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

2. 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

3. 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

4. PubChem Access & Search …
Entrez
BioAssay Classification Browser
PubChem FTP

5. 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.

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

7. 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

8. Exercise #1
Collect bioactivity data for a compound …

9. Exercise #1 … Pick a compound (with name “MyCompound”, for example)
Go to NCBI Entrez:
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

10. Exercise #2
Search and view BioAssay data …

11. Exercise #2 …
Pick a protein or gene (with protein name or gene symbol MyAssayTarget)
Go to NCBI Entrez:
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

12. Exercise #3
Collect bioactivity data for a gene …

13. Exercise #3 … Pick a gene (with gene symbol MyGene)
Go to NCBI Entrez:
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