These are the slides I will be giving here at the Science Commons Symposium Pacific Northwest at the Microsoft Campus here in Redmond in about 5 minutes time

1. ChemSpider: Collecting and Curating the
World’s Chemistry with the Community

2. A Pragmatic Vision
“Build a Structure Centric Community”
 December 2006 – A hobby project initiated to
connect chemistry on the web
 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

3. Where is chemistry online?
 Encyclopedic articles (Wikipedia)
 Chemical vendor databases
 Metabolic pathway databases
 Property databases
 Patents with chemical structures
 Drug Discovery data
 Scientific publications
 Compound aggregators
 Blogs/Wikis and Open Notebook Science

4. Chemistry on the Internet TODAY
 Chemistry searches are generally limited to text-
based searches across the internet
 Data are dirty: sorting the wheat from the chaff.
Who can you trust?
 Too many searches required to resource data

5. media.obsessable.com
As few interfaces as possible
What do humans want?

6. Chemistry on the Internet FUTURE
 The semantic web for chemistry is in place
 Crowdsourced contributions are commonplace
 Chemists will search by structure/substructure
 Chemistry articles indexed and searchable
 Reduced number of searches to find data
 Data are integrated – compounds, vendors,
syntheses, data, publications and patents
 A world of Open Access and Open Data
 Classical business models will have to morph

7. Getting it done
 March 2007 – A beta system opened online
 One purchased computer, two home-built
 Seeded with 10.5 million structures
 Structure/substructure searching
 June 2007
 A curating layer to flag data
 A deposition interface to add to the data
 And so it continued….

8. ChemSpider Searches

9. Search Cholesterol

10. Search Cholesterol

11. Search Cholesterol

12. Search Cholesterol

13. Search Cholesterol

14. Linked across the internet

15. Kyoto Encyclopedia of Genes and Genomes

16. Links to Patents based on structure

17. Articles Linked

18. ChemSpider Complex Searches

19. Link off a structure in ChemSpider
 Chemical suppliers
 Other publications
 Analytical Data
 Related Reactions
 Wikipedia
 Patents
 “Everything”

20. Answering Questions for Chemists
 Questions a chemist might ask…
 What is the melting point of n-butanol?
 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?

21. What is a compound?

22. ChemSpider is a structure-centric hub
 ChemSpider aggregates and links out across the
internet
 Data aggregate based on “structures and links”
 What defines a chemical compound?

23. Linked Data on the Web
Taken from: Rafael Sidis’ Blog

24. Where Would You look?
What Do You Trust?

25. Question Everything online: www.dhmo.org

26. Di-Hydrogen Monoxide
2H

27. Di-Hydrogen Monoxide
2H + 1O

28. Di-Hydrogen Monoxide
H2O

29. Di-Hydrogen Monoxide
H2O
Water

30. It’s all on Wikipedia…

31. Chemistry on The Internet Is Messy

32. It’s Methane…

33. What’s Methane?

34. What’s Methane?

35. What ELSE is Methane???

36. PubChem

37. Chemistry is REALLY Messy

38. Vancomycin
 Who will curate?
 How would you clean such
a large dataset?
 Assertions!!!

39. Vancomycin on ChemSpider
1 compound – 3 days

40. The EXPERTS must get it right?!

41. Wikipedia, C&E News, PubChem
C&E News (from ACS)

42. The InChI Identifier

43. Multiple Layers

44. InChIStrings Hash to InChIKeys

45. InChIs for Taxol

46. InChIKeys for Taxol
 DrugBank: RCINICONZNJXQF-CLDWUXIMDD
 ChEBI: RCINICONZNJXQF-GXKQXQCDDN
 Wikipedia: RCINICONZNJXQF-MZXODVADBJ
 ChEBI and Wikipedia are the SAME structure
 Drugbank is a DIFFERENT structure – ONE
stereocenter

