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

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 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 EPI (donated all
dataset 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. 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 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. “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 learn
How 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