RSC Open Source Cheminformatics
Platforms and Libraries
Valery Tkachenko
A Memorial Symposium celebrating
the work of Jean...
Chemical data entry
Unification attempt
Further simplification - pure technical view
Proof of concept designs
Proof of con...
PubChem Deposition System
Thesis abstract
GInAS (NCATS) – ISO 11238
Micropublishing article
Compounds
Reaction
Analytical Data
Text and References
Chemical data entry
Unification attempt
Further simplification - pure technical view
Proof of concept designs
Proof of con...
Technical view - unification
Chemical data entry
Unification attempt
Further simplification - pure technical view
Proof of concept designs
Proof of con...
Input pipeline
Output pipeline
Chemical data entry
Unification attempt
Further simplification - pure technical view
Proof of concept designs
Proof of con...
Chemistry Validation and Standardization
Platform
Compounds domain
Reactions domain
Analytical data domain
Crystallography data domain
APIs, endpoints and widgets
Chemical data entry
Unification attempt
Further simplification - pure technical view
Proof of concept designs
Proof of con...
• 3-year Innovative Medicines Initiative project
• Integrating chemistry and biology data using
semantic web technologies
...
Chemical data entry
Simplification attempt
Further simplification - pure technical view
Proof of concept designs
Proof of ...
Handling complex content
What’s the
structure?
What’s the
structure?
Are they in
our file?
Are they in
our file?
What’s
si...
Federated repositories
Machine learning
Thank you
Email: tkachenkov@rsc.org
Slides: http://www.slideshare.net/valerytkachenko16
Royal Society of Chemistry open source cheminformatics platforms and libraries
Royal Society of Chemistry open source cheminformatics platforms and libraries
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Royal Society of Chemistry open source cheminformatics platforms and libraries

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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.

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Royal Society of Chemistry open source cheminformatics platforms and libraries

  1. 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. 2. Chemical data entry Unification attempt Further simplification - pure technical view Proof of concept designs Proof of concepts applications Where further?
  3. 3. PubChem Deposition System
  4. 4. Thesis abstract
  5. 5. GInAS (NCATS) – ISO 11238
  6. 6. Micropublishing article Compounds Reaction Analytical Data Text and References
  7. 7. Chemical data entry Unification attempt Further simplification - pure technical view Proof of concept designs Proof of concepts applications Where further?
  8. 8. Technical view - unification
  9. 9. Chemical data entry Unification attempt Further simplification - pure technical view Proof of concept designs Proof of concepts applications Where further?
  10. 10. Input pipeline
  11. 11. Output pipeline
  12. 12. Chemical data entry Unification attempt Further simplification - pure technical view Proof of concept designs Proof of concepts applications Where further?
  13. 13. Chemistry Validation and Standardization Platform
  14. 14. Compounds domain
  15. 15. Reactions domain
  16. 16. Analytical data domain
  17. 17. Crystallography data domain
  18. 18. APIs, endpoints and widgets
  19. 19. Chemical data entry Unification attempt Further simplification - pure technical view Proof of concept designs Proof of concepts applications Where further?
  20. 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…
  21. 21. Chemical data entry Simplification attempt Further simplification - pure technical view Proof of concept designs Proof of concepts applications Where further?
  22. 22. 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?
  23. 23. Federated repositories
  24. 24. Machine learning
  25. 25. Thank you Email: tkachenkov@rsc.org Slides: http://www.slideshare.net/valerytkachenko16
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