We are all benefiting from a shift towards openness fed by Open Source, Open Standards, Open Data and Open Access. Open Notebook Science is likely the scientific revolution of the near term. As more scientists become comfortable with the concepts of openly sharing their experiments and data, often in near real time, we are seeing a shift to significant increases in the availability of new data that does not have to be extracted from publications but is available as data feeds that can be delivered to the community. This presentation will provide an overview of how the ChemSpider database from the RSC supports Open Notebook Science using programmatic access to both data and services and how ChemSpider ingests data feeds to mesh together with our existing database of over 27 million chemical compounds.

1. Feeding and consuming data to
support Open Notebook Science via
the ChemSpider Platform
Antony Williams, Jean-Claude Bradley, Andrew Lang and
Valery Tkachenko
ACS Philadelphia August 2012

2. Setting the Stage
 Chemists want access to tools and data
 The more capabilities the better
 The more data the better
 And give us an API with that…
 And it should be free…
 And constantly updated…
 And all data should be Open…
 And make it fully Open Source…
 And it needs to be on my mobile…

3. Setting the Stage
 Chemists have access to tools and data
 The more capabilities the better – we’ll see
 The more data the better – changing daily
 And give us an API with that… - not just one
 And it should be free… - sure
 And constantly updated… - indeed..please help!
 And all data should be Open…- licensing
 And make it fully Open Source… - kinda, sorta
 And it needs to be on my mobile… - sure

4. Welcome to ChemSpider
 5 years, 28 million chemicals, linking 400 data
sources and growing daily
 Hosted by the Royal Society of Chemistry
 An important part of our long term strategic vision
 Free to access
 With lots/most/all (?) of the functionality
necessary to support chemists and Open
Notebook Science…

5. Why Use ChemSpider?

6. Why Use ChemSpider?

7. Why Use ChemSpider?

8. Why Use ChemSpider?

9. Why Use ChemSpider? LINKING OUT

10. Why Use ChemSpider?

11. Why Use ChemSpider

12. Why Use ChemSpider

13. Why Use ChemSpider

14. Why Use ChemSpider

15. What about Syntheses?

16. ChemSpider SyntheticPages

17. Work in Progress – 300k Reactions

18. Storing ONS Reactions
 Working with JC Bradley to host ONS reactions
 Linking directly back to ONS reactions
 What if the links decay?
 Host all related ONS data – benefits of Openness!
 Future applications for RInChIs

19. What we have been asked for
 “Allow us to grab data”
 “Let us link”
 “Give us web services to integrate”
 “Can we store our data with you?”
 “Can you give us predictions to validate data?”

20. What we have been asked for
 “Allow us to grab data”
 “Let us link”
 “Give us web services to integrate”
 “Can we store our data with you?”
 “Can you give us predictions to validate data?”
 “Can you build us an ELN?”

21. Simple Linking to ChemSpider
 Link using ChemSpiderID
 http://www.chemspider.com/1234567

22. ChemSpider IDs Proliferating Now

23. Simple Querying Example
 http://
www.chemspider.com/Search.aspx?q=InChIKey=XXO

24. Or InChI, or SMILES
 http://www.chemspider.com/Search.aspx?q=InChI=1S
m1/s1
 http://www.chemspider.com/Search.aspx?
q=Clc1ccc(cc1)C(O)=C3C(=O)C(=O)N([C@@H]3
c2cccc(F)c2)CCc5c4ccccc4nc5

25. Better to provide APIs….

26. Various Flavors of API

27. Various Flavors of API

28. MANY Web Services for integration

29. Feeding ONS Data into ChemSpider
 ONS data can be deposited into ChemSpider and
linked out to the ONS pages
 Simply deposit structure(s) and links

31. Feeding ONS Data into ChemSpider
 ONS Solubility Challenge

32. Feeding ONS Data into ChemSpider

33. So isn’t ONS all about ELNs?
 Open Notebook Science is about
 Making records of research publicly available
online as it is recorded
 ONS is enabled by software tools and platforms
 Keep the notebook of the researcher online
with all raw and processed data as it is
generated (close to or near real time)
 Notebooks as Wikis, Commercial or Free ELNs
published to the web (choose public/private –
what data to expose)

34. Feeding ELN Data into ChemSpider
 Integrate e-Notebooks into ChemSpider
 IDBS e-Workbook plug-in allows direct
deposition of chemical structures
 Can be extended to more ELN content
 Spectra
 Reactions
 Properties etc.
 Integration Video http://tinyurl.com/9xnprqr

35. Feeding ELN Data into ChemSpider

36. How much data is lost?
 How many reactions in a thesis never get
published?
 How many spectra of common materials could be
shared?
 How many properties are measured and lost?
 What stands in the way of sharing?
 Is it technology?
 Permissions? “The Boss”, Licensing?
 And yes – there are data quality issues but there
is algorithmic checking and data curation to help

37. What could the future look like?
 “Publicly funded” research data flows onto the web
 Licensing is clear and NOT a challenge
 Machines are picking up data and depositing
 EXAMPLE project – Any interest?
 Put your spectra/structure in folders (Dropbox)
 ChemSpider robot scoops, processes and
deposits – opportunity with JC Bradley
 While processing also predicts spectra and
compares for validation

38. Leaving the Stage
 Chemists have access to tools and data
 The more capabilities the better – what’s missing?
 The more data the better – anyone want to share?
 And give us an API with that… - ask us for help
 And it should be free… - it is
 And constantly updated… - help annotate/curate
 And all data should be Open…- licensing
 And make it fully Open Source… - book chapter
 And it needs to be on my mobile… - it is

39. ChemSpider Mobile

40. New URLs to try out
 ChemSpider Reactions:
www.chemspider.com/reactions
 ChemSpider Validation and Standardization
Platform: www.chemspider.com/cvsp
 ChemSpider Google:
www.chemspider.com/google

41. ChemSpider Google

42. ChemSpider Google

43. Acknowledgments
 RSC Cheminformatics team
 JC Bradley’s lab
 Daniel Lowe – reactions
 Commercial Software – GGA Software,
ACD/Labs, OpenEye
 Open Source Components

44. Thank you
Email: williamsa@rsc.org
Blog: www.chemconnector.com
SLIDES: www.slideshare.net/AntonyWilliams