The Royal Society of Chemistry is building a Global Chemistry Network which will connect chemical resources and chemists across the globe in a single scientific information network dynamically updated in real time. We have been working on a number of the foundation technologies for a number of years including a structure database containing almost 30 million chemicals, a micropublishing environment, a platform for the validation and standardization of chemical structure representations and a text-mining and semantic markup platform for data enabling our published articles. Our goal is to provide seamless tools for researchers, librarians, publishers, informational technology specialists and government agencies to facilitate scientific research by providing a free flow of information. This talk will review our work to date to provide a chemistry data platform for the community and will highlight some of the challenges we face as we expand the architecture for our Global Chemistry Network platform.

1. Building Global Chemistry
Network at the Royal Society of
Chemistry
Valery Tkachenko
ICSTI Workshop
Data and Non-Data Integration –
A Journey Across Disciplines
Ottawa, October 16th 2013

2. The World we live in
Internet World
20+ years into the Internet Revolution
Web 2.0 -> Web 3.0
Connected World
Social Networks
Real-time Communications
Big Data World
Semantic content
New Interfaces

3. Big Data challenge
RSC/ChemSpider platforms
Crowdsourcing and AltMetrics
New interfaces
Building Global Chemistry Network

5. Science map

6. Chemistry on the Internet

7. Why disproportion?
Scientific complexity
Conservative nature

8. Big Data challenge
RSC/ChemSpider platforms
Crowdsourcing and AltMetrics
New interfaces
Building Global Chemistry Network

9. Royal Society of Chemistry (RSC)
Largest European organisation for advancing the chemical
sciences
Founded 1841
Not-for profit “To be the leading voice and
trusted partner for science and humanity”
Professional body with a worldwide network
of 48,000 members
International publisher ~400 employees
Education facilitator, Science leader,
E-Science leaders

10. About the RSC
• Headquarters in London
• Offices in Cambridge, Beijing,
Shanghai, Philadelphia, Tokyo
Bangalore, Sao Paulo

11. STM publisher
Knowledge
Delivery Magic
Our User Interfaces
(Desktop, Web, Mobile, etc)
Customers
3rd party integrations
(our web services)

12. ChemSpider Suite
UIs
ChemSpider
Reactions
mobile web app
ChemSpider
website
ChemSpider
desktop app
Depositions client
Components Layer
Java Beans
JS Components
Python widgets
ASP.NET
Components
PHP snippets
Google Apps
Components
SharePoint
Components
APIs Layer
Search API
CSC API
Export API
CSR API
DS API
Processing API
CSS API
CSM API
CSA API
CSAs API
CSR BO
CSS BO
CSM BO
CSA BO
CSAs BO
ChemSpider
Reactions
ChemSpider
Spectra
ChemSpider
Materials
ChemSpider
Algorithms
ChemSpider
Assays
Business Objects Layer
CSC BO
Data Layer
ChemSpider
Compounds

13. •
•
•
•
29 million chemicals and growing
Data sourced from >500 different sources
Crowdsourced curation and annotation
Ongoing deposition of data from our
journals and our collaborators
• A structure centric hub for web-searching

14. ChemSpider

15. ChemSpider

16. ChemSpider

17. ChemSpider

18. ChemSpider

19. ChemSpider

20. ChemSpider

21. ChemSpider

22. ChemSpider

26. ChemSpider Reactions

27. ChemSpider Reactions

28. ChemSpider Reactions

29. ChemSpider Reactions

30. RSC Archive – since 1841

31. DERA Digitally Enabling RSC Archive

32. Semantic Mark-up of Articles

33. It is so difficult to navigate…
IP?
IP?
What’s the
What’s the
structure?
structure?
Are they in
Are they in
our file?
our file?
What’s
What’s
similar?
similar?
Pharmacology
Pharmacology
data?
data?
What’s the
What’s the
target?
target?
Known
Known
Pathways?
Pathways?
Competitors?
Competitors?
Connections
Connections
to disease?
to disease?
Working On
Working On
Now?
Now?
Expressed in
Expressed in
right cell type?
right cell type?

34. DERA Architecture
Structures
Reactions
DERA
(Text Mining)
Text, PDF, XML
Chemistry Validation and
Standardization Platform
(CVSP)
Spectra
Materials
Biological
Activities

35. Data quality issue and CVSP
Robochemistry
Proliferation of errors in public and
private databases
Automated quality control system

36. DrugBank dataset (6516
records)
~60 records that can’t be dearomatized unambiguously
DB04283
DB04462

37. ~30 records with bonds that do not make
sense
DB04283
DDB04009

38. 7 records with 2 stereo bonds at chiral
atoms
J. Brechner, IUPAC
Graphical Representation of
stereochem. configurations
Section: ST-1.1.10
DB08128
DB06287

39. “Direction of bond makes no sense” –
63%

40. “Stereo types of non-opposite bonds match” – 2%

41. ChemSpider Suite
UIs
ChemSpider
Reactions
mobile web app
ChemSpider
website
ChemSpider
desktop app
Depositions client
Components Layer
Java Beans
JS Components
Python widgets
ASP.NET
Components
PHP snippets
Google Apps
Components
SharePoint
Components
APIs Layer
Search API
CSC API
Export API
CSR API
DS API
Processing API
CSS API
CSM API
CSA API
CSAs API
CSR BO
CSS BO
CSM BO
CSA BO
CSAs BO
ChemSpider
Reactions
ChemSpider
Spectra
ChemSpider
Materials
ChemSpider
Algorithms
ChemSpider
Assays
Business Objects Layer
CSC BO
Data Layer
ChemSpider
Compounds

42. Big Data challenge
RSC/ChemSpider platforms
Crowdsourcing and AltMetrics
New interfaces
Building Global Chemistry Network

43. AltMetrics

44. Plum Analytics

45. RSC/Rewards and Recognition
The First Step badge is
awarded when a user
submits (& has published)
their 1st CSSP article.
Congratulations! Your 1st CSSP
article has been published.
Philosopher Lao Tzu said “A
journey of a thousand miles begins
with a single step”. In the same
way we hope that this will be the
first of many submissions that you
make to CSSP.

46. Big Data challenge
RSC/ChemSpider platforms
Crowdsourcing and AltMetrics
New interfaces
Building Global Chemistry Network

47. Visualization

48. Navigation

49. ChemSpider APIs

50. Big Data challenge
RSC/ChemSpider platforms
Crowdsourcing and AltMetrics
New interfaces
Building Global Chemistry Network

51. We are a part of a larger world

52. National Chemistry Database

53. National Data Repository
Scientists
Funding bodies
External clients
Publishers
Indexes
Data Repository
indexed storage
Chemically
intelligent services
Data
Data Repository provided
data storage
University 1
University 2
Data Hub
Workstations
Company 3
Data Hub
Workstations
Data Hub
Workstations

54. http://www.openphacts.org
Open PHACTS is an Innovative
Medicines Initiative (IMI) project,
aiming to reduce the barriers to
drug discovery in industry,
academia and for small
businesses.
Semantic web is one of the
corner stones

56. We know about Natural Products

57. Marinlit

58. OSDD

59. The Future
Internet Data
Small organic molecules
Undefined materials
Organometallics
Nanomaterials
Polymers
Minerals
Particle bound
Links to Biologicals
Commercial Software
Pre-competitive Data
Open Science
Open Data
Publishers
Educators
Open Databases
Chemical Vendors

60. Thank you
Email: tkachenkov@rsc.org
Slides: http://www.slideshare.net/valerytkachenko16