RSC Open Source Cheminformatics Platforms and Libraries
Valery Tkachenko
A Memorial Symposium celebrating
the work of Jean-Claude Bradley
Cambridge, UK
July 14th 2014
Chemical data entry
Unification attempt
Further simplification - pure technical view
Proof of concept designs
Proof of concepts applications
Where further?
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 concepts applications
Where further?
Technical view - unification
Chemical data entry
Unification attempt
Further simplification - pure technical view
Proof of concept designs
Proof of concepts applications
Where further?
Input pipeline
Output pipeline
Chemical data entry
Unification attempt
Further simplification - pure technical view
Proof of concept designs
Proof of concepts applications
Where further?
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 concepts applications
Where further?
• 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…
Chemical data entry
Simplification attempt
Further simplification - pure technical view
Proof of concept designs
Proof of concepts applications
Where further?
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?
Federated repositories
Machine learning
