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

2. 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

3. Access, search, data retrieval, use…

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

5. 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

6. 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

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

8. 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.

9. Goal #1
Collect bioactivity data for a compound …

10. How to get here???
Bioactivity data for androgen …

11. Goal 2
Collect bioactivity data for a gene …

12. Bioactivity data for alpha4 nicotinic acetylcholine receptor …
How to get here???

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

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

15. Search Androgen …

16. Search result …

17. Access tools …

18. Subset of rule 5 & bioactivity data …

19. Subset with annotations …

20. Links, related data, cross-references …

21. Specific search using index field …

22. Specific search using index field …
follow up

23. Androgen page … https://pubchem.ncbi.nlm.nih.gov/compound/5995
Goal #1
Androgen page …

24. 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

25. Search “nicotinic acetylcholine receptors” …

26. Search rattus …

27. Access search history …

28. Search history …

29. Combine search query …

30. Advanced search …

31. Complex query …

32. Index fields …

33. 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

34. 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

35. Access BioAssay from Entrez Gene …

36. Search “nicotinic acetylcholine receptors” in Gene …

37. Retrieve genes associated with BioAssay …

38. Search history …

39. Retrieve assays targeting nicotinic acetylcholine receptors …

40. Gene page for …

41. Links of BioAssay data targeting CHRNA4 …

42. Bioactivity data for CHRNA4 …
Goal #2

43. 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.

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

45. BioAssay Tools …

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

48. PubChem BioAssay FTP …
ftp://ftp.ncbi.nlm.nih.gov/pubchem/Bioassay/

49. 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
Wang Y, et al. PubChem BioAssay: 2017 update. Nucleic Acids Res , 45(D1):D
Li Q, Cheng T, Wang Y*, Bryant SH*. PubChem as a public resource for drug discovery. Drug Discov Today. 2010, 15(23-24):
Pan Y, Cheng, T, Wang Y*, Bryant SH*. Pathway Analysis for Drug Repositioning Based on Public Database Mining. J Chem Inf Model , 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),