Apps and approaches to
mobilizing chemistry from the
Royal Society of Chemistry
Antony Williams*, Valery Tkachenko, Dmitry...
Chemistry has gone Mobile..
• Read Publications
• Access databases
• Perform calculations
• Draw chemicals
• Retrieve reac...
RSC Mobile
Chemistry World
• 29 million chemicals and growing
• Data sourced from >500 different sources
• Crowdsourced curation and annotation
• Dep...
NAME Lookup of ChemSpider
NAME Lookup of ChemSpider
Molecular Sketching to Search
•First hard problem: drawing
chemical structures on tiny
touchscreen (iPhones, etc.)
•Requir...
MMDS Sketcher
• Molecule editor combines:
• drawing primitives
• template placement
• gesture shortcuts
• ... but there is...
Structure Drawing
ChemSpider Mobile
• Released 2011 for iOS.
• When released, the
only way to issue
mobile structure search
• Simple workflo...
ChemSpider Mobile Android
• Released 2012 for
Android.
• Similar feature set to
iOS version
Focus is to access ChemSpider
• Substructure searching
• Similarity searching
• Depends on responsive
services and infrast...
Infrastructure Architecture
Infrastructure Architecture
ChemDraw for iPad
Full APIs for ChemSpider etc.
• All chemistry sketchers can access
ChemSpider for searching
Sponsoring Apps
Green Solvents
• Released 2011 for iOS.
Sponsored by RSC.
• Reponse to ACS GCI report
on greenness of solvents...
• identi...
Lab Solvents
• Released 2012 for Android.
Sponsored by RSC.
• Similar content to Green
Solvents
Open Drug Discovery Teams
• Released 2012 for iOS.
Coproduced with
Collaborations in Chemistry.
• Scientific newsreader fo...
Open Drug Discovery Teams
• Chemistry aware
• Users can
• emit data
• acquire data
• Long term plan is
to accumulate
open ...
Why is Open Source Drug data of
interest to RSC?
From Compounds to Reactions
• Chemical reactions are very amenable to
serving up on mobile applications
• What is availabl...
Some Reaction apps available….
SPRESImobile database
• Released 2011 for iOS.
• Search names,
structures and reactions
• ChemReact subset free,
full SPRE...
RSC and Chemical Reactions
RSC and Chemical Reactions
RSC and Chemical Reactions
RSC Journal Content
• Many 10s/100s of thousands of reactions
contained in our journals
• Electronic Supplementary informa...
Extracting Spectra from Figures
ChemSpider SyntheticPages
ChemSpider SyntheticPages
ChemSpider SyntheticPages
Text Mining
The N-(β-hydroxyethyl)-N-methyl-N'-(2-trifluoromethyl-1,3,4-
thiadiazol-5-yl)urea prepared in Example 6, thion...
Text Mining
The N-(β-hydroxyethyl)-N-methyl-N'-(2-trifluoromethyl-1,3,4-
thiadiazol-5-yl)urea prepared in Example 6 , thio...
ChemSpider Reactions
…and data too
Spectral Display in the hand
So what is ultimately feasible?
Conclusion
• Access to chemistry on mobile is clearly here
• RSC’s commitment to a mobile strategy is
obvious and includes...
• SciMobileApps Wiki: scimobileapps.com
• Add your own apps or one you discovered
• Open content and community-driven
• Ca...
SciMobileApps Wiki
Categorization of Mobile Apps
Mobile Tools in Drug Discovery
Acknowledgments
• RSC eScience Team
• Alex Clark – ChemSpider Mobile, Green Solvents,
Open Drug Discovery team, Lab Solven...
Thank You
Email: williamsa@rsc.org
Twitter: ChemConnector
Personal Blog: www.chemconnector.com
SLIDES: www.slideshare.net/...
Apps and approaches to mobilizing chemistry from the Royal Society of Chemistry
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Apps and approaches to mobilizing chemistry from the Royal Society of Chemistry

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Mobilizing chemistry by delivering data and content from Royal Society of Chemistry resources has become an important component of our activities to increase accessibility. Content includes access to our publications, our magazine content and our chemistry databases. Mobile devices also allow us to deliver access to tools to support teaching, game-based learning, annotation and curation of data. This presentation will provide an overview of our varied activities in enhancing access to chemistry related data and materials. This will include providing data feeds associated with RSC graphical databases, our experiences in optical structure recognition using smartphone apps and our future vision for supporting chemistry on mobile devices.

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Apps and approaches to mobilizing chemistry from the Royal Society of Chemistry

