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Taming The Wild West Of Internet Based Chemistry You Can Help

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I am an adjunct prof at University of North Carolina Chapel Hill so when I stopped by yesterday for a business meeting I was informed that I had been lined up to give a talk to the students at 1pm. I …

I am an adjunct prof at University of North Carolina Chapel Hill so when I stopped by yesterday for a business meeting I was informed that I had been lined up to give a talk to the students at 1pm. I had 20 minutes to prepare and assembled a mish-mash of information that might be of value to Citizen Chemists, those who might want to contribute to chemistry on the internet

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  • 1. Taming the Wild, Wild West of Chemistry on the Internet. Maybe YOU Can Help?
  • 2. Citizen Scientists Enable the Web
    • Who is writing about chemical compounds on Wikipedia?
    • Who is writing critical reviews of Chemistry online?
    • Who is blogging about chemistry on the web?
  • 3. For Synthesis…TotallySynthetic.com
  • 4. Org Prep Daily (Blog)
  • 5. Molbank (Open Access Journal)
  • 6. Synthetic Pages (Website)
  • 7. Encyclopedic Articles (Wikipedia)
  • 8.  
  • 9. Chemistry online – An Overview
    • Encyclopedic articles (Wikipedia)
    • Chemical vendor databases
    • Metabolic pathway databases
    • Property databases
    • Chemical Synthesis procedures
    • Scientific publications
    • Chemical vendors
    • Blogs
    • Wikis
    • Open Notebook Science
  • 10. What and who do you trust?
  • 11. Compounds and Identifiers
  • 12. What is ChemSpider?
    • ChemSpider is:
      • Building a Structure Centric Community for Chemists
      • >23 million compounds, ca. 250 data sources
      • A deposition and curation platform
      • A publishing platform for the community
      • Grows daily – more depositions, more links, more data sources
  • 13. Search Cholesterol
  • 14. Search Cholesterol
  • 15. Search Cholesterol
  • 16. Search Cholesterol
  • 17. Search Cholesterol
  • 18. Linked across the internet
  • 19. Link off a structure in ChemSpider
      • Chemical suppliers
      • Other publications
      • Analytical Data
      • Related Reactions
      • Wikipedia
      • Patents
      • “ Everything”
  • 20. Linked to Millions of Articles
  • 21. 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?
  • 22. What is the structure of Flibanserin?
  • 23. What is the structure of Flibanserin?
  • 24. Complex Data and Information
  • 25. Various Searches
    • Structure searching
    • Substructure searching
    • Subset searching – choose from 200 data sources
    • Property searching
    • Searches are used in various ways by different types of chemists…
  • 26. ChemSpider Searches
  • 27. ChemSpider Searches
  • 28. Antony Williams vs Identifiers Passport ID Dad, Tony, others SSN Green Card License 5 email addresses ChemSpiderman (blog, Twitter account, Facebook, Friendfeed) OpenID … .
  • 29. Aspirin vs Chemical Identifiers
  • 30. Aspirin names and synonyms
    • Text searches depend on correct association
    • 335 suggested identifiers for Aspirin just on PubChem!
    • Disambiguation dictionaries are necessary
  • 31.  
  • 32.  
  • 33.  
  • 34. The Final Search Strategy
  • 35. All Those Names, One Structure
  • 36. Connections Can Lead Anywhere
  • 37. The InChI Identifier
  • 38. Multiple Layers
  • 39. InChIStrings Hash to InChIKeys
  • 40. Oleoylethanolamine
  • 41. Search Engine Dependencies
  • 42. Search Engine Dependencies
  • 43. Vancomycin
  • 44. Vancomycin
    • Who will curate?
    • How would you clean such a large dataset?
  • 45. Chemistry on the Internet
