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Royal society of chemistry developments to support open drug discovery


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In recent years the Royal Society of Chemistry has become known for our development of freely accessible data platforms including ChemSpider, ChemSpider Reactions and our new chemistry data repository. In order to support drug discovery RSC participates in a number of projects including the Open PHACTS semantic web project, the PharmaSea natural products discovery project and the Open Source Drug Discovery project in collaboration with a team in India. Our most recent developments include extending our efforts to support neglected diseases by the provision of high quality datasets resulting from our curation efforts to support modeling, the delivery of enhanced application programming interfaces to allow open source drug discovery teams to both source and deposit data from our chemistry databases and the provision of a micropublishing platform to report on various aspects of work supporting neglected disease drug discovery. This presentation will review our existing efforts and our plans for extended development.

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Royal society of chemistry developments to support open drug discovery

  1. 1. 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
  2. 2. 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
  3. 3. 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
  4. 4. • ~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
  5. 5. ChemSpider
  6. 6. ChemSpider
  7. 7. Properties – ACD/Labs
  8. 8. Properties – EPI Suite
  9. 9. Properties - ChemAxon
  10. 10. Literature references
  11. 11. Patents references
  12. 12. Books
  13. 13. Chemical vendors and data sources
  14. 14. 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
  15. 15. ChemSpider SyntheticPages
  16. 16. ChemSpider SyntheticPages
  17. 17. ChemSpider Reactions
  18. 18. ChemSpider Spectra
  19. 19. 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
  20. 20. Open Source Drug Discovery India
  21. 21. • Tuberculosis kills 1.6-1.7 million people every year (~1 every 8 seconds) • 1/3 of the worlds population is infected
  22. 22. OSDD Collaboration Recently sponsored cheminformatics jamboree – training by skilled specialists in the applications of cheminformatics to medicinal chemistry and drug design
  23. 23. 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
  24. 24. 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 (
  25. 25. Antibiotic resistance
  26. 26. Discovery Curve Decay
  27. 27. 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
  28. 28. Marinlit • RSC acquired Marinlit. Goes online in April • All Marinlit chemical compounds in ChemSpider • Marinlit developers are dereplication experts
  29. 29. Cancer Deaths Worldwide
  30. 30. Top Treatments for Cancer
  31. 31. • Over half of all drugs introduced between 1940 and 2006 were of natural origin or inspired by natural compounds Importance of Natural Products
  32. 32. Natural Products for all of us!
  33. 33. Natural Products Data Availability
  34. 34. • 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…
  35. 35. The Open PHACTS community ecosystem
  36. 36. Chemistry Registration Normalisatio n & 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)
  37. 37. OPS1 DrugBank ID DB07241 OPS5OPS4 OPS3 OPS2 OPS6 ops:OPS1 skos:exactMatch <http://www4.wiwiss.fu-> . 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 .
  38. 38. ChemSpider Validation & Standardization Platform Quality Assurance
  39. 39. 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)
  40. 40. Enabling Academic Researchers UK National Chemical Database
  41. 41. 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!
  42. 42. 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
  43. 43. We are doing it…we will do more Royal Society of Chemistry developments to support open drug discovery
  44. 44. Thank you Email: ORCID: 0000-0002-2668-4821 Twitter: @ChemConnector Personal Blog: SLIDES: