ChemSpider – The Free Chemistry

Database for the Community

Antony Williams
Duke University, September 17th 2012
We Have …Too Much Data!!!
The World of Online Chemistry
 Property databases
 Compound aggregators
 Screening assay results
 Scientific publications
 Encyclopedic articles (Wikipedia)
 Metabolic pathway databases
 ADME/Tox data – eTOX for example
 Blogs/Wikis and Open Notebook Science
 Contributing Open Source code to projects
ChemSpider
 The Free Chemical Database

 A central hub for chemists to source information

 >28 million unique chemical records
 Aggregated from >400 data sources
 Chemicals, spectra, CIF files, movies, images,
podcasts, links to patents, publications,
predictions

 A central hub for chemists to deposit & curate data

We Want to Answer Questions
 Questions a chemist might ask…
 What is the melting point of n-heptanol?
 What is the chemical structure of Xanax?
 Chemically, what is phenolphthalein?
 What are the stereocenters of cholesterol?
 Where can I find publications about xylene?
 What are the different trade names for Ketoconazole?
 What is the NMR spectrum of Aspirin?
 What are the safety handling issues for Thymol Blue?
I want to know about “Vincristine”
Vincristine: Identifiers and Properties
Vincristine: Vendors and Sources
Vincristine: Patents
Vincristine: Articles
ChemSpider : Spectra Linked
Sources of Spectra
 Sourced from online sources with permission

 Private collections

 The MAJORITY deposited by ChemSpider users

Data Uploading – YOU HELP
 Locate the structure of interest and deposit
spectrum
Multiple Spectra for One Structure
ChemSpider ID 24528095 H1 NMR
ChemSpider ID 24528095 C13 NMR
ChemSpider ID 24528095 HHCOSY
Spectra Linked
CURATION Search “Vitamin H”
“Curate” Identifiers
“Curate” Identifiers
“Curate” Identifiers
The InChI Identifier
Multiple Layers
InChIStrings Hash to InChIKeys
Vancomycin – Search the Internet
Vancomycin

Search Molecular Search Full Molecule

SKELETON
Searches: The INTERNET
Validated Names for Searching…
And InChIs…
ChemSpider Interface
www.SpectralGame.com
http://www.jcheminf.com/content/1/1/9
Spectral Game
Increasing Complexity
Structure Database Lookup
ChemSpider SyntheticPages
ChemSpider Everywhere : ChemMobi
SpectralGame in the hand
ChemSpider Resources for Chemistry
 Conclusions
 ChemSpider is a FREE resource for the community
 Grows daily with new data – do you have any to
share?
 Concerned about data quality! YOU SHOULD BE!
 Crowdsourced and algorithmic curation is working
 API is available to access data – any informatics
people want access??

 If you want hands on training I can come and give it

Thank you

Email: williamsa@rsc.org
Twitter: ChemConnector
Blog: www.chemspider.com/blog
Personal Blog: www.chemconnector.com
SLIDES: www.slideshare.net/AntonyWilliams