The cheminformatics group at the Royal Society of Chemistry has supported a number of national and international grants for the last 5 years with the deployment of Cheminformatics tools and platforms. Among them is the Open PHACTS project which is intended to help reducing the barriers to drug discovery in industry, academia and for small businesses by providing the Open PHACTS Discovery Platform. The PharmaSea project targets the identification of leads for new antibiotics in deep sea trenches. The National Chemistry Database Service and Data Repository is a collaborative platform for handling research data. Our contribution to all of these projects has been the development of a number of open source cheminformatics library and user interface components that can be freely used in 3rd party websites and applications. In this presentation we will cover our approach to the development as well as give particular examples of applications built using our toolkits. These software components will likely be very important in the future deployment of Open Notebook Science platforms to help deliver on the vision of Jean-Claude Bradley.

1. RSC Open Source Cheminformatics
Platforms and Libraries
Valery Tkachenko
A Memorial Symposium celebrating
the work of Jean-Claude Bradley
Cambridge, UK
July 14th
2014

2. Chemical data entry
Unification attempt
Further simplification - pure technical view
Proof of concept designs
Proof of concepts applications
Where further?

3. PubChem Deposition System

4. Thesis abstract

5. GInAS (NCATS) – ISO 11238

6. Micropublishing article
Compounds
Reaction
Analytical Data
Text and References

7. Chemical data entry
Unification attempt
Further simplification - pure technical view
Proof of concept designs
Proof of concepts applications
Where further?

8. Technical view - unification

9. Chemical data entry
Unification attempt
Further simplification - pure technical view
Proof of concept designs
Proof of concepts applications
Where further?

10. Input pipeline

11. Output pipeline

12. Chemical data entry
Unification attempt
Further simplification - pure technical view
Proof of concept designs
Proof of concepts applications
Where further?

13. Chemistry Validation and Standardization
Platform

14. Compounds domain

15. Reactions domain

16. Analytical data domain

17. Crystallography data domain

18. APIs, endpoints and widgets

19. Chemical data entry
Unification attempt
Further simplification - pure technical view
Proof of concept designs
Proof of concepts applications
Where further?

20. • 3-year Innovative Medicines Initiative project
• Integrating chemistry and biology data using
semantic web technologies
• Open source code, open data and open
standards
• Academics, Pharmas, Publishers…
• To put medicines in the pipeline…

22. Chemical data entry
Simplification attempt
Further simplification - pure technical view
Proof of concept designs
Proof of concepts applications
Where further?

23. Handling complex content
What’s the
structure?
What’s the
structure?
Are they in
our file?
Are they in
our file?
What’s
similar?
What’s
similar?
What’s the
target?
What’s the
target?Pharmacology
data?
Pharmacology
data?
Known
Pathways?
Known
Pathways?
Working On
Now?
Working On
Now?Connections
to disease?
Connections
to disease?
Expressed in
right cell type?
Expressed in
right cell type?
Competitors?Competitors?
IP?IP?

24. Federated repositories

25. Machine learning

27. Thank you
Email: tkachenkov@rsc.org
Slides: http://www.slideshare.net/valerytkachenko16