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.

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. 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. 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. • ~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. ChemSpider

6. ChemSpider

7. Properties – ACD/Labs

8. Properties – EPI Suite

9. Properties - ChemAxon

10. Literature references

11. Patents references

12. Books

13. Chemical vendors and data sources

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. ChemSpider SyntheticPages

16. ChemSpider SyntheticPages

17. ChemSpider Reactions

18. ChemSpider Spectra

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. Open Source Drug Discovery
India

21. • Tuberculosis kills 1.6-1.7 million people
every year (~1 every 8 seconds)
• 1/3 of the worlds population is infected

22. OSDD Collaboration
Recently sponsored
cheminformatics
jamboree – training
by skilled specialists
in the applications of
cheminformatics to
medicinal chemistry
and drug design

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. 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)

26. Antibiotic resistance

27. Discovery Curve Decay

29. 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

30. Marinlit
• RSC acquired Marinlit. Goes online in April
• All Marinlit chemical compounds in ChemSpider
• Marinlit developers are dereplication experts

31. Cancer Deaths Worldwide

32. Top Treatments for Cancer

33. • Over half of all drugs introduced between
1940 and 2006 were of natural origin or
inspired by natural compounds
Importance of Natural Products

34. Natural Products for all of us!

35. Natural Products Data Availability

36. • 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…

37. The Open PHACTS community ecosystem

39. 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)

40. 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 .

41. ChemSpider Validation & Standardization Platform
Quality Assurance

42. 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)

43. Enabling Academic Researchers
UK National Chemical Database

44. 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!

45. 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

46. We are doing it…we will do more
Royal Society of Chemistry
developments to support
open drug discovery

47. Thank you
Email: williamsa@rsc.org
ORCID: 0000-0002-2668-4821
Twitter: @ChemConnector
Personal Blog: www.chemconnector.com
SLIDES: www.slideshare.net/AntonyWilliams