  1. 1. Apps and approaches to mobilizing chemistry from the Royal Society of Chemistry Antony Williams*, Valery Tkachenko, Dmitry Ivanov, Will Russell, Alex Clark and Sean Ekins ACS Indianapolis September 8th 2013
  2. 2. Chemistry has gone Mobile.. • Read Publications • Access databases • Perform calculations • Draw chemicals • Retrieve reactions • Tap into the ever-increasing cloud of data… • For students “Chemistry in the Hand” is to be expected….
  3. 3. RSC Mobile
  4. 4. Chemistry World
  5. 5. • 29 million chemicals and growing • Data sourced from >500 different sources • Crowdsourced curation and annotation • Deposition of new data • Linked to prediction models
  6. 6. NAME Lookup of ChemSpider
  7. 7. NAME Lookup of ChemSpider
  8. 8. Molecular Sketching to Search •First hard problem: drawing chemical structures on tiny touchscreen (iPhones, etc.) •Requirements: ★complicated structures ★publication quality ★fast to draw •Needed to redesign the interface
  9. 9. MMDS Sketcher • Molecule editor combines: • drawing primitives • template placement • gesture shortcuts • ... but there is a learning curve.
  10. 10. Structure Drawing
  11. 11. ChemSpider Mobile • Released 2011 for iOS. • When released, the only way to issue mobile structure search • Simple workflow: objective is to locate the ChemSpider page
  12. 12. ChemSpider Mobile Android • Released 2012 for Android. • Similar feature set to iOS version
  13. 13. Focus is to access ChemSpider • Substructure searching • Similarity searching • Depends on responsive services and infrastructure
  14. 14. Infrastructure Architecture
  15. 15. Infrastructure Architecture
  16. 16. ChemDraw for iPad
  17. 17. Full APIs for ChemSpider etc. • All chemistry sketchers can access ChemSpider for searching
  18. 18. Sponsoring Apps
  19. 19. Green Solvents • Released 2011 for iOS. Sponsored by RSC. • Reponse to ACS GCI report on greenness of solvents... • identified by Sean Ekins • available only as PDF • behind a login • listed by name only • Free app, structure-centric
  20. 20. Lab Solvents • Released 2012 for Android. Sponsored by RSC. • Similar content to Green Solvents
  21. 21. Open Drug Discovery Teams • Released 2012 for iOS. Coproduced with Collaborations in Chemistry. • Scientific newsreader for rare & neglected diseases and precompetitive topics • Source material: Twitter & RSS • Crowd-curation paradigm • Micropublication capability
  22. 22. Open Drug Discovery Teams • Chemistry aware • Users can • emit data • acquire data • Long term plan is to accumulate open drug data
  23. 23. Why is Open Source Drug data of interest to RSC?
  24. 24. From Compounds to Reactions • Chemical reactions are very amenable to serving up on mobile applications • What is available now? • Teaching basics of chemical reactions • Look-ups against reaction databases • Reaction mechanisms
  25. 25. Some Reaction apps available….
  26. 26. SPRESImobile database • Released 2011 for iOS. • Search names, structures and reactions • ChemReact subset free, full SPRESIweb with trial or license
  27. 27. RSC and Chemical Reactions
  28. 28. RSC and Chemical Reactions
  29. 29. RSC and Chemical Reactions
  30. 30. RSC Journal Content • Many 10s/100s of thousands of reactions contained in our journals • Electronic Supplementary information data contains lots more • Lots of analytical data also but that’s a topic for another talk on Wednesday
  31. 31. Extracting Spectra from Figures
  32. 32. ChemSpider SyntheticPages
  33. 33. ChemSpider SyntheticPages
  34. 34. ChemSpider SyntheticPages
  35. 35. Text Mining The N-(β-hydroxyethyl)-N-methyl-N'-(2-trifluoromethyl-1,3,4- thiadiazol-5-yl)urea prepared in Example 6, thionyl chloride ( 5 ml ) and benzene ( 50 ml ) were charged into a glass reaction vessel equipped with a mechanical stirrer, thermometer and reflux condenser . The reaction mixture was heated at reflux with stirring, for a period of about one-half hour . After this time the benzene and unreacted thionyl chloride were stripped from the reaction mixture under reduced pressure to yield the desired product N-(β-chloroethyl)-N- methyl-N'-(2-trifluoromethyl-1,3,4-thiaidazol-5-yl)urea as a solid residue
  36. 36. Text Mining The N-(β-hydroxyethyl)-N-methyl-N'-(2-trifluoromethyl-1,3,4- thiadiazol-5-yl)urea prepared in Example 6 , thionyl chloride ( 5 ml ) and benzene ( 50 ml ) were charged into a glass reaction vessel equipped with a mechanical stirrer , thermometer and reflux condenser . The reaction mixture was heated at reflux with stirring , for a period of about one-half hour . After this time the benzene and unreacted thionyl chloride were stripped from the reaction mixture under reduced pressure to yield the desired product N-(β-chloroethyl)-N- methyl-N'-(2-trifluoromethyl-1,3,4-thiaidazol-5-yl)urea as a solid residue
  37. 37. ChemSpider Reactions
  38. 38. …and data too
  39. 39. Spectral Display in the hand
  40. 40. So what is ultimately feasible?
  41. 41. Conclusion • Access to chemistry on mobile is clearly here • RSC’s commitment to a mobile strategy is obvious and includes: • Access to Journal Content • Access to Database Content • Structure/substructure searching across all content
  42. 42. • SciMobileApps Wiki: scimobileapps.com • Add your own apps or one you discovered • Open content and community-driven • Can someone add ChemDraw for iPad? Sourcing information about SciApps
  43. 43. SciMobileApps Wiki
  44. 44. Categorization of Mobile Apps
  45. 45. Mobile Tools in Drug Discovery
  46. 46. Acknowledgments • RSC eScience Team • Alex Clark – ChemSpider Mobile, Green Solvents, Open Drug Discovery team, Lab Solvents • JC Bradley, Andy Lang, Bob Lancashire – SpectralGame • Kevin Thiesen – ChemDoodle • ACD/Labs – SpectraSchool HTML5 NMR Display • Daniel Lowe – Chemical reactions dataset • Sean Ekins – SciMobileApps wiki
  47. 47. Thank You Email: williamsa@rsc.org Twitter: ChemConnector Personal Blog: www.chemconnector.com SLIDES: www.slideshare.net/AntonyWilliams
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