Rapid dissemination of chemical information for people and machines using Open Notebook Science<br />American Chemical Soc...
Motivation: Faster Science,Better Science<br />
There are NO FACTS, <br />only measurements embedded within assumptions<br />Open Notebook Science maintains the integrity...
TRUST<br />PROOF<br />
Strategy for an Open Notebook:<br />First record then abstract structure<br />In order to be discoverable use Google frien...
Crowdsourcing Solubility Data<br />
ONS Challenge Judges<br />
ONS Challenge Award Winners<br />
Data provenance: <br />From Wikipedia to…<br />
…the lab notebook and raw data<br />
Calculations Made Public on <br />Google Spreadsheets<br />
Interactive NMR spectra using JSpecView and JCAMP-DX<br />
Raw Data As Images<br />Splatter?<br />Some liquid<br />
YouTube for demonstrating experimental set-up<br />
The importance of raw data availability<br />Missed in a prior publication on solubility for this compound<br />
Solubilities collected in a Google Spreadsheet<br />
Rajarshi Guha’s Live Web Query using Google Viz API<br />
Web services for summary data<br />(Andrew Lang)<br />
Web service calls from within a Google Spreadsheet for solubility measurement and prediction<br />(Andrew Lang)<br />
Integration of Multiple Web Services to Recommend Solvents for Reactions<br />(Andrew Lang)<br />
Reaction Attempts Book<br />
Reaction Attempts Book: Reactants listed Alphabetically<br />
ONS Challenge Solubility Book cited for nanotechnology application<br />
Lulu.com Data Disks<br />
Visualizing molecule-researcher connection maps reveals link between 2 Open Notebooks (Todd and Bradley)<br />(Don Pellegr...
The Intersection of Open Notebooks (Bradley/Todd) and IP implications<br />Open Notebook could have blocked patent if done...
The Chemical Information Validation Sheet <br />567 curated and referenced measurements from <br />Fall 2010 Chemical Info...
The Chemical Information Validation Explorer <br />(Andrew Lang)<br />
Discovering outliers for melting points (stdev/average)<br />
Investigating the m.p. inconsistencies of EGCG<br />
Investigating the m.p. inconsistencies of cyclohexanone<br />
Sigma-Aldrich, Acros and Wolfram Alpha apparently use the same sources for melting points<br />
Sigma-Aldrich, Acros and Wolfram Alpha apparently use the same sources for boiling points<br />
Sigma-Aldrich, Acros and Wolfram Alpha apparently <br />DO NOT use the same sources for flash points<br />
Most popular data sources<br />
Alfa Aesar donates melting points to the public<br />
Open Melting Point Explorer<br />
Outliers<br />MDPI <br />dataset<br />EPI (via ChemSpider)<br />
Outliers<br />Alfa Aesar<br />
Inconsistencies and SMILES problems within MDPI dataset<br />
MDPI Dataset labeled with High Trust Level<br />
Open Melting Point Datasets<br />
Open Random Forest modeling of Open Melting Point data using CDK descriptors<br />(Andrew Lang)<br />R2 = 0.78, TPSA and n...
Melting point prediction service<br />
Using melting point for temperature dependent solubility prediction<br />
Decanoic acid<br />Water<br />NaCl<br />
Phrase searching for useful solubility applications<br />
The challenge of modeling inorganic solubility openly<br />
All ONS web services <br />
Dynamic links to private tagged <br />Mendeley collections<br />(Andrew Lang)<br />
For all Formats of ONS Projects<br />
Conclusions<br /><ul><li>Abstraction of ONS experimental data into a clear semantic format can be done quickly and easily ...
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Open Notebook Science Web Services - ACS Spring 2011

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Jean-Claude Bradley presents on March 30, 2011 at the American Chemical Society on Rapid Dissemination of Chemical Information for people and machines using Open Notebook Science.

