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RSC ChemSpider for students

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This is a presentation I gave the the students at Duke University regarding RSC ChemSpider

This is a presentation I gave the the students at Duke University regarding RSC ChemSpider

Published in: Technology, Education

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Transcript

  • 1. ChemSpider – The Free Chemistry Database for the Community Antony Williams Duke University, September 17th 2012
  • 2. We Have …Too Much Data!!!
  • 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. 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. 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. I want to know about “Vincristine”
  • 7. Vincristine: Identifiers and Properties
  • 8. Vincristine: Vendors and Sources
  • 9. Vincristine: Patents
  • 10. Vincristine: Articles
  • 11. ChemSpider : Spectra Linked
  • 12. Sources of Spectra Sourced from online sources with permission Private collections The MAJORITY deposited by ChemSpider users
  • 13. Data Uploading – YOU HELP Locate the structure of interest and deposit spectrum
  • 14. Multiple Spectra for One Structure
  • 15. ChemSpider ID 24528095 H1 NMR
  • 16. ChemSpider ID 24528095 C13 NMR
  • 17. ChemSpider ID 24528095 HHCOSY
  • 18. Spectra Linked
  • 19. CURATION Search “Vitamin H”
  • 20. “Curate” Identifiers
  • 21. “Curate” Identifiers
  • 22. “Curate” Identifiers
  • 23. The InChI Identifier
  • 24. Multiple Layers
  • 25. InChIStrings Hash to InChIKeys
  • 26. Vancomycin – Search the Internet
  • 27. VancomycinSearch Molecular Search Full Molecule SKELETON
  • 28. Searches: The INTERNET
  • 29. Validated Names for Searching…
  • 30. And InChIs…
  • 31. ChemSpider Interface
  • 32. www.SpectralGame.comhttp://www.jcheminf.com/content/1/1/9
  • 33. Spectral Game
  • 34. Increasing Complexity
  • 35. Structure Database Lookup
  • 36. ChemSpider SyntheticPages
  • 37. ChemSpider Everywhere : ChemMobi
  • 38. SpectralGame in the hand
  • 39. ChemSpider Resources for Chemistry
  • 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. Thank youEmail: williamsa@rsc.orgTwitter: ChemConnectorBlog: www.chemspider.com/blogPersonal Blog: www.chemconnector.comSLIDES: www.slideshare.net/AntonyWilliams