Download 1. Pubchem database access

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