ChemSpider – An Online Database and Registration System Linking the Web

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

This presentation was given at the EBI Meeting in Cambridge on October 11th 2011 regarding Chemical Registration and Standardization.

Technologie

ChemSpider – An Online Database and Registration System Linking the Web Antony Williams and Valery Tkachenko EBI Chemical Registry Systems Workshop, October 2011

ChemSpider… ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Vancomycin Search Molecular SKELETON Search Full Molecule

ChemSpider… ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

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

Vincristine: Vendors and Sources Linked by Structure

ORIGINAL ChemSpider ,[object Object],[object Object],[object Object],[object Object]

How do we build it? ,[object Object],[object Object],[object Object],[object Object],[object Object]

Downsides of InChI ,[object Object],[object Object],[object Object]

Standardization Issues Depiction based on molfile

Downsides of Overall Approach ,[object Object],[object Object],[object Object]

Originally 15 compounds “called” Yohimbine 54 Skeletons for Yohimbine

ChemSpider as an Aggregator ,[object Object],[object Object],[object Object],[object Object],[object Object]

Chemistry Databases on the Internet ,[object Object],[object Object],[object Object]

PHYSPROP Database ,[object Object],[object Object]

The Stereochemistry challenge. 12500 chemicals with “missed” stereo

Searches on ChemSpider ,[object Object],[object Object]

Synonyms on PubChem ,[object Object],[object Object],[object Object],[object Object],[object Object]

What is getting into Our Databases? ,[object Object],[object Object],[object Object]

Identifier Dictionaries ,[object Object],[object Object],[object Object]

Structure Validation using feed ,[object Object],[object Object],[object Object]

[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Adopting Modified FDA Rules ,[object Object]

Parent and Child ,[object Object],[object Object],[object Object],[object Object]

ChemSpider Standardization ,[object Object],[object Object],[object Object]

Project Status ,[object Object],[object Object],[object Object],[object Object]

Conclusions ,[object Object],[object Object],[object Object],[object Object]

Acknowledgments ,[object Object],[object Object],[object Object]

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 – An Online Database and Registration System Linking the Web

1. ChemSpider – An Online Database and Registration System Linking the Web Antony Williams and Valery Tkachenko EBI Chemical Registry Systems Workshop, October 2011

2. www.chemspider.com

4. Vancomycin

5. Vancomycin Search Molecular SKELETON Search Full Molecule

6. Full Skeleton Search: 104 Hits

7. Full Molecule Search: 4 Hits

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

10. Vincristine: Identifiers and Properties

11. Vincristine: Vendors and Sources Linked by Structure

12. Vincristine: Patents Linked by Name

13. Vincristine: Articles Linked by Name

14.

15.

16. InChIs – both on ChemSpider

17.

18. Side Effects of InChI Usage

19. SMILES by comparison…

20. Side Effects of InChI Usage

21. Standardization Issues Depiction based on molfile

22.

23. Yohimbine

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

25.

26.

27.

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

29.

30. NIST Webbook

31. PubChem

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

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

34.

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

36.

37. Synonyms on PubChem

38. Data Proliferation

39.

40.

41.

42.

43.

44. What is meant by a name?

45. Choose a Starting Point

46. “ The First 10”

47.

48. Standardization of Patent Data???

49. Standardization of Patent Data???

50. WYSIWYG compounds

51. WYSIWYG compounds

52. Text Mining Chemical Name Errors

53. “ DPA”

54. All aggegators suffer dilution!

55. Structures have timelines

56. Name-Structure Dictionaries…

57. Depiction for Humans

58. Human Depiction versus Algorithms

59. Human Depiction versus Algorithms

60.

61. Proof of Concept Data Curation Sharing

62.

63.

64.

65. Nitro groups

66. Salt and Ionic Bonds

67. Ammonium salts

68.

69.

70.

71.

72.

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

ChemSpider – An Online Database and Registration System Linking the Web

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