The document discusses the creation of ChemSpider, a crowdsourced chemical database aimed at the chemistry community, emphasizing the challenges of finding and validating chemical data online. It outlines the importance of structure-centric data aggregation and the role of community contributions in improving data accuracy. The future vision includes enhanced searching capabilities by chemical structure and a push for open access to chemical information.

1. ChemSpider - Building a Crowdsourced Chemical Database for the Chemistry Community OpenSciNY, New York, May 2010,

2. Once Upon a Time Over a “Coffee”

3. Which is better for Plants? Vodka, Sprite or Viagra?

4. It Works – Viagra Wins the Day

5. Now Which is Better? Viagra or Cialis? Images sourced from Wikipedia

6. Cialis I want… The structure Any patent information Related publications Where can I buy it? Metabolic pathway info What else is easy to find…

7. Cialis on Google?

8. What is Cialis?

9. What is Cialis? Can we trust Wikipedia?

10. What is Cialis? 6 hits on PubChem

11. What is Cialis?

12. Search by Trade Name

13. Are there other names???

14. Are there other names??? PubMed hits: 736 Tadalafil 744 Cialis

15. Are there other names???

16. Are There Other Names?

17. IC351 on PubChem? 5 HITS for IC351 ZERO HITS for IC 351

18. Chemistry on the Web Text searching the web is far from optimal The quality of data on the web is a problem It may be hard to find but it is “out there” What was once locked up behind an expensive license can generally be found Structure searching the web is already possible!

19. Text Searching the Web Text searching the web for chemical compounds is an enormous challenge RSC has multiple databases, >500,000 articles and a lot of other resources. How do we do?

20. The RSC Publishing Platform (Beta)

21. 2+2 = 4 Articles?

22. CAS Number Search

23. Text Searching the Web Disambiguation dictionaries of name-structure relationships would be very enabling. IC351 = IC 351 = Tadalafil = Cialis = … Creating validated dictionaries is an enormous challenge to cover chemistry

24. CAS Registry – LOTS of Chemicals!

27. The Final Search Strategy A “Disambiguation Query!”

28. All Those Names, One Structure A problem to solve…

29. ChemSpider - A Pragmatic Vision “ Build a Structure Centric Community to Serve Chemists” Aggregate and integrate chemical structure data on the web – names, structures, links Create a “structure-based hub” to information, data and algorithmic predictions Let chemists contribute their own data Allow the community to curate/correct data

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

31. Aggregating Data – Who to Trust??? 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

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

33. Question Everything online: www.dhmo.org

34. Di-Hydrogen Monoxide 2H

35. Di-Hydrogen Monoxide 2H + 1O

36. Di-Hydrogen Monoxide H2O

37. Di-Hydrogen Monoxide H2O Water

38. It’s all on Wikipedia…

39. What About Gases? Methane…

40. What’s Methane?

41. What’s Methane?

42. What ELSE is Methane???

43. Structural Data for Life Sciences DailyMed

44. Lack of Stereochemisty

45. Incorrect Structures

46. Pragmatic Vision Delivered… Aggregate, integrate and link data from across the internet Almost 25 million structures from > 300 data sources Linked to vendors, literature, online databases (open and commercial), open notebook science, patents and…. Robotic and Crowdsourced Curation

47. Search “OEA”

48. Search OEA

49. Search OEA

50. Search OEA

51. Linked Patents for OEA

52. Answering Questions… Questions a student might ask… What is the structure of levulinic acid? 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? How can I synthesize 2,4-dichlorophenol? What are the safety handling issues for Thymol Blue?

53. Back to Cialis…

54. Cialis on ChemSpider : 1 hit Chemicals are curated/validated on ChemSpider by ourselves and the community Based on assertions from various sources. Iterative, time-consuming and exacting! We believe we know the structure now What is linked and available?

55. Google Patents

56. ChemSpider – Patents Linked SURECHEM PATENTS GOOGLE

57. Google Books

58. Microsoft Academic Search

59. Google Scholar – Articles were found by CAS Number !

60. Identifiers for Tadalafil

61. How Many Articles in RSC Journals ? Based on 171596-29​-5 there are 13 articles in RSC journals What about if we VALIDATE identifiers?

