This is a general presentation about our efforts to build an internet based community for chemists using ChemSpider. A general overview of data quality online, crowdsourced deposition and curation and our progress to deliver a solution to the community for resourcing data.

1. RSC ChemSpider – Building an Internet Based Community for Chemists

2. 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

3. Chemistry on the Internet TODAY Chemistry searches are generally limited to text-based searches across the internet Poor quality and little curation/validation work Too many searches required to resource data

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

5. Chemistry on the Internet FUTURE Search by chemical structure and substructure Chemistry articles indexed and searchable Reduced number of searches to find data Data are integrated – compounds, vendors, syntheses, data, publications and patents

6. For Synthesis…TotallySynthetic.com

7. Org Prep Daily (Blog)

8. Lots of “Public Compound” Databases PubChem Drugbank ChEBI/ChEMBL KEGG LipidMAPs ChemIDPlus eMolecules ZINC Lots of chemical vendors ChemSpider

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

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

11. What is a compound?

12. What is ChemSpider? ChemSpider is: Building a Structure Centric Community for Chemists >23 million compounds, >300 data sources A deposition and curation platform A publishing platform for the community Grows daily – more depositions, more links, more data sources

13. How Was ChemSpider Built? ChemSpider was a “hobby project” Housed in a basement and running off three servers – one bought, two built Sensitive to weather and power stability Went live at ACS Spring 2007 in Chicago

14. Search Cholesterol

15. Search Cholesterol

16. Search Cholesterol

17. Search Cholesterol

18. Search Cholesterol

19. Linked across the internet

20. Kyoto Encyclopedia of Genes and Genomes

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

22. Links to Patents based on structure

23. Clickthrough to Patents

24. Articles Linked

25. 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?

26. Complex Data and Information

27. 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?

28. What is a compound?

29. Question Everything online: www.dhmo.org

30. Di-Hydrogen Monoxide 2H

31. Di-HydrogenMonoxide 2H + 1O

32. Di-Hydrogen Monoxide H2O

33. Di-Hydrogen Monoxide H2O Water

34. It’s all on Wikipedia…

35. It’s all on Wikipedia…

36. Chemistry on The Internet Is Messy

37. It’s Methane…

38. What’s Methane?

39. What’s Methane?

40. What ELSE is Methane???

41. PubChem

42. Truly “I Love You”

43. Chemistry is REALLY Messy

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

45. Vancomycin Who will curate? How would you clean such a large dataset?

46. Vancomycin on ChemSpider 1 compound – 3 days

47. The EXPERTS must get it right?!

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

49. What About Digitonin?

50. CAS as an authority

51. The Blogging Community Participate

52. The FDA’s DailyMed

53. Structures on DailyMed

54. Lack of Stereochemisty

55. Incorrect Structures

56. Wow!

57. The InChI Identifier

58. Multiple Layers

59. InChIStrings Hash to InChIKeys

60. InChIs for Taxol

61. Back to Taxol DrugBank: RCINICONZNJXQF-CLDWUXIMDD ChEBI: RCINICONZNJXQF-GXKQXQCDDN Wikipedia: RCINICONZNJXQF-MZXODVADBJ Which one is correct???

62. 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

63. Does one stereocenter matter?

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

66. 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…

67. ChemSpider Searches

68. ChemSpider Searches

69. ChemSpider Complex Searches

70. Vancomycin – Search the Internet

71. Full Molecule Search: 4 Hits

72. Full Skeleton Search: 104 Hits

73. The InChI “Resolver”

74. Citizen Scientists

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

76. Building a Structure Centric Community for Chemists Multi-level Curation and Approval

77. Citizens as Data Sources

79. Entity-Extraction, Mark-up, Annotate

80. Success Depends on Dictionaries

81. Project Prospect

82. ChemMantis and CJOC

83. Name-Structure Pairs

84. Species – linked to Wikipedia

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

86. ChemSpider Everywhere Linked from Wikipedia Linked from Open Notebook Science sites using EMBED Linked from Blogs using Structure/Spectra EMBED Integrated into structure drawing packages such as ACD/ChemSketch, Symyx Draw, Open Source applets Integrated to software offerings from Thermo, Waters, Agilent, Bruker

87. ChemSpider Everywhere : Embed

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

89. ChemSpider Everywhere: Spectral Game

90. ChemSpider EverywhereCrowdsourced Curation of Spectra

91. ChemSpider EverywhereChemMobi

92. There are always gaps... What ChemSpider doesn’t deal with yet... Markush structures and other “non-defineds” Materials Minerals Polymers Biological macromolecules

93. What’s next? Continue the curation effort and keep cleaning Finish depositions – millions left to deposit Layer on RDF to allow the semantic web to benefit from our efforts Integrate RSC content – a massive archive! Integrate RSC publishing workflows and databases

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