1. ChemSpider compound database as
one of the pillars of a semantic web
for chemistry
of the pillars of a
Valery Tkachenko, Antony J Williams,
Ken Karapetyan, Colin Batchelor, Jon Steele, Aileen Day
and David Sharpe
ACS Philly August 2012

2. Outline
 The world we live in
 Pillars of the world
 ChemSpider as a semantic web system
 Example of federated semantic web system

3. The World we live in
 Internet World
 ~20 years of WWW and inflationary expansion
 Web 2.0
 Connected World
 Social Networks
 Mobile Communications
 Internet TV
 Big Data World
 Semantic content
 New Interfaces

4. Pillars of the World
 Data is King
 New data model approach: SQL  NoSQL
 Inflow of data
 Structured data
 Search and Navigation
 Search by all domain specific information
 Navigate inside and link out
 Cloud
 Data and code are distributed and self-sustained
 Federated systems take precedence over standalone solutions
 Interfaces
 Sophisticated HCI (human computer interface)
 Pervasive M2M (machine to machine)

5. Chemistry on the Internet

6. What’s wrong?!?!
 Is science (and chemistry in particular) so miserable in the
world we live in?
 Or too obscure and complex to be easily presented?
 Or scientists are rather conservative beasts?

7. Scientific data complexity

8. Chemical data complexity

9. ChemCloud

10. ChemSpider
 Database of small organic molecules
 Properties
 Names and synonyms
 Spectra
 Contribute in an easy way
 New data depositions
 Existing data curations
 Search engine for chemistry
 Search a chemical by a, b, c
 Cluster and navigate relationships
 Extensive infrastructure
 Computer farm
 Components
 Standard interfaces
 SOAP
 REST
 JSON

11. ChemSpider UI
Filters
APIs
Data
BPF
(distributed computing)

12. Deposition System

13. ChemSpider UI
Filters
APIs
Data
BPF
(distributed computing)

14. Validation and Standardization

15. ChemSpider UI
Filters
APIs
Data
BPF
(distributed computing)

16. User Interface
 Web
 Mobile
 GUI components

17. JS Components

18. Google Search

19. UI
Filters
APIs
Data
BPF
(distributed computing)

20. APIs
 SOAP
 Traditional web services
 REST/JSON
 Used in JS applications
 RDF
 Exchange format for semantic web
 SPARQL
 Query language

21. OpenPHACTS
 Open PHACTS is an Innovative Medicines
Initiative (IMI) – 3 years project
 To reduce the barriers to drug discovery in
industry, academia and for small businesses
 To build an open platform, integrating chemistry
and biology data from public domain resources
 Open Standards, Open Data and Open Source

22. Acknowledgements
 RSC Cheminformatics group
 Open PHACTS consortium
 Software: GGA Software, ACD/Labs, Scilligence,
OpenEye, Accelrys, ChemDoodle, ChemAxon,
Dotmatics, OpenBabel, Jmol, JSpecView,

23. Thank you
Email: tkachenkov@rsc.org
Blog: www.chemspider.com/blog
SLIDES:
http://www.slideshare.net/valerytkachenko16