    • Much of the information is based on assertions and User Beware!
    • The Quality of information available is diverse and how does the user know what is and is not “correct”?
  • 46. Caution! Question Everything!
  • 47. Question Everything online: www.dhmo.org
  • 48. Vancomycin on ChemSpider
  • 49. Vancomycin
  • 50. Vancomycin Search Molecular SKELETON Search Full Molecule
  • 51. Full Skeleton Search: 104 Hits
  • 52. Full Molecule Search: 4 Hits
  • 53. The EXPERTS must get it right?!
  • 54. Wikipedia, C&E News, PubChem
    • C&E News (from ACS)
  • 55. “ Lathosterol”
  • 56. “ Lathosterol”
  • 57. “ Lathosterol”
  • 58. “ Lathosterol” Removed
  • 59.  
  • 60. “ Lathosterol” on PubChem
  • 61. Crowd-sourcing Chemistry Curation
    • Crowd-sourced curation: identify/tag errors, edit names, synonyms, identify records to deprecate
  • 62. Citizen Scientists
  • 63. Become a Data Source
  • 64.  
  • 65. Synthesis Procedures
  • 66. Links to Data or Deposit Data
  • 67. Your Blog Posted Online?
  • 68. Upload Spectral Data, OPEN Data?
  • 69. Semantic Mark-up for Chemistry
    • Semantic mark-up for chemistry is here
      • RSC project prospect (structure linking, IUPAC Gold Book ontology and other ontologies). Based on the OSCAR system
      • ChemSpider Journal of Chemistry
      • Nature publishing group compound linking
  • 70. ChemMantis and CJOC
  • 71. Name-Structure Pairs
  • 72. Deposit Structures
  • 73. Species – linked to Wikipedia
  • 74. In Development ChemSpider Synthesis
    • ChemSpider Synthesis will be a home for all things “synthetic”
    • An online resource for synthetic procedures from blogs, other online resources, RSC supplementary info, other publishers etc.
    • Public peer-review and feedback for synthetic procedures
  • 75. Online Journals and Live Data
  • 76. ChemSpider Everywhere : Embed
  • 77. ChemSpider Everywhere: Spectral Game
  • 78. ChemSpider Everywhere Crowdsourced Curation of Spectra
  • 79. ChemSpider Everywhere ChemMobi Building a Structure Centric Community for Chemists
  • 80. ChemSpider Everywhere
    • Linked from Wikipedia
    • Linked from Open Notebook Science sites
    • Linked from Blogs using Structure/Spectra
    • Integrated into structure drawing packages such as ACD/ChemSketch, Symyx Draw, Open Source applets
  • 81. Where is ChemSpider Lacking?
    • ChemSpider is limited to “defined chemicals”. No support for:
      • Polymers
      • Minerals
      • Markush structures
    • ChemSpider is very dependent on InChIs
      • Stereochemistry around non-carbon centers
      • Organometallics are not correctly represented
    • There are millions of errors on ChemSpider
  • 82. What’s next?
    • Keep cleaning and depositing data
    • Enable discovery via the semantic web (RDF)
    • Integrate software: Symyx Jdraw, NMRShiftDB
    • Integrate RSC content – a massive archive!
    • Integrate RSC publishing workflows and databases
  • 83.
    • Continue Building Community for Chemistry
    • Building a Public ADME/Tox database
    • Delivering ChemSpider Synthetic Pages
    • Delivering ChemSpider Analytical Data
    • Delivering ChemSpider Education
    Project Focus
  • 84. People Make Change Happen You are invited..
    • Curate ChemSpider data and link to us
    • Deposit your data with us
      • Structures
      • Spectra
      • Synthesis procedures
    • ChemSpider Synthesis is under development
  • 85. People Make Change Happen
    • 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
    • ca. 6000 visitors a day, >50,000 transactions daily
  • 86. Organizations Scale Innovation
  • 87. Thank you [email_address] Twitter: ChemSpiderman www.chemspider.com/blog SLIDES: www.slideshare.net/AntonyWilliams