62. Validated Dictionaries Hit APIs This is data curation...

63. Does this generate more results?

64. RSC Journals

65. RSC Journals REMEMBER 2+2 = 4

66. PubMed

67. Google Scholar – Expanded Hit Set

68. Microsoft Academic Search

69. Microsoft Academic Search Be careful! More mussels than drugs…

70. Searching Chemistry on the Internet Do we get complete a result set will we get if we search for “chemicals” only by name? Is there a better way to link chemistry databases? Linking by “names” is dangerous Chemists want structure and SUBstructure searching

71. Structure Searching the Web We have resources about Tadalafil actively linked to ChemSpider What about searching the web for Tadalafil by structure…not based on the various identifiers How?

72. Link the Internet with InChIKeys! Taken from: Rafael Sidis’ Blog

73. The InChI Identifier

74. Multiple Layers

75. InChIStrings Hash to InChIKeys

76. Cialis – Searching the Web by InChI Search Molecular SKELETON Search Full Molecule

77. InChI Search the Web by Skeleton 78 Hits by Skeleton

78. InChI Search the Web Exact Match 32 Hits by InChIKey

79. InChI Search the Web Exact Match 6 Hits by Standard InChIKey

80. InChifying the Web There are more than 2X “skeletons” for Cialis than exact matches – different stereo? Mistakes? Our judgment…MISTAKES

81. Vancomycin – Search the Internet

82. Full Molecule Search: 4 Hits

83. Full Skeleton Search: 104 Hits

84. InChIKeys Make the internet searchable by adding InChIKeys Publishers add InChIKeys to papers now… But what is the structure???

85. We need an InChI “Resolver”

86. InChI Resolver to DOIs Structure Search the Web

87. Semantic Markup: Project Prospect

88. Depends on Validated Dictionaries Link to a Structure or the Right Structure?

89. Name-Structure Pairs

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

91. Unpublished Chemistry Only a fraction of chemistry is published Only a tiny fraction of chemistry is patented What of the “Lost Chemistry”- never published and cannot be abstracted Reactions performed Structures made and studied Spectra acquired and then disposed of Available chemicals never found

92. Org Prep Daily (Blog)

93. ChemSpider SyntheticPages

94. Submission process Register as a user Use the Submit button and fill in the fields…

95. Submission Process Submissions reviewed by editorial board Published as is or comments sent to author Online Peer Review process Data supported include web movies, images, live spectra etc.

96. Micro- and Nano-publications Blogs, wiki entries and even Amazon book reviews are micro/nano-publications ChemSpider SyntheticPages will be DOI’ed – students can add these “micro-publications” to their resume Structures and spectra are nano-publications – these can be tracked and referenced also. (depositions, curations etc). Students participate in building one of the premier sources of chemistry data.

97. ChemSpider : Spectra Linked

98. Spectra Linked

99. Spectra Linked

100. Not Just NMR Data

101. www.SpectralGame.com http://www.jcheminf.com/content/1/1/9

102. Spectral Game

103. Increasing Complexity

104. Spectral Game

105. ChemSpider Content ChemSpider is a container…supports multimedia Spectra Crystal structures Images MP3s Videos

106. Roses’ Crystal Image Collection

107. MP3s and Videos : Titanium

108. Periodic Table Images

109. How Can You Help ChemSpider? Deposit your data and share with the community Structures – one or many Spectra Links Syntheses into SyntheticPages Curate data – most basic level…just add comments Spread the word – ChemSpider is an untapped resource

110. Community Contribution We can make a bigger contribution to the community if the community shares via ChemSpider Don’t underestimate what others will find of value ChemSpider wins “Community contribution” best practice award”

111. 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

112. Thank you [email_address] Twitter: ChemSpiderman www.chemspider.com/blog SLIDES: www.slideshare.net/AntonyWilliams