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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
SKELETON
Search Full Molecule
Searches: The INTERNET
Validated Names for Searching…
And InChIs…
ChemSpider Interface
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: [email protected]
Twitter: ChemConnector
Blog: www.chemspider.com/blog
Personal Blog: www.chemconnector.com
SLIDES: www.slideshare.net/AntonyWilliams