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Antony Williams, Ken Karapetyan, Valery Tkachenko, Colin Batchelor Alexey Pshenichnov and Jon Steele ACS Dallas March 2014. Royal Society of Chemistry developments to support open drug discovery. Supporting Open Drug Discovery. As a publisher As a host of chemistry databases
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As a publisher
As a host of chemistry databases
As a charity and community support
As a provider of grant-based services
As an innovator in cheminformatics
One of the world’s top publishers for chemistry – journals, books and databases
High quality, high impact journals – direct journals of relevance for drug discovery
Databases to support drug discovery – Merck Index, ChemSpider, Natural Product Updates…
Innovative publisher – semantic markup, mobile developments
~30 million chemicals and growing
Data sourced from >500 different sources
Crowdsourced curation and annotation
Ongoing deposition of data from our journals and our collaborators
Structure centric hub for web-searching
Ongoing expansion of integrated services of value to open drug discovery
Integration to Mcule online docking and toxicity checker – in development
New grant to integrate to improved patent service with Cambridge IP (UK)
Integration to enhance MedChemComm journal articles for property extraction and data management
Acts as host and funder for networking meetings
Funds trainings and onsite participation
Provides funding for RSC cheminformatics team to work on open drug discovery projects
1/3 of the worlds population is infected
Recently sponsored cheminformatics jamboree – training by skilled specialists in the applications of cheminformatics to medicinal chemistry and drug design
We will provide access and support to the ChemSpider API to integrate to their OSDD cheminformatics platform
We will extend our data model to support their Open Data – compounds, pharmacology data
Synthetic reactions will be published to ChemSpider SyntheticPages and Reactions
Analytical Data to be published to ChemSpider Spectra
RSC cheminformatics participates in multiple European consortium-based grants
PharmaSea (FP7 funded)
Open PHACTS (IMI funded)
RSC hosts the UK National Chemical Database Service (http://cds.rsc.org)
RSC cheminformatics support to include:
Provide access to natural products subset (make available on ChemSpider)
Develop “dereplication techniques”
Searching NMR features against database
Develop advanced searches for MS data
Host Open Data from the PharmaSea project and make available to the community
RSC acquired Marinlit. Goes online in April
All Marinlit chemical compounds in ChemSpider
Marinlit developers are dereplication experts
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…
Normalisation & Q/C
ops:OPS1 skos:exactMatch <http://www4.wiwiss.fu-berlin.de/drugbank/resource/drugs/DB07241> .
ops:OPS2 skos:relatedMatch ops:OPS1 .
ops:OPS3 skos:relatedMatch ops:OPS1 .
ops:OPS3 skos:closeMatch ops:OPS4 .
ops:OPS3 skos:closeMatch ops:OPS5 .
ops:OPS4 skos:closeMatch ops:OPS6 .
ops:OPS5 skos:closeMatch ops:OPS6 .
DrugBank ID DB07241
ChemSpider Validation & Standardization Platform
All Open PHACTS data is licensed as Open Data and available from Open PHACTS website – ca. 2 Million chemicals
The Chemical Registration Service, including Chemical Validation and Standardization Platform will be released as Open Source code to the community (from Open PHACTS github site)
Data on ChemSpider is curated in an ongoing fashion - take what you need!
Used a lot for accessing the “dictionary of chemicals” to build models – right Sean?
Pharmacalogy data will increasingly be available – from PharmaSea and OSDD
All Open PHACTS data already available!
Hopefully self-evident by now?
Support of Open PHACTS, PharmaSea and Chemical Database Service
Releasing Open Source code to community
Chemical Data Repository in development
Hosting models for the community
Royal Society of Chemistry developments to support open drug discovery
Personal Blog: www.chemconnector.com