royal society of chemistry open source cheminformatics platforms and libraries
DESCRIPTION
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.TRANSCRIPT
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
