1. The RSC & e-Science:
Reflecting the Change in the
World we Live In
Valery Tkachenko
RSC-OSDD Consultative Workshop on
Cheminformatics
Delhi, September 28th
2013

2. Royal Society of Chemistry and Global
Chemistry Network

3. 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

4. Pillars of the World
Data
Data (knowledge) is a King
Dataflow
Navigation
Domain-specific search and navigation
Navigate inside and link out - federation
Interfaces
HCI (human computer interface)
M2M (machine to machine)

5. Science map

6. Chemical sciences map

7. Chemistry on the Internet

8. What’s wrong?!?!
Complexity

9. Royal Society of Chemistry and Global
Chemistry Network

10. Knowledgebases and delivery systems
Big Data challenge
Crowdsourcing and altmetrics
New interfaces

11. Knowledgebases and delivery systems
Big Data challenge
Crowdsourcing and altmetrics
New interfaces

12. 50000ft view at STM publisher
Knowledge
Our User Interfaces
(Desktop, Web, Mobile, etc)
Customers
Delivery Magic
3rd
party integrations
(our web services)

13. ChemSpider Suite
Data Layer
ChemSpider
Assays
ChemSpider
Compounds
ChemSpider
Reactions
ChemSpider
Spectra
ChemSpider
Materials
ChemSpider
Algorithms
Business Objects Layer
CSAs BOCSC BO CSR BO CSS BO CSMBO CSABO
APIs Layer
DS APIExport APISearch API Processing API
CSAs APICSC API CSR API CSS API CSMAPI CSAAPI
Components Layer
JS Components
Google Apps
Components
Python widgets
SharePoint
Components
PHP snippets
ASP.NET
Components
UIs
ChemSpider
website
ChemSpider
Reactions
mobileweb app
ChemSpider
desktop app
Depositions client
Java Beans

14. • 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

15. ChemSpider and Atovaquone

16. ChemSpider and Atovaquone

17. ChemSpider and Atovaquone

18. ChemSpider and Atovaquone

19. ChemSpider and Atovaquone

20. ChemSpider and Atovaquone

21. ChemSpider and Atovaquone

22. ChemSpider and Atovaquone

23. ChemSpider and Atovaquone

24. ChemSpider and Atovaquone

25. ChemSpider and Atovaquone

26. ChemSpider and Atovaquone

27. Micropublishing

28. Micropublishing

29. Micropublishing

30. ChemSpider Reactions

31. ChemSpider Reactions

32. Knowledge in our own archives

33. DERA and Text Mining
The N-(β-hydroxyethyl)-N-methyl-N'-(2-trifluoromethyl-1,3,4-
thiadiazol-5-yl)urea prepared in Example 6, thionyl chloride ( 5
ml ) and benzene ( 50 ml ) were charged into a glass reaction
vessel equipped with a mechanical stirrer, thermometer and
reflux condenser .
The reaction mixture was heated at reflux with stirring, for a
period of about one-half hour .
After this time the benzene and unreacted thionyl chloride
were stripped from the reaction mixture under reduced
pressure to yield the desired product N-(β-chloroethyl)-N-
methyl-N'-(2-trifluoromethyl-1,3,4-thiaidazol-5-yl)urea as a solid
residue

34. Text Mining
The N-(β-hydroxyethyl)-N-methyl-N'-(2-trifluoromethyl-1,3,4-
thiadiazol-5-yl)urea prepared in Example 6 , thionyl chloride ( 5
ml ) and benzene ( 50 ml ) were charged into a glass reaction
vessel equipped with a mechanical stirrer , thermometer and
reflux condenser .
The reaction mixture was heated at reflux with stirring , for a
period of about one-half hour .
After this time the benzene and unreacted thionyl chloride
were stripped from the reaction mixture under reduced
pressure to yield the desired product N-(β-chloroethyl)-N-
methyl-N'-(2-trifluoromethyl-1,3,4-thiaidazol-5-yl)urea as a solid
residue

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

36. Digitally Enabling RSC Archive
Text, PDF, XML
Structures
Reactions
Spectra
Materials
Chemistry Validation and
Standardization Platform
(CVSP)
DERA
(Text Mining)
Biological
Activities

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

38. ChemSpider issues

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

40. ~30 records with bonds that do not make
sense
DB04283
DDB04009

41. 2 records where Smiles, InChI, and name did not match
the structure
DB00611 DB01547

42. ~40 records where InChIs did not match the structure
DrugBank ID: DB00755
InChI=1S/C20H28O2/c1-15(8-6-9-16(2)14-19(21)22)11-12-18-17(3)10-7-13-
20(18,4)5/h6,8-9,11-12,14H,7,10,13H2,1-5H3,(H,21,22)/b9-6+,12-11+,15-8+,16-14+
DruGBank ID: DB00614

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

44. CVSP validation of ChEMBL 16 (~1.3 mln. records)
• Overall 0.7% of records had validation issues
• Stereo problems (~82%)
• Directions of bonds do not make sense (~63%)
• Ambiguous stereo : 2 stereo bonds at chiral center (~19%)

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

46. “Stereo types of the opposite bonds mismatch” -15%
http://www.iupac.org/publications/pac/2006/pdf/7810x1897.pdf

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

48. “atom not recognized” – 3% isotopes
Should be atom from periodic table
No mass difference in atom line
No “M ISO” in connection table
In molfile:

49. ChemSpider Suite
Data Layer
ChemSpider
Assays
ChemSpider
Compounds
ChemSpider
Reactions
ChemSpider
Spectra
ChemSpider
Materials
ChemSpider
Algorithms
Business Objects Layer
CSAs BOCSC BO CSR BO CSS BO CSMBO CSABO
APIs Layer
DS APIExport APISearch API Processing API
CSAs APICSC API CSR API CSS API CSMAPI CSAAPI
Components Layer
JS Components
Google Apps
Components
Python widgets
SharePoint
Components
PHP snippets
ASP.NET
Components
UIs
ChemSpider
website
ChemSpider
Reactions
mobileweb app
ChemSpider
desktop app
Depositions client
Java Beans

50. Knowledgebases and delivery systems
Big Data challenge
Crowdsourcing and altmetrics
New interfaces

51. Started with 2 servers in a basement
Presently – two farms ~40 servers each
Future – in the Clouds

52. Compute intensive calculations
Delivery systems

53. Knowledgebases and delivery systems
Big Data challenge
Crowdsourcing and altmetrics
New interfaces

54. AltMetrics

55. Curation in ChemSpider

56. Knowledgebases and delivery systems
Big Data challenge
Crowdsourcing and altmetrics
New interfaces

57. Visualization

58. Navigation

59. ChemSpider APIs

60. We are a part of a larger world

61. National Chemistry Database

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

63. 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

64. What does e-Science do in
?
ChemSpider provides many of the
physicochemical properties within the
Open PHACTS Discovery Platform
e-Science develop tools to check and
standardise chemical structures
•
•
e-Science is creating the Open PHACTS
chemical registration system
•

65. RDF Export
Data:
ChEMBL
HMDB
DrugBankChemistry Validation and Standardization
Platform (CVSP)
at cvsp.chemspider.com
•Validation
•Standardization
•Parent generation
•Run on Hadoop-based farm

67. We know about Natural Products

68. Marinlit

69. OSDD

70. The Global Chemistry Network