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,, 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.

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Delivering The Vision Of An Online Database Of Nmr Spectra

  1. 1. ChemSpider: Delivering the Vision of an Online Database of NMR Spectra
  2. 2. A Pragmatic Vision <ul><ul><li>“ Build a Structure Centric Community to </li></ul></ul><ul><ul><li>Serve Chemists” </li></ul></ul><ul><ul><li>Integrate chemical structure data on the web </li></ul></ul><ul><ul><li>Create a “structure-based hub” to information and data </li></ul></ul><ul><ul><li>Provide access to structure-based “algorithms” </li></ul></ul><ul><ul><li>Let chemists contribute their own data </li></ul></ul><ul><ul><li>Allow the community to curate/correct data </li></ul></ul>
  3. 3. ChemSpider Searches
  4. 4. Search Cholesterol
  5. 5. Search Cholesterol
  6. 6. Linked to Content
  7. 7. Patents Linked
  8. 8. Articles Linked
  9. 9. ChemSpider Content <ul><li>The database presently contains: </li></ul><ul><ul><li>Almost 25 million unique chemical compounds </li></ul></ul><ul><ul><li>From almost 400 data sources </li></ul></ul><ul><li>Content changes daily </li></ul><ul><ul><li>New chemistry from RSC Articles and databases </li></ul></ul><ul><ul><li>New or existing data sources with updated content </li></ul></ul><ul><ul><li>Spectral data added regularly </li></ul></ul>
  10. 10. NMR Spectroscopy on the Internet <ul><li>Access to presentations, tutorials and guidance </li></ul><ul><li>Tables of information – solvent shifts, coupling constants etc </li></ul><ul><li>Spectral data for download – binary files and JCAMP files </li></ul><ul><li>Assigned NMR spectra – tables and interactive displays </li></ul><ul><li>Access to NMR prediction algorithms – free and commercial </li></ul>
  11. 11. ChemSpider : Spectra Linked
  12. 12. Spectra Linked
  13. 13. Spectra Linked
  14. 14. Spectra on ChemSpider
  15. 15. Sources of Spectra <ul><li>Sourced from online sources with permission </li></ul><ul><li>Private collections </li></ul><ul><li>The MAJORITY deposited by ChemSpider users </li></ul>
  16. 16. Spectral Uploading <ul><li>Locate the structure of interest and deposit spectrum </li></ul>
  17. 17. Spectral Uploading <ul><li>Various types of NMR spectra supported </li></ul>
  18. 18. Multiple Spectra for One Structure
  19. 19. ChemSpider ID 24528095 H1 NMR
  20. 20. ChemSpider ID 24528095 C13 NMR
  21. 21. ChemSpider ID 24528095 HHCOSY
  22. 22. ChemSpider ID 24528095 HSQC
  23. 23. ChemSpider ID 24528095 HMBC
  24. 24. Full C13 assignment uploaded
  25. 25. Deposit spectra against new structure <ul><li>If a NEW compound has spectral data then deposit the structure onto ChemSpider first </li></ul>
  26. 26. Available Spectra
  27. 27. Embedding Data
  28. 28. Embedding Structures
  29. 29. Web Services
  30. 30.
  31. 31. Spectral Game
  32. 32. Increasing Complexity
  33. 33. Spectral Game
  34. 34. Data Curation
  35. 35. Reversed Spectrum
  36. 36. Download, reprocess, redeposit
  37. 37. True Curation of Data
  38. 38. 2DNMR Spectral Game
  39. 40. Not Just NMR Data
  40. 41. ChemSpider SyntheticPages
  41. 42. Invitations <ul><li>Spectral data are welcomed from associated syntheses, lab experiments etc </li></ul><ul><li>Companies especially encouraged to provide non-proprietary data for the community </li></ul><ul><li>Upload structures, spectra, analyses etc to ChemSpider to share with the community </li></ul><ul><li>Use and encourage your students </li></ul><ul><li>And presently in beta… </li></ul>
  42. 43. NMRShiftDB
  43. 44. NMRShiftDB:
  44. 46. NMR Prediction
  45. 47. NMRShiftDB Data Review <ul><li>High quality NMR shift set of ca. 100,000 shifts </li></ul><ul><li>Multiple outliers identified </li></ul><ul><li>Removed following publication </li></ul><ul><li>Integration has highlighted prediction bugs </li></ul><ul><li>ACD/NMR predictions do outperform NMRShiftDB </li></ul>
  46. 48. ChemSpider Integrated NMR Prediction <ul><li>Initial integration in place </li></ul>
  47. 49. Acknowledgments <ul><li>Jean-Claude Bradley, Andrew Lang and Robert Lancashire </li></ul><ul><li>Christoph Steinbeck and Stefan Kuhn, EBI/NMRShiftDB </li></ul><ul><li>Depositors of data </li></ul>
  48. 50. Thank you [email_address] Twitter: ChemSpiderman SLIDES: