This document discusses ChemSpider, an online database of chemical compounds. It summarizes ChemSpider's capabilities, including searching by mass or formula for structure identification. ChemSpider contains over 34 million chemicals from various sources that can be searched and filtered. The document outlines how ChemSpider provides value to mass spectrometrists and discusses efforts to integrate more spectral data like NMR spectra directly into ChemSpider from publications and individual submissions. Future goals include hosting over a million spectra online and improving visualization of spectral data.

1. Dealing with the complex challenge
of managing diverse analytical
chemistry data online
Antony Williams, Valery Tkachenko
and Alexey Pshenichnov
Pittcon
March 2015

2. Free and Easy
• Everything I will show in terms of ChemSpider
is available for free online today
• To make it easy to “take notes” these slides
will be available at:
www.slideshare.net/AntonyWilliams/

3. Two posters from this week
• Using an online database of chemical compounds
for the purpose of structure identification
• ChemSpider - building an online database of open
spectra

4. www.ChemSpider.com

5. ChemSpider

6. What will ChemSpider give us?

7. What will ChemSpider give us?

8. For Mass Spectrometrists
• Valuable searches for Mass Spec would be:
• Search the database by mass or formula for
structure identification
• Search subsets of data – e.g. “metabolism”,
pesticides etc
• Link structure-based data across the internet
• Provide “programming interfaces” to integrate
• Does ChemSpider provide value to Mass
Spectrometrists?

9. Pre-calculated data

10. Data Source Selection
• >34 million chemicals include
• Vendor collections
• Government databases
• Individual/Lab data
• Publication data
• All segregated allowing for data source
selection

11. Data Source Selection - Type

12. Data Source Selection -
Individual

13. Mass Spec Analysis
Jim Little, Eastman Chemical

14. ChemSpider Interface

15. 1287 Hits Ranked by Defect

16. 1287 Hits Ranked by # of
References

17. Top Ranked Hit

18. Tinuvin 328

19. What can I find on ChemSpider?

20. What can I find?

21. What can I find?

22. Source and Purchase…

23. What can I find on ChemSpider?

24. External Calculation Engines

25. What can I find on ChemSpider?

26. …and in the RSC Databases..

27. Linked to the Publisher

28. What can I find?

29. And out to Google Patents

30. What About the Entire Web?

31. The InChI Identifier

32. InChIStrings Hash to InChIKeys

33. Searching Internet by Structure

34. Extended Study
Sorting by references

35. Position sorted by references

36. Position 1 only

37. Web Services For Collaboration
• Many instrument vendors are using or
investigating our web-based services for
compound lookup
• Many academic sites integrating directly –
metabonomics, name lookup, mass-based
searching

38. Results of the ChemSpider Search
in the MarkerLynx Worksheet

39. Hit Details in ChemSpider

40. “REAL Spectral Data”
• Masses on ChemSpider are clearly valuable!
• We’d like to host “spectral curves”
• But we’re a publisher so what can we do?

41. PDF files with images…

42. ESI – Text Spectra…

43. We want this…we need YOU!

44. Spectra: Cholesterol

45. ChemSpider ID 24528095 H1 NMR

46. ChemSpider ID 24528095 C13 NMR

47. ChemSpider ID 24528095 HHCOSY

48. Managing Assignments?

49. Visualization of Spectra
• We would like to view “interactive spectra”

50. The challenges of analytical data
• Vendors produce complex proprietary data
formats – tough to manage but some do it:
ACD/Labs, Mestre, others
• Standard formats are required (JCAMP,
NetCDF, AniML, “Allotrope” in future?)

51. ACD/Labs

52. Jmol

53. ChemDoodle Components

54. Publications & “Real Spectra”
• We are turning text into spectra
• We are turning figures into spectra

55. ESI – Text Spectra

56. 1H NMR (CDCl3, 400 MHz):
δ = 2.57 (m, 4H, Me, C(5a)H), 4.24 (d, 1H, J = 4.8 Hz, C(11b)H), 4.35 (t,
1H, Jb = 10.8 Hz, C(6)H), 4.47 (m, 2H, C(5)H), 4.57 (dd, 1H, J = 2.8 Hz,
C(6)H), 6.95 (d, 1H, J = 8.4 Hz, ArH), 7.18–7.94 (m, 11H, ArH)

57. 13C NMR (CDCl3, 100 MHz): δ = 14.12 (CH3), 30.11 (CH, benzylic methane),
30.77 (CH, benzylic methane), 66.12 (CH2), 68.49 (CH2), 117.72, 118.19,
120.29, 122.67, 123.37, 125.69, 125.84, 129.03, 130.00, 130.53 (ArCH), 99.42,
123.60, 134.69, 139.23, 147.21, 147.61, 149.41, 152.62, 154.88 (ArC)

58. “Where is the real data please?”
FIGURE
DATA

59. Future Developments
• We have extracted 100s of 1000s of text strings
from patents – next we go into our archive
• We estimate many 1000s of figures with spectral
data in our ESI and articles
• We are aiming for a million spectra online…
• But YOU can submit your data today and share it

60. New Repository Architecture
doi: 10.1007/s10822-014-9784-5

61. Acknowledgments
• Jim Little, Eastman Chemical Company
• Kevin Thiesen & Rudy Potenzone – ChemDoodle
• Daniel Lowe – NextMove Software
• Bill Brouwer – Plot2Txt Development
• Carlos Cobas and Santi Dominguez – MestreLabs
• Bob Hanson - Jmol/JSpecView Javascript version
• David Hardy, Patrick Wheeler, Arvin Moser -
ACD/Labs

62. Thank you
Email: williamsa@rsc.org
ORCID: 0000-0002-2668-4821
Twitter: @ChemConnector
Personal Blog: www.chemconnector.com
SLIDES: www.slideshare.net/AntonyWilliams