47. Does one stereocenter matter?

48. Does one stereocenter matter?
 Distaval, Talimol, Nibrol,
Sedimide, Quietoplex,
Contergan, Neurosedyn,
and Softenon

49. Does one stereocenter matter?
 Distaval, Talimol, Nibrol,
Sedimide, Quietoplex,
Contergan, Neurosedyn,
and Softenon

50. Assertion and Chemical Entities
 Who says what Taxol is?
 What is the “timeline” for a molecule?
 How do we clean up the Public data?
 The Quality source is Chemical Abstracts Service…

51. Vancomycin – Search the Internet

52. Full Molecule Search: 4 Hits

53. Full Skeleton Search: 104 Hits

54. The InChI “Resolver”

55. Citizen Scientists

56. Crowd-sourcing Chemistry Curation
 Crowd-sourced curation: identify/tag errors, edit
names, synonyms, identify records to deprecate

57. Building a Structure Centric
Multi-level Curation and Approval

58. Citizens as Data Sources

60. Semantic Markup: Project Prospect

61. Entity-Extraction, Mark-up, Annotate

62. Success Depends on Dictionaries

63. ChemMantis and CJOC

64. Name-Structure Pairs

65. Species – linked to Wikipedia

66. Semantic Linking of Structures
 What would you want
to link off a structure?
 Chemical suppliers
 Other publications
 Analytical Data
 Related Reactions
 Wikipedia
 Patents
 “Everything”

67. ChemSpider Everywhere : Embed

68. ChemSpider Everywhere: Spectral Game

69. ChemSpider Everywhere
Crowdsourced Curation of Spectra

70. ChemSpider Everywhere:
What do computers want?
Web services
flickr.com/photos/microcosmos

71. ChemSpider Everywhere
 Linked from Wikipedia and many Public Databases
 Linked from Open Notebook Science sites
 Linked from Blogs using Structure/Spectra EMBED
 Integrated into structure drawing packages
 Integrated to software offerings from Thermo,
Waters, Agilent, Bruker

72. ChemSpider Everywhere: ChemMobi

73. There will always be gaps...
 What ChemSpider does not deal with, yet...
 Materials
 Minerals
 Polymers
 Biological macromolecules

74. Open Source, Access and Data
 ChemSpider is NOT Open Source but we do use
Open Source components (OpenBabel,
JSpecView, Jmol). Thanks Microsoft!
 ChemSpider is not an “Open Access Database” –
it’s a “free access” resource
 We do not assume copyright. Rights to the data
and the creative works remain with the depositor
 Is ChemSpider “Open Data”?

75. Open Data?

76. Who declares data as Open?
 Data licensing is very interesting and can spark
“interesting” conversations. Opinions differ:
 Are images data? Are assertions data?
 What on a ChemSpider record is data?
 Is PubChem or PubMed Open Data?
 We allow people to declare their data as Open and
add an Open Data button at upload
 A lot of data on ChemSpider are free but not Open
 Pragmatism: Our focus is a community resource

77. Conclusions: ChemSpider Today
 ChemSpider is an established community resource
 >23 million compounds from >300 data sources
 About 7000 unique users per day and up to ½ million
transactions per day
 A crowdsourced deposition and curation platform
 Grows daily – more depositions, more links, more data
 Web services provider
 Linked to commercial and open source software
 Supporting analytical companies: Agilent, Thermo, Waters, Bruker
 Serving ONS, providing games to students, ChemSpidey robot
 A publishing platform for the community

78. ChemSpider Tomorrow
 Continue the curation effort and keep cleaning
 Finish depositions – millions left to deposit
 Integrate RSC content – a massive archive!
 Integrate RSC publishing workflows and databases
 Enable the semantic web for chemistry

79. Acknowledgments
 Royal Society of Chemistry
 Valery Tkachenko and Sergey Shevelev
 Commercial Software: Microsoft, Advanced
Chemistry Development, OpenEye and Symyx
 Open Source Software: Jmol, OpenBabel,
JSpecView
 JC Bradley, Andrew Lang – The Spectral Game
and Open Notebook Science integration
 The “Crowd” of curators
 306 Data Source providers
 SyntheticPages.org

80. Thank you
antony.williams@chemspider.com
Twitter: ChemSpiderman
www.chemspider.com/blog
SLIDES: www.slideshare.net/AntonyWilliamsSLIDES: www.slideshare.net/AntonyWilliams