royal society of chemistry developments to support open drug discovery
TRANSCRIPT
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Royal Society of Chemistry developments to support open drug discovery
Antony Williams, Ken Karapetyan, Valery Tkachenko, Colin Batchelor Alexey Pshenichnov and Jon Steele
ACS Dallas
March 2014
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Supporting Open Drug Discovery
• 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
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RSC as a Publisher• 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
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• ~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
As host of chemistry databases
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ChemSpider
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ChemSpider
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Properties – ACD/Labs
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Properties – EPI Suite
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Properties - ChemAxon
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Literature references
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Patents references
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Books
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Chemical vendors and data sources
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ChemSpider
• 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
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ChemSpider SyntheticPages
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ChemSpider SyntheticPages
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ChemSpider Reactions
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ChemSpider Spectra
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RSC as a Charity
• 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
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Open Source Drug DiscoveryIndia
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• Tuberculosis kills 1.6-1.7 million people every year (~1 every 8 seconds)
• 1/3 of the worlds population is infected
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OSDD Collaboration
Recently sponsored cheminformatics jamboree – training by skilled specialists in the applications of cheminformatics to medicinal chemistry and drug design
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OSDD Collaboration
• 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
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As a provider of grant-based services
• 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)
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Antibiotic resistance
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Discovery Curve Decay
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Focus on Marine Natural Products
• 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
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Marinlit
• RSC acquired Marinlit. Goes online in April
• All Marinlit chemical compounds in ChemSpider• Marinlit developers are dereplication experts
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Cancer Deaths Worldwide
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Top Treatments for Cancer
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• Over half of all drugs introduced between 1940 and 2006 were of natural origin or inspired by natural compounds
Importance of Natural Products
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Natural Products for all of us!
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Natural Products Data Availability
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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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The Open PHACTS community ecosystem
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Chemistry RegistrationNormalisation & Q/C
• New Chemical Registration System• Utilizes ChemSpider Validation
and Standardization platform• Utilizes FDA rule set as basis for
standardizations • Generate Open PHACTS identifier
(OPS ID)
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OPS1
DrugBank ID DB07241
OPS5OPS4
OPS3
OPS2
OPS6
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 .
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ChemSpider Validation & Standardization Platform
Quality Assurance
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Open Sourcing Data and Code
• 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)
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Enabling Academic ResearchersUK National Chemical Database
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Data for the Community
• 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!
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As Innovator in Cheminformatics
• Hopefully self-evident by now?• ChemSpider• Support of Open PHACTS, PharmaSea and
Chemical Database Service• Releasing Open Source code to community
• To come:• Chemical Data Repository in development• Hosting models for the community
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We are doing it…we will do more
Royal Society of Chemistry developments to support
open drug discovery
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Thank you
Email: [email protected]: 0000-0002-2668-4821 Twitter: @ChemConnectorPersonal Blog: www.chemconnector.com SLIDES: www.slideshare.net/AntonyWilliams