The collection, curation and modeling of Open Melting Point measurements

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Jean-Claude Bradley and Andrew Lang present at the 5th Meeting on U.S. Government Chemical Databases and Open Chemistry on August 26, 2011 about "The collection, curation and modeling of Open Melting Point measurements". The talk also covers the role of Open Notebook Science and Google Apps Scripts in this effort.

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The collection, curation and modeling of Open Melting Point measurements 5th Meeting on U.S. Government Chemical Databases and Open Chemistry Jean-Claude Bradley Andrew Lang Antony Williams Department of Chemistry Drexel University ChemSpider Royal Society of Chemistry Department of Mathematics Oral Roberts University August 26, 2011

The Problem of Data Quality in Chemistry ,[object Object]

Reliance on a system of “trusted sources”In the case of melting points: ,[object Object]

Chemical Vendor Catalogs (e.g. Sigma-Aldrich)

The Chemical Information Validation Sheet 567 curated and referenced measurements from Fall 2010 Chemical Information Retrieval course

Investigating the m.p. inconsistencies of EGCG

Alfa Aesar donates melting points to the public

Outliers EPA/PhysProp (donated all data to public also) MDPI dataset

Outliers for ethanol: Alfa Aesar and Oxford MSDS

Inconsistencies and SMILES problems within MDPI dataset

MDPI Dataset labeled with High Trust Level

EPA/PHYSPROP Structure Errors (Incorrect Valence): 2315 out of 43543 were contained pentavalentnitrogens

EPA/PHYSPROP Errors: Structure displayed is for the neutral compound dopamine but the associated CAS Number and chemical name in the file are for the hydrobromidesalt.

Common errors in datasets multiple melting points for the same compound in the same database stereochemistry issues sign inversion conversion errors (Kelvin/CelciusFahrenheit/Celcius) bad SMILES (non-rendering) salts associated with SMILES for free base using boiling point for melting point

Open melting point datasets Double+ validated: 2706 compounds (7413 highly curated measurements. range: 0.01-5 C. Compounds that had at least one chiral center, possessed cis/trans isomerism, were inorganic or a salt removed.) Entire dataset: 19933 unique compounds (27684 measurements – no inorganics or salts)

Open Models with Open Data Using Open Descriptors (CDK)

Melting point predictions and measurements on iPhone/iPad(Alex Clark)

Publication of double+ validated melting point dataset to Nature Precedings and LuLu

Open Melting Point Datasets Currently 20,000 compounds with Open MPs

Some melting points can’t be resolved only with literature: 4-benzyltoluene

Motivation: Faster Science,Better Science

Open Lab Notebook page measuring the melting point of 4-benzyltoluene

Using melting point for temperature dependent solubility prediction

Integration of Multiple Web Services to Recommend Solvents for Reactions

Google Apps Scripts for conveniently exploring melting point data

Comparison of model with triple validated measurements Straight chain carboxylic acids from 1 to 10 carbons Straight chain alcohols from 1 to 10 carbons

Cyclic primary amines from 3 to 6 carbons (cyclobutylamine flagged for validation – only single source available)

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The collection, curation and modeling of Open Melting Point measurements

1. The collection, curation and modeling of Open Melting Point measurements 5th Meeting on U.S. Government Chemical Databases and Open Chemistry Jean-Claude Bradley Andrew Lang Antony Williams Department of Chemistry Drexel University ChemSpider Royal Society of Chemistry Department of Mathematics Oral Roberts University August 26, 2011

4. Merck Index

5. Chemical Vendor Catalogs (e.g. Sigma-Aldrich)

7. The Chemical Information Validation Sheet 567 curated and referenced measurements from Fall 2010 Chemical Information Retrieval course

8. Investigating the m.p. inconsistencies of EGCG

9. Most popular data sources

10. Alfa Aesar donates melting points to the public

11. Open Melting Point Explorer

12. Outliers EPA/PhysProp (donated all data to public also) MDPI dataset

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. EPA/PHYSPROP Structure Errors (Incorrect Valence): 2315 out of 43543 were contained pentavalentnitrogens

17. EPA/PHYSPROP Errors: Structure displayed is for the neutral compound dopamine but the associated CAS Number and chemical name in the file are for the hydrobromidesalt.

18. Common errors in datasets multiple melting points for the same compound in the same database stereochemistry issues sign inversion conversion errors (Kelvin/CelciusFahrenheit/Celcius) bad SMILES (non-rendering) salts associated with SMILES for free base using boiling point for melting point

19. Open melting point datasets Double+ validated: 2706 compounds (7413 highly curated measurements. range: 0.01-5 C. Compounds that had at least one chiral center, possessed cis/trans isomerism, were inorganic or a salt removed.) Entire dataset: 19933 unique compounds (27684 measurements – no inorganics or salts)

20. Open Models with Open Data Using Open Descriptors (CDK)

21. Modeling Results

22. Melting point prediction service

23. Melting point predictions and measurements on iPhone/iPad(Alex Clark)

24. Publication of double+ validated melting point dataset to Nature Precedings and LuLu

25. For all Formats of ONS Projects

26. Open Melting Point Datasets Currently 20,000 compounds with Open MPs

27. Some melting points can’t be resolved only with literature: 4-benzyltoluene

28. Motivation: Faster Science,Better Science

29. Open Lab Notebook page measuring the melting point of 4-benzyltoluene

30. Using melting point for temperature dependent solubility prediction

31. Crowdsourcing Solubility Data

32. Integration of Multiple Web Services to Recommend Solvents for Reactions

33.

34. All ONS web services

35. Google Apps Scripts web services

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. Google Apps Scripts for planning reactions and creating schemes

40. Open Melting Points in Supplementary Data Pages of Wikipedia (Martin Walker)

41.

42. Open Notebook Science offers an efficient way to make research transparent and discoverable

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