RSC ChemSpider for students

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This presentation is an overview of ChemSpider delivered to a group of students at Duke University in North Carolina on September 17th 2012.

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RSC ChemSpider for students

  1. 1. ChemSpider – The Free Chemistry Database for the Community Antony Williams Duke University, September 17th 2012
  2. 2. We Have …Too Much Data!!!
  3. 3. The World of Online Chemistry Property databases Compound aggregators Screening assay results Scientific publications Encyclopedic articles (Wikipedia) Metabolic pathway databases ADME/Tox data – eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source code to projects
  4. 4. ChemSpider The Free Chemical Database A central hub for chemists to source information  >28 million unique chemical records  Aggregated from >400 data sources  Chemicals, spectra, CIF files, movies, images, podcasts, links to patents, publications, predictions A central hub for chemists to deposit & curate data
  5. 5. We Want to Answer Questions Questions a chemist might ask…  What is the melting point of n-heptanol?  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?
  6. 6. I want to know about “Vincristine”
  7. 7. Vincristine: Identifiers and Properties
  8. 8. Vincristine: Vendors and Sources
  9. 9. Vincristine: Patents
  10. 10. Vincristine: Articles
  11. 11. ChemSpider : Spectra Linked
  12. 12. Sources of Spectra Sourced from online sources with permission Private collections The MAJORITY deposited by ChemSpider users
  13. 13. Data Uploading – YOU HELP Locate the structure of interest and deposit spectrum
  14. 14. Multiple Spectra for One Structure
  15. 15. ChemSpider ID 24528095 H1 NMR
  16. 16. ChemSpider ID 24528095 C13 NMR
  17. 17. ChemSpider ID 24528095 HHCOSY
  18. 18. Spectra Linked
  19. 19. CURATION Search “Vitamin H”
  20. 20. “Curate” Identifiers
  21. 21. “Curate” Identifiers
  22. 22. “Curate” Identifiers
  23. 23. The InChI Identifier
  24. 24. Multiple Layers
  25. 25. InChIStrings Hash to InChIKeys
  26. 26. Vancomycin – Search the Internet
  27. 27. VancomycinSearch Molecular Search Full Molecule SKELETON
  28. 28. Searches: The INTERNET
  29. 29. Validated Names for Searching…
  30. 30. And InChIs…
  31. 31. ChemSpider Interface
  32. 32. www.SpectralGame.comhttp://www.jcheminf.com/content/1/1/9
  33. 33. Spectral Game
  34. 34. Increasing Complexity
  35. 35. Structure Database Lookup
  36. 36. ChemSpider SyntheticPages
  37. 37. ChemSpider Everywhere : ChemMobi
  38. 38. SpectralGame in the hand
  39. 39. ChemSpider Resources for Chemistry
  40. 40. Conclusions ChemSpider is a FREE resource for the community Grows daily with new data – do you have any to share? Concerned about data quality! YOU SHOULD BE! Crowdsourced and algorithmic curation is working API is available to access data – any informatics people want access?? If you want hands on training I can come and give it
  41. 41. Thank youEmail: williamsa@rsc.orgTwitter: ChemConnectorBlog: www.chemspider.com/blogPersonal Blog: www.chemconnector.comSLIDES: www.slideshare.net/AntonyWilliams
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