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Open Notebook Science Web Services - ACS Spring 2011

  1. 1. Rapid dissemination of chemical information for people and machines using Open Notebook Science<br />American Chemical Society Meeting<br />Jean-Claude Bradley<br />Andrew Lang<br />Department of Chemistry<br />Drexel University<br />Department of Mathematics<br />Oral Roberts University<br />March 30, 2011<br />
  2. 2. Motivation: Faster Science,Better Science<br />
  3. 3. There are NO FACTS, <br />only measurements embedded within assumptions<br />Open Notebook Science maintains the integrity of data provenance by making assumptions explicit<br />
  4. 4. TRUST<br />PROOF<br />
  5. 5. Strategy for an Open Notebook:<br />First record then abstract structure<br />In order to be discoverable use Google friendly formats (simple HTML, no login) <br />In order to be replicable use free hosted tools (Wikispaces, Google Spreadsheets)<br />
  6. 6. Crowdsourcing Solubility Data<br />
  7. 7. ONS Challenge Judges<br />
  8. 8. ONS Challenge Award Winners<br />
  9. 9. Data provenance: <br />From Wikipedia to…<br />
  10. 10. …the lab notebook and raw data<br />
  11. 11. Calculations Made Public on <br />Google Spreadsheets<br />
  12. 12. Interactive NMR spectra using JSpecView and JCAMP-DX<br />
  13. 13. Raw Data As Images<br />Splatter?<br />Some liquid<br />
  14. 14. YouTube for demonstrating experimental set-up<br />
  15. 15. The importance of raw data availability<br />Missed in a prior publication on solubility for this compound<br />
  16. 16. Solubilities collected in a Google Spreadsheet<br />
  17. 17. Rajarshi Guha’s Live Web Query using Google Viz API<br />
  18. 18. Web services for summary data<br />(Andrew Lang)<br />
  19. 19. Web service calls from within a Google Spreadsheet for solubility measurement and prediction<br />(Andrew Lang)<br />
  20. 20. Integration of Multiple Web Services to Recommend Solvents for Reactions<br />(Andrew Lang)<br />
  21. 21.
  22. 22.
  23. 23.
  24. 24. Reaction Attempts Book<br />
  25. 25. Reaction Attempts Book: Reactants listed Alphabetically<br />
  26. 26. ONS Challenge Solubility Book cited for nanotechnology application<br />
  27. 27. Lulu.com Data Disks<br />
  28. 28. Visualizing molecule-researcher connection maps reveals link between 2 Open Notebooks (Todd and Bradley)<br />(Don Pellegrino)<br />
  29. 29. The Intersection of Open Notebooks (Bradley/Todd) and IP implications<br />Open Notebook could have blocked patent if done earlier<br />
  30. 30. The Chemical Information Validation Sheet <br />567 curated and referenced measurements from <br />Fall 2010 Chemical Information Retrieval course<br />
  31. 31. The Chemical Information Validation Explorer <br />(Andrew Lang)<br />
  32. 32. Discovering outliers for melting points (stdev/average)<br />
  33. 33. Investigating the m.p. inconsistencies of EGCG<br />
  34. 34. Investigating the m.p. inconsistencies of cyclohexanone<br />
  35. 35. Sigma-Aldrich, Acros and Wolfram Alpha apparently use the same sources for melting points<br />
  36. 36. Sigma-Aldrich, Acros and Wolfram Alpha apparently use the same sources for boiling points<br />
  37. 37. Sigma-Aldrich, Acros and Wolfram Alpha apparently <br />DO NOT use the same sources for flash points<br />
  38. 38. Most popular data sources<br />
  39. 39. Alfa Aesar donates melting points to the public<br />
  40. 40. Open Melting Point Explorer<br />
  41. 41. Outliers<br />MDPI <br />dataset<br />EPI (via ChemSpider)<br />
  42. 42. Outliers<br />Alfa Aesar<br />
  43. 43. Inconsistencies and SMILES problems within MDPI dataset<br />
  44. 44. MDPI Dataset labeled with High Trust Level<br />
  45. 45. Open Melting Point Datasets<br />
  46. 46. Open Random Forest modeling of Open Melting Point data using CDK descriptors<br />(Andrew Lang)<br />R2 = 0.78, TPSA and nHdon most important<br />
  47. 47. Melting point prediction service<br />
  48. 48. Using melting point for temperature dependent solubility prediction<br />
  49. 49. Decanoic acid<br />Water<br />NaCl<br />
  50. 50. Phrase searching for useful solubility applications<br />
  51. 51. The challenge of modeling inorganic solubility openly<br />
  52. 52. All ONS web services <br />
  53. 53. Dynamic links to private tagged <br />Mendeley collections<br />(Andrew Lang)<br />
  54. 54. For all Formats of ONS Projects<br />
  55. 55. Conclusions<br /><ul><li>Abstraction of ONS experimental data into a clear semantic format can be done quickly and easily and greatly leverages the utility of the data
  56. 56. No information is lost as long as a link to the Open Notebook is captured</li>
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