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

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….

RSC Mobile

Chemistry World

• 29 million chemicals and growing

• Data sourced from >500 different sources

• Crowdsourced curation and annotation

• Deposition of new data

• Linked to prediction models

NAME Lookup of ChemSpider

NAME Lookup of ChemSpider

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

MMDS Sketcher

• Molecule editor combines:• drawing primitives• template placement• gesture shortcuts

• ... but there is a learning curve.

Structure Drawing

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

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 infrastructure

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...• identified by Sean Ekins• available only as PDF• behind a login• listed by name only

• Free app, structure-centric

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 for rare & neglected diseases and precompetitive topics

• Source material: Twitter & RSS

• Crowd-curation paradigm• Micropublication capability

Open Drug Discovery Teams

• Chemistry aware

• Users can• emit data• acquire data

• Long term plan is to accumulate open drug data

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 available now?• Teaching basics of chemical reactions• Look-ups against reaction databases• Reaction mechanisms

Some Reaction apps available….

SPRESImobile database

• Released 2011 for iOS.

• Search names, structures and reactions

• ChemReact subset free, full SPRESIweb with trial or license

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 information data contains lots more

• Lots of analytical data also but that’s a topic for another talk on Wednesday

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, 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

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

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:• Access to Journal Content• Access to Database Content• Structure/substructure searching across all

content

• 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

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 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

Thank YouEmail: williamsa@rsc.org

Twitter: ChemConnector

Personal Blog: www.chemconnector.com

SLIDES: www.slideshare.net/AntonyWilliams