The document discusses the messy state of chemistry data online and proposes crowdsourcing as a way to curate and clean up public compound databases. It describes efforts by the ChemSpider database to leverage crowdsourcing for tasks like identifying errors, standardizing names and structures, and linking related information. The author argues that widespread adoption of data standards like InChI could help bring order to chemistry information on the internet.

1. Delivering Curated Chemistry to the World via Crowdsourced Deposition and Annotation on ChemSpider Antony Williams University of Chicago, January 27 th 2012

3. We Have …Too Much Data!!!

5. TotallySynthetic.com

7. PubChem

8. ChEMBL

9. Collaborative Knowledge Management

11. RSC’s ChemSpider

13. Available Information….

16. Spectra

17. Spectra

18. Data on the Web

20. The Structure of Vitamin K?

22. The Structure of Vitamin K1?

23. What is the Structure of Vitamin K1?

24. CAS’s Common Chemistry

25. Wikipedia

28. ChEBI – Manual Curation

33. Question Everything online: www.dhmo.org

34. It’s all on Wikipedia…

35. Chemistry on The Internet Is Messy

36. It’s Methane…

37. What’s Methane?

38. What’s Methane?

39. What ELSE is Methane???

41. EPA’s DailyMed

42. EPA’s DailyMed

43. EPA’s DailyMed

45. The Stereochemistry challenge. 12500 chemicals with “missed” stereo

46. With Great Fanfare…

47. NPC Browser http://tripod.nih.gov/npc/

48. NPC Browser http://tripod.nih.gov/npc/

50. Openness and Quality Issues Williams and Ekins, DDT, 16: 747-750 (2011) Science Translational Medicine 2011

52. Stop Whining – Fix it

54. Search “Vitamin H”

55. “ Curate” Identifiers

56. “ Curate” Identifiers

57. “ Curate” Identifiers

58. Standards : Structure Standardization

59. Standards : Structure Standardization

60. Standards : Structure Standardization

62. The InChI Identifier

63. Multiple Layers

64. InChIStrings Hash to InChIKeys

65. Vancomycin – Search the Internet

66. Vancomycin Search Molecular SKELETON Search Full Molecule

67. Full Skeleton Search: 104 Hits

68. Full Molecule Search: 4 Hits

71. Antony Williams vs Identifiers Passport ID Dad, Tony, others SSN Green Card License 5 email addresses ChemSpiderman (blog, Twitter account, Facebook, Friendfeed) OpenID … .

75. The Final Search Strategy

76. All Those Names, One Structure

77. Ambiguity in Identifiers

78. Curated Dictionaries Matter

79. Success Depends on Dictionaries

81. I want to know about “Vincristine” If all algorithms work then everything on the page is correct by default except the name-structure relationship!

82. Vincristine: Identifiers and Properties

83. Vincristine: Vendors and Sources Linked by Structure

84. Vincristine: Patents Linked by Name

85. Vincristine: Articles Linked by Name

86. Challenges of Complex Molecules Yohimbine

87. Originally 15 compounds “called” Yohimbine 54 Skeletons for Yohimbine

90. It is so difficult to navigate… What’s the structure? Are they in our file? What’s similar? What’s the target? Pharmacology data? Known Pathways? Working On Now? Connections to disease? Expressed in right cell type? Competitors? IP?

93. ChemSpider Resources for Chemistry

94. The Future Commercial Software Pre-competitive Data Open Science Open Data Publishers Educators Open Databases Chemical Vendors Small organic molecules Undefined materials Organometallics Nanomaterials Polymers Minerals Particle bound Links to Biologicals Internet Data

97. Thank you Email: williamsa@rsc.org Twitter: ChemConnector Blog: www.chemspider.com/blog Personal Blog: www.chemconnector.com SLIDES: www.slideshare.net/AntonyWilliams