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Chemical Information Retrieval Class 1
Chemical Information Retrieval Class 1
Chemical Information Retrieval Class 1
Chemical Information Retrieval Class 1
Chemical Information Retrieval Class 1
Chemical Information Retrieval Class 1
Chemical Information Retrieval Class 1
Chemical Information Retrieval Class 1
Chemical Information Retrieval Class 1
Chemical Information Retrieval Class 1
Chemical Information Retrieval Class 1
Chemical Information Retrieval Class 1
Chemical Information Retrieval Class 1
Chemical Information Retrieval Class 1
Chemical Information Retrieval Class 1
Chemical Information Retrieval Class 1
Chemical Information Retrieval Class 1
Chemical Information Retrieval Class 1
Chemical Information Retrieval Class 1
Chemical Information Retrieval Class 1
Chemical Information Retrieval Class 1
Chemical Information Retrieval Class 1
Chemical Information Retrieval Class 1
Chemical Information Retrieval Class 1
Chemical Information Retrieval Class 1
Chemical Information Retrieval Class 1
Chemical Information Retrieval Class 1
Chemical Information Retrieval Class 1
Chemical Information Retrieval Class 1
Chemical Information Retrieval Class 1
Chemical Information Retrieval Class 1
Chemical Information Retrieval Class 1
Chemical Information Retrieval Class 1
Chemical Information Retrieval Class 1
Chemical Information Retrieval Class 1
Chemical Information Retrieval Class 1
Chemical Information Retrieval Class 1
Chemical Information Retrieval Class 1
Chemical Information Retrieval Class 1
Chemical Information Retrieval Class 1
Chemical Information Retrieval Class 1
Chemical Information Retrieval Class 1
Chemical Information Retrieval Class 1
Chemical Information Retrieval Class 1
Chemical Information Retrieval Class 1
Chemical Information Retrieval Class 1
Chemical Information Retrieval Class 1
Chemical Information Retrieval Class 1
Chemical Information Retrieval Class 1
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Chemical Information Retrieval Class 1

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Jean-Claude Bradley presents the first lecture of Chemical Information Retrieval in the Fall of 2012 at Drexel University.

Jean-Claude Bradley presents the first lecture of Chemical Information Retrieval in the Fall of 2012 at Drexel University.

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  • 1. Chemical Information Retrieval 2012 First Class CHEM367/767 Drexel University Jean-Claude Bradley Associate Professor of Chemistry Drexel University September 28, 2012
  • 2. Finding reliablechemical information can be really hard
  • 3. After this class, you should feel that you can never blindly trustchemical data sources again
  • 4. But…You will learn how to do the best you can with imperfect information
  • 5. The Chemical Information Validation Sheet 567 curated and referenced measurements from Fall 2010 Chemical Information Retrieval course
  • 6. Discovering outliers for melting points (stdev/average)
  • 7. Investigating the m.p. inconsistencies of EGCG
  • 8. Investigating the m.p. inconsistencies of cyclohexanone
  • 9. Most popular data sources
  • 10. Alfa Aesar donates melting points to the public
  • 11. Open Melting Point Explorer (Andrew Lang)
  • 12. OutliersMDPI EPI (donated alldataset data to public also)
  • 13. Outliers for ethanol: Alfa Aesar and Oxford MSDS
  • 14. Inconsistencies and SMILES problems within MDPI dataset
  • 15. MDPI Dataset labeled with High Trust Level
  • 16. Open Melting Point DatasetsCurrently 20,000 compounds with Open MPs
  • 17. What is the melting point of 4-benzyltoluene? American Petroleum Institute5 C PHYSPROP -30 C PHYSPROP 125 C peer reviewed journal (2008) 97.5 C government database -30 C government database 4.58 C
  • 18. The quest to resolve the melting pointof 4-benzyltoluene: liquid at room temp and can be frozen <-30C
  • 19. Open Lab Notebook page measuring the melting point of 4-benzyltoluene
  • 20. Motivation: Faster Science, Better Science
  • 21. Ruling out all melting points above -15C?
  • 22. Oops – 4-benzyltoluene freezes after 16 days at -15C!
  • 23. Measuring the melting point by slowly heating from -15 C gives 5 C
  • 24. There are NO FACTS, only measurements embedded within assumptionsOpen Notebook Science maintainsthe integrity of data provenance by making assumptions explicit
  • 25. “Simple” aldol condensation synthesis Top Hit (no reports of synthesis) In top ten (a few reports of synthesis) (Andrew Lang)
  • 26. Information from the literature on the target synthesis
  • 27. Information from the literature on the target synthesis
  • 28. An example of a “failed experiment” in an Open Notebook with useful information
  • 29. A successful synthesis by avoiding water, dramatically increasing NaOH and long reaction time
  • 30. Open Random Forest modeling of Open Melting Point data using CDK descriptors (Andrew Lang) R2 = 0.78, TPSA and nHdon most important
  • 31. Melting point prediction service
  • 32. Web services for summary data (Andrew Lang)
  • 33. Using a Google Spreadsheet as a “dashboard interface” for reaction planning and analysis
  • 34. Calling Google App Scripts
  • 35. Calling Google App Scripts (Andrew Lang and Rich Apodaca)
  • 36. Google Apps Scripts for conveniently exploring melting point data
  • 37. Comparison of model with triple validated measurements Straight chain carboxylic acids from 1 to 10 carbons Straight chain alcohols from 1 to 10 carbons
  • 38. Cyclic primary amines from 3 to 6 carbons (cyclobutylamine flagged for validation – only single source available)
  • 39. Open Melting Points in Supplementary Data Pages of Wikipedia (Martin Walker)
  • 40. Google Apps Scripts web services
  • 41. Integration of Multiple Web Services to Recommend Solvents for Reactions (Andrew Lang)
  • 42. What are good solvents to recrystallize benzoic acid? (Andrew Lang)
  • 43. Click on the solvent to see temp curve (Andrew Lang)
  • 44. Deliver melting point data via App (Andrew Lang)
  • 45. Web services from data collected in this class will be added here
  • 46. In this class you will learnHow to search Science1.0 resources •Peer-Reviewed journals •Commercial databases •Patents •Conference Proceedings
  • 47. In this class you will learn How to participate in Science2.0•wikis (Wikipedia, class wiki)•blogs•interactive databases (ChemSpider)•social software (Twitter, FriendFeed)
  • 48. In this class you will learn How to leverage Science3.0 •machine readable web-services(via collaboration with Andrew Lang)
  • 49. Now lets take a look at the class wiki

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