Citizen Scientists and Their Contributions to Internet Based Chemistry


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This is a presentation I gave to a group of students at Drexel University via webex and skype. This is the Powerpoint presentation component but it was intersected with a live demo of multiple online databases. The movie of the presentation is online at SciVee here:

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Citizen Scientists and Their Contributions to Internet Based Chemistry

  1. 1. Citizen Scientists and Their Contributions to Internet Based Chemistry
  2. 2. Citizen Scientists Enable the Web <ul><li>Who is writing about chemical compounds on Wikipedia? </li></ul><ul><li>Who is writing critical reviews of Chemistry online? </li></ul><ul><li>Who is blogging about chemistry on the web? </li></ul>
  3. 3. Org Prep Daily (Blog)
  4. 4. Encyclopedic Articles (Wikipedia)
  5. 5. Chemistry online – An Overview <ul><li>Encyclopedic articles (Wikipedia) </li></ul><ul><li>Chemical vendor databases </li></ul><ul><li>Metabolic pathway databases </li></ul><ul><li>Property databases </li></ul><ul><li>Chemical Synthesis procedures </li></ul><ul><li>Scientific publications </li></ul><ul><li>Chemical vendors </li></ul><ul><li>Blogs </li></ul><ul><li>Wikis </li></ul><ul><li>Open Notebook Science </li></ul>
  6. 6. What and who do you trust?
  7. 7. Compounds and Identifiers
  8. 8. What is ChemSpider? <ul><li>ChemSpider is: </li></ul><ul><ul><li>Building a Structure Centric Community for Chemists </li></ul></ul><ul><ul><li>>23 million compounds, ca. 250 data sources </li></ul></ul><ul><ul><li>A deposition and curation platform </li></ul></ul><ul><ul><li>A publishing platform for the community </li></ul></ul><ul><ul><li>Grows daily – more depositions, more links, more data sources </li></ul></ul>
  9. 9. Search Cholesterol
  10. 10. Search Cholesterol <ul><li>Perform Real Search on Cholesterol </li></ul>
  11. 11. Link off a structure in ChemSpider <ul><ul><li>Chemical suppliers </li></ul></ul><ul><ul><li>Other publications </li></ul></ul><ul><ul><li>Analytical Data </li></ul></ul><ul><ul><li>Related Reactions </li></ul></ul><ul><ul><li>Wikipedia </li></ul></ul><ul><ul><li>Patents </li></ul></ul><ul><ul><li>“ Everything” </li></ul></ul>
  12. 12. Answering Questions for Chemists <ul><li>Questions a chemist might ask… </li></ul><ul><ul><li>What is the melting point of n-butanol? </li></ul></ul><ul><ul><li>What is the chemical structure of Xanax? </li></ul></ul><ul><ul><li>Chemically, what is phenolphthalein? </li></ul></ul><ul><ul><li>What are the stereocenters of cholesterol? </li></ul></ul><ul><ul><li>Where can I find publications about xylene? </li></ul></ul><ul><ul><li>What are the different trade names for Ketoconazole? </li></ul></ul><ul><ul><li>What is the NMR spectrum of Aspirin? </li></ul></ul><ul><ul><li>What are the safety handling issues for Thymol Blue? </li></ul></ul>
  13. 13. What is Flibanserin?
  14. 14. What is the structure of Flibanserin?
  15. 15. What is the structure of Flibanserin?
  16. 16. Complex Data and Information
  17. 17. Various Searches <ul><li>Structure searching </li></ul><ul><li>Substructure searching </li></ul><ul><li>Subset searching – choose from 200 data sources </li></ul><ul><li>Property searching </li></ul><ul><li>Searches are used in various ways by different types of chemists… </li></ul>
  18. 18. ChemSpider Searches
  19. 19. ChemSpider Searches
  20. 20. Aspirin On Wikipedia
  21. 21. Aspirin names and synonyms <ul><li>Text searches depend on correct association </li></ul><ul><li>335 suggested identifiers for Aspirin just on PubChem! </li></ul><ul><li>Disambiguation dictionaries are necessary </li></ul>
  22. 25. The Final Search Strategy
  23. 26. All Those Names, One Structure
  24. 27. The InChI Identifier
  25. 28. Multiple Layers
  26. 29. InChIStrings Hash to InChIKeys
  27. 30. Oleoylethanolamine
  28. 31. Search Engine Dependencies
  29. 32. Search Engine Dependencies
  30. 33. Vancomycin
  31. 34. Vancomycin on PubChem
  32. 35. Methane on PubChem
  33. 36. Question Everything online:
  34. 37. Vancomycin on ChemSpider
  35. 38. Vancomycin
  36. 39. Vancomycin Search Molecular SKELETON Search Full Molecule
  37. 40. The EXPERTS must get it right?!
  38. 41. Wikipedia, C&E News, PubChem <ul><li>C&E News (from ACS) </li></ul>
  39. 42. Citizen Scientists
  40. 43. Crowd-sourcing Chemistry Curation <ul><li>Crowd-sourced curation: identify/tag errors, edit names, synonyms, identify records to deprecate </li></ul>
  41. 44. Curate Fostriecin <ul><li>Search Fostriecin on ChemSpider </li></ul><ul><li>Curate it </li></ul>
  42. 45. Become a Data Source
  43. 47. Synthesis Procedures
  44. 48. Links to Data or Deposit Data
  45. 49. Upload Spectral Data, OPEN Data?
  46. 50. Semantic Mark-up for Chemistry <ul><li>Semantic mark-up for chemistry is here </li></ul><ul><ul><li>RSC project prospect (structure linking, IUPAC Gold Book ontology and other ontologies). Based on the OSCAR system </li></ul></ul><ul><ul><li>ChemSpider Journal of Chemistry </li></ul></ul><ul><ul><li>Nature publishing group compound linking </li></ul></ul>
  47. 51. ChemMantis and CJOC
  48. 52. Name-Structure Pairs
  49. 53. Deposit Structures
  50. 54. Species – linked to Wikipedia
  51. 55. In Development ChemSpider Synthesis <ul><li>ChemSpider Synthesis will be a home for all things “synthetic” </li></ul><ul><li>An online resource for synthetic procedures from blogs, other online resources, RSC supplementary info, other publishers etc. </li></ul><ul><li>Public peer-review and feedback for synthetic procedures </li></ul>
  52. 56. Online Journals and Live Data
  53. 57. ChemSpider Everywhere : Embed
  54. 58. ChemSpider Everywhere: Spectral Game
  55. 59. ChemSpider Everywhere Crowdsourced Curation of Spectra
  56. 60. ChemSpider Everywhere ChemMobi
  57. 61. People Make Change Happen You are invited.. <ul><li>Curate ChemSpider data and link to us </li></ul><ul><li>Deposit your data with us </li></ul><ul><ul><li>Structures </li></ul></ul><ul><ul><li>Spectra </li></ul></ul><ul><ul><li>Synthesis procedures </li></ul></ul><ul><li>ChemSpider Synthesis is under development </li></ul>
  58. 62. Thank you [email_address] Twitter: ChemSpiderman SLIDES: