Introduction to PubChem BioAssay

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Presentation transcript:

Introduction to PubChem BioAssay Yanli Wang MCBIOS Little Rock, Arkansas March 24, 2017

Hand-on practice Outline Overview of PubChem Access, search, data retrieval, use Hand-on practice *at PubChem we have several goals *public depo system *various sources

PubChem Access & Search … Entrez PubChem Home PubChem FTP Structure Search Public search engine, such as Google Bioactivity analysis tools, data view PUG-REST E-utils

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.

Entrez Substance & Compound … Chemical name Synonym Chemical Property Links: Tools Cross-reference Related data

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

Exercise #1 Collect bioactivity data for a compound …

Exercise #1 … Pick a compound (with name “MyCompound”, for example) Go to NCBI Entrez: https://www.ncbi.nlm.nih.gov/ Select “PubChem Compound” database Search with “MyCompound” Search with “MyCompound”[synonym] Search with “MyCompound”[completesynonym] Compare the results Any compounds associated with BioAssay data? Any compounds associated with protein 3D structure? Check the compound page Navigate to bioactivity data, download data

Exercise #2 Search and view BioAssay data …

Exercise #2 … Pick a protein or gene (with protein name or gene symbol MyAssayTarget) Go to NCBI Entrez: https://www.ncbi.nlm.nih.gov/ Select “PubChem BioAssay” database Search with MyAssayTarget Pick one BioAssay entry and view the assay page Review the page Drill down to active test results Download data table with CSV format

Exercise #3 Collect bioactivity data for a gene …

Exercise #3 … Pick a gene (with gene symbol MyGene) Go to NCBI Entrez: https://www.ncbi.nlm.nih.gov/ Select “Gene” database Search with MyGene Search gene_pcassay_target[filter] Combine results from step 3) and 4) Pick one entry and view the Gene page Find links to BioAssay Navigate to the gene specific bioactivity data view Download data table with CSV format

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