Royal Society of Chemistry open source cheminformatics platforms and libraries
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Transcript of Royal Society of Chemistry open source cheminformatics platforms and libraries
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RSC Open Source Cheminformatics Platforms and Libraries
Valery Tkachenko
A Memorial Symposium celebrating
the work of Jean-Claude Bradley
Cambridge, UK
July 14th 2014
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Chemical data entry
Unification attempt
Further simplification - pure technical view
Proof of concept designs
Proof of concepts applications
Where further?
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PubChem Deposition System
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Thesis abstract
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GInAS (NCATS) – ISO 11238
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Micropublishing article
Compounds
Reaction
Analytical Data
Text and References
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Chemical data entry
Unification attempt
Further simplification - pure technical view
Proof of concept designs
Proof of concepts applications
Where further?
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Technical view - unification
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Chemical data entry
Unification attempt
Further simplification - pure technical view
Proof of concept designs
Proof of concepts applications
Where further?
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Input pipeline
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Output pipeline
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Chemical data entry
Unification attempt
Further simplification - pure technical view
Proof of concept designs
Proof of concepts applications
Where further?
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Chemistry Validation and Standardization Platform
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Compounds domain
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Reactions domain
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Analytical data domain
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Crystallography data domain
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APIs, endpoints and widgets
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Chemical data entry
Unification attempt
Further simplification - pure technical view
Proof of concept designs
Proof of concepts applications
Where further?
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• 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…
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Chemical data entry
Simplification attempt
Further simplification - pure technical view
Proof of concept designs
Proof of concepts applications
Where further?
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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?
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Federated repositories
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Machine learning
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