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ChemInfo 2011 class1
ChemInfo 2011 class1
ChemInfo 2011 class1
ChemInfo 2011 class1
ChemInfo 2011 class1
ChemInfo 2011 class1
ChemInfo 2011 class1
ChemInfo 2011 class1
ChemInfo 2011 class1
ChemInfo 2011 class1
ChemInfo 2011 class1
ChemInfo 2011 class1
ChemInfo 2011 class1
ChemInfo 2011 class1
ChemInfo 2011 class1
ChemInfo 2011 class1
ChemInfo 2011 class1
ChemInfo 2011 class1
ChemInfo 2011 class1
ChemInfo 2011 class1
ChemInfo 2011 class1
ChemInfo 2011 class1
ChemInfo 2011 class1
ChemInfo 2011 class1
ChemInfo 2011 class1
ChemInfo 2011 class1
ChemInfo 2011 class1
ChemInfo 2011 class1
ChemInfo 2011 class1
ChemInfo 2011 class1
ChemInfo 2011 class1
ChemInfo 2011 class1
ChemInfo 2011 class1
ChemInfo 2011 class1
ChemInfo 2011 class1
ChemInfo 2011 class1
ChemInfo 2011 class1
ChemInfo 2011 class1
ChemInfo 2011 class1
ChemInfo 2011 class1
ChemInfo 2011 class1
ChemInfo 2011 class1
ChemInfo 2011 class1
ChemInfo 2011 class1
ChemInfo 2011 class1
ChemInfo 2011 class1
ChemInfo 2011 class1
ChemInfo 2011 class1
ChemInfo 2011 class1
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ChemInfo 2011 class1

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Jean-Claude Bradley presents the introductory lecture for Chemical Information Retrieval at Drexel University for Fall 2011 on September 23, 2011. Examples are given to demonstrate how difficult it …

Jean-Claude Bradley presents the introductory lecture for Chemical Information Retrieval at Drexel University for Fall 2011 on September 23, 2011. Examples are given to demonstrate how difficult it can be to find and assess chemical information such as melting points. An overview of the class wiki is then given

Published in: Education, Technology
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Transcript

  • 1. Chemical Information Retrieval 2011 Jean-Claude Bradley September 23, 2011 First Class Associate Professor of Chemistry Drexel University CHEM367/767 Drexel University
  • 2. Finding reliable chemical information can be really hard
  • 3. After this class, you should feel that you can never blindly trust chemical 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. Outliers MDPI dataset EPI (donated all 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 Datasets Currently 20,000 compounds with Open MPs
  • 17. American Petroleum Institute 5 C PHYSPROP -30 C PHYSPROP 125 C peer reviewed journal (2008) 97.5 C government database -30 C government database 4.58 C What is the melting point of 4-benzyltoluene?
  • 18. The quest to resolve the melting point of 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 assumptions Open Notebook Science maintains the integrity of data provenance by making assumptions explicit
  • 25. Open Random Forest modeling of Open Melting Point data using CDK descriptors (Andrew Lang) R2 = 0.78, TPSA and nHdon most important
  • 26. Melting point prediction service
  • 27. Melting point predictions and measurements on iPhone/iPad (Andrew Lang and Alex Clark)
  • 28. Using melting point for temperature dependent solubility prediction
  • 29. Web services for summary data (Andrew Lang)
  • 30. Web service calls from within a Google Spreadsheet for solubility measurement and prediction (Andrew Lang)
  • 31. Integration of Multiple Web Services to Recommend Solvents for Reactions (Andrew Lang)
  • 32. Publication of double+ validated melting point dataset to Nature Precedings and LuLu
  • 33.  
  • 34.  
  • 35. Reaction Attempts Book
  • 36. Reaction Attempts Book: Reactants listed Alphabetically
  • 37.  
  • 38. All ONS web services
  • 39. Google Apps Scripts web services
  • 40. Google Apps Scripts for conveniently exploring melting point data
  • 41. Straight chain carboxylic acids from 1 to 10 carbons Straight chain alcohols from 1 to 10 carbons Comparison of model with triple validated measurements
  • 42. Cyclic primary amines from 3 to 6 carbons (cyclobutylamine flagged for validation – only single source available)
  • 43. Google Apps Scripts for planning reactions and creating schemes
  • 44. Open Melting Points in Supplementary Data Pages of Wikipedia (Martin Walker)
  • 45. Web services from data collected in this class will be added here
  • 46. In this class you will learn How to search Science1.0 resources <ul><li>Peer-Reviewed journals </li></ul><ul><li>Commercial databases </li></ul><ul><li>Patents </li></ul><ul><li>Conference Proceedings </li></ul>
  • 47. In this class you will learn How to participate in Science2.0 <ul><li>wikis (Wikipedia, class wiki) </li></ul><ul><li>blogs </li></ul><ul><li>interactive databases (ChemSpider) </li></ul><ul><li>social software (Twitter, FriendFeed) </li></ul>
  • 48. In this class you will learn How to leverage Science3.0 (via collaboration with Andrew Lang) <ul><li>machine readable web-services </li></ul>
  • 49. Now lets take a look at the class wiki

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