide: AID 1637 GEO Taxonomy Structure a mirror of Protein Data Bank (PDB) CDD conserved protein family domain
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