Delivering The Vision Of An Online Database Of Nmr Spectra
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ChemSpider: Delivering the Vision of an Online Database of NMR Spectra
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ChemSpider is an online database of over 20 million chemical compounds sourced from over 300 different sources including government laboratories, chemical vendors, public resources and publications. Developed with the intention of building community for chemists ChemSpider allows its users to deposit data including structures, properties, links to external resources and various forms of spectral data. Over the past three years ChemSpider has aggregated almost 3000 high quality NMR spectra and continues to expand as the community deposits additional data. The majority of spectral data is licensed as Open Data allowing it to be downloaded and reused in presentations, lesson plans and for teaching purposes. Using the spectral data as a basis a web-based game, www.spectralgame.com, has been developed where players try to match molecules to various forms of interactive spectra including 1D/2D NMR. Each correct selection earns the player one point and play continues until the player supplies an incorrect answer. The spectra are displayed using JSpecView, an Open Source spectrum viewing applet which affords zooming and integration of JCAMP spectra. Players of the game provide both active and passive feedback regarding the quality of the spectral data resulting in crowd sourced curation and validation of the data. This presentation will provide an overview of ChemSpider and our mission to provide access to a free integrated database of various forms of spectral data.
Transcript of Delivering The Vision Of An Online Database Of Nmr Spectra
ChemSpider: Delivering the Vision of an Online Database of NMR Spectra
A Pragmatic Vision“Build a Structure Centric Community to
Serve Chemists”
Integrate chemical structure data on the web Create a “structure-based hub” to information and
data Provide access to structure-based “algorithms” Let chemists contribute their own data Allow the community to curate/correct data
ChemSpider Searches
Search Cholesterol
Search Cholesterol
Linked to Content
Patents Linked
Articles Linked
ChemSpider Content
The database presently contains: Almost 25 million unique chemical compounds From almost 400 data sources
Content changes daily New chemistry from RSC Articles and
databases New or existing data sources with updated
content Spectral data added regularly
NMR Spectroscopy on the Internet
Access to presentations, tutorials and guidance Tables of information – solvent shifts, coupling
constants etc Spectral data for download – binary files and
JCAMP files Assigned NMR spectra – tables and interactive
displays Access to NMR prediction algorithms – free and
commercial
ChemSpider : Spectra Linked
Spectra Linked
Spectra Linked
Spectra on ChemSpider
Sources of Spectra
Sourced from online sources with permission
Private collections
The MAJORITY deposited by ChemSpider users
Spectral Uploading
Locate the structure of interest and deposit spectrum
Spectral Uploading Various types of NMR spectra supported
Multiple Spectra for One Structure
ChemSpider ID 24528095 H1 NMR
ChemSpider ID 24528095 C13 NMR
ChemSpider ID 24528095 HHCOSY
ChemSpider ID 24528095 HSQC
ChemSpider ID 24528095 HMBC
Full C13 assignment uploaded
Deposit spectra against new structure
If a NEW compound has spectral data then deposit the structure onto ChemSpider first
Available Spectra http://www.chemspider.com/spectra.aspx
Embedding Data
Embedding Structures
Web Services
Spectral Game
Increasing Complexity
Spectral Game
Data Curation
Reversed Spectrum
Download, reprocess, redeposit
True Curation of Data
2DNMR Spectral Game
Not Just NMR Data
ChemSpider SyntheticPages
Invitations
Spectral data are welcomed from associated syntheses, lab experiments etc
Companies especially encouraged to provide non-proprietary data for the community
Upload structures, spectra, analyses etc to ChemSpider to share with the community
Use www.SpectralGame.com and encourage your students
And presently in beta…
NMRShiftDB
NMRShiftDB: http://www.ebi.ac.uk/nmrshiftdb/
NMR Prediction
NMRShiftDB Data Review
• High quality NMR shift set of ca. 100,000 shifts• Multiple outliers identified • Removed following publication• Integration has highlighted prediction bugs• ACD/NMR predictions do outperform NMRShiftDB
ChemSpider Integrated NMR Prediction
Initial integration in place
Acknowledgments
Jean-Claude Bradley, Andrew Lang and Robert Lancashire
Christoph Steinbeck and Stefan Kuhn, EBI/NMRShiftDB
Depositors of data
Thank you
[email protected]: ChemSpidermanwww.chemspider.com/blogSLIDES: www.slideshare.net/AntonyWilliams
