ChemSpider as a Platform for Crowd Participation in Curating Chemistry

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US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure

This is a presentation I gave at the International Digital Curation Conference in Chicago, December 7th 2010, #idcc10. The presentation discusses the issues of data quality and the need for collective, crowdsourced efforts to improve the quality of chemistry related data on the Internet

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ChemSpider as a Platform for Crowd Participation in Curating Chemistry Antony Williams IDCC, Chicago, December 2010

Di-Hydrogen Monoxide ,[object Object],[object Object]

Chemistry on the Internet – Not All Bad ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

A Pragmatic Vision ,[object Object],[object Object],[object Object],[object Object],[object Object]

Answering Questions for Chemists ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

ChemSpider Today ,[object Object],[object Object],[object Object],[object Object],[object Object]

Three Years of Experience ,[object Object],[object Object],[object Object],[object Object],[object Object]

Where is chemistry online? ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

MeSH – Medical Subject Headings ,[object Object]

Chemical Abstracts “Common Chemistry” Database

Does stereochemistry matter? ,[object Object]

Internet-Based Chemistry is a Mess ,[object Object],[object Object],[object Object]

Crowd-sourcing Chemistry Curation ,[object Object]

“ Curate” Identifiers ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Crowdsourcing Works ,[object Object],[object Object],[object Object],[object Object]

Crowdsourcing Works ,[object Object],[object Object],[object Object],[object Object],[object Object]

Vancomycin on ChemSpider 1 compound – 3 days

Crowdsourced “Annotations” ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

ChemSpider Everywhere Crowdsourced Curation of Spectra

Drug Name Generic Name ChEBI ChemSpider CAS Com. Chem ChemIDPlus DailyMed DrugBank PubChem Wikipedia Spiriva Tiotropium Bromide No Hits  No Hits    4/0  Depakote Valproate semisodium        No Structure Basen Voglibose   No Hits  No Hits  2/1  Symbicort 1) Budesonide       8/1  Symbicort 2) Formoterol WRONG  No Hits    6/1  Vytorin 1) Ezetimibe   No Hits      Vytorin 2) Simvastatin       2/1  Taxol Paclitaxel       44/1  Thalidomid Thalidomide No Hits        Zocor Simvastatin       2/1  Crestor Rosuvastatin   No Hits    2/1 

Sharing Our Activities ,[object Object],[object Object],[object Object]

First request to Database Hosts! ,[object Object]

Second request to Database Hosts! Show Comments

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

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ChemSpider as a Platform for Crowd Participation in Curating Chemistry

1. ChemSpider as a Platform for Crowd Participation in Curating Chemistry Antony Williams IDCC, Chicago, December 2010

2. WARNING: Chemistry is Dangerous

3. Di-Hydrogen Monoxide

8. It’s all on Wikipedia…

10. Dialects describing chemicals

11.

12. www.chemspider.com

13.

14. Search for a Chemical…by name

15.

16. Available Information….

17.

18.

19. Linked Data on the Web

20.

21. What is the Structure of Vitamin K?

22.

23. What is the Structure of Vitamin K1?

24. What is the Structure of Vitamin K1?

25. Chemical Abstracts “Common Chemistry” Database

26. Wikipedia

27.

28. Incorrect Structures

29. Lack of Stereochemistry

30.

31.

32. PubChem

33.

34.

35. What’s Methane?

36. What’s Methane?

37. What ELSE is Methane???

38.

39. Search “Vitamin H”

40. Search “Vitamin H”

41. “ Curate” Identifiers

42. “ Curate” Identifiers

43. “ Curate” Identifiers

44.

45.

46.

47.

48. Vancomycin – Curate This!!!

49. Vancomycin on ChemSpider 1 compound – 3 days

50.

51. Multimedia Content Holder

52. Gaming for Curation of Spectra

53. ChemSpider Everywhere Crowdsourced Curation of Spectra

54. Data Curation

55. True Curation of Data

56. ChemSpider SyntheticPages

57. Drug Name Generic Name ChEBI ChemSpider CAS Com. Chem ChemIDPlus DailyMed DrugBank PubChem Wikipedia Spiriva Tiotropium Bromide No Hits  No Hits    4/0  Depakote Valproate semisodium        No Structure Basen Voglibose   No Hits  No Hits  2/1  Symbicort 1) Budesonide       8/1  Symbicort 2) Formoterol WRONG  No Hits    6/1  Vytorin 1) Ezetimibe   No Hits      Vytorin 2) Simvastatin       2/1  Taxol Paclitaxel       44/1  Thalidomid Thalidomide No Hits        Zocor Simvastatin       2/1  Crestor Rosuvastatin   No Hits    2/1 

58.

59. Mobile ChemSpider

60.

61. Second request to Database Hosts! Show Comments

62. Question Quality

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

ChemSpider as a Platform for Crowd Participation in Curating Chemistry

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