ChemSpider is being built with the intention of being a chemical structure centric community for chemists. With over 16 million chemical structures as of August 2007, and with data deposition and curation mechanisms in place for text, structure and spectra ChemSpider intends to be a meeting place and collaborative environment for chemists to work together.

1. An Introduction to
ChemSpider
Antony Williams

2. The ChemSpider Mission
ChemSpider intends to build a structure centric
community for chemists by:
Providing an environment for chemical structure drawing,
manipulation, visualization, modeling & databasing
Providing methods by which to deposit, curate and enhance
data associated with chemical structures
Providing structure-based access to federated Chemistry
databases representing chemical vendors, literature, online
data, patents and other forms of Chemistry data
Building a Structure Centric Community for Chemists

3. Every Journey Starts with a Single Step
March 2007
ChemSpider Beta opened to the public for exposure at
the Spring ACS (March 2007)
Initial database exposed only PubChem Data as a proof of
concept (10.5 Million compounds)
Structure/substructure searching available
Online prediction services available
Accompanying Spinneret Blog released
Building a Structure Centric Community for Chemists

4. Execution of the Mission
August 2007
An online database of over 16.5 million structures
Systems in place for:
Single structure and data collection depositions
Association of analytical data with structures
Ability to curate data for each individual record
Indexing of and Integration to:
Over 70 individual databases
Patents from the US, European and Asian Patent offices
Text-based searching of over 50,000 Open Access articles
Over a thousand unique users access ChemSpider per day
Building a Structure Centric Community for Chemists

5. Search Text “Prozac”
Building a Structure Centric Community for Chemists

6. Predicted Properties Details “Prozac”
Building a Structure Centric Community for Chemists

7. Flexible Boolean Searching
Building a Structure Centric Community for Chemists

8. Integrated Searching from Online Applet or
Desktop Drawing Packages
Building a Structure Centric Community for Chemists

9. Integrated Structure/Substructure and
Property Searches
Building a Structure Centric Community for Chemists

10. Search result: 49 hits in 2.8 seconds
Building a Structure Centric Community for Chemists

11. Integrated Visualization Tools
Building a Structure Centric Community for Chemists

12. Integrated Analytical Data Management
for Public Domain Data
Building a Structure Centric Community for Chemists

13. Integrated Prediction Engines
Input a chemical structure
and predict the properties
in real time using server-
based transactions.
Predictions furnished by
ACD/Labs at present.
Building a Structure Centric Community for Chemists

14. Integrated Access to Open Access
Literature
Text-based searching of
over 50,000 Open Access
Chemistry Articles
Building a Structure Centric Community for Chemists

15. External Integrations - Wikipedia
The links between Wikipedia and
ChemSpider are formed automatically
Building a Structure Centric Community for Chemists

16. External Integrations - Google
Search Across
Google Using
InChI string
Building a Structure Centric Community for Chemists

17. External Integrations – Patents
Reel Two Surechem Portal
Building a Structure Centric Community for Chemists

18. External Integrations – Plug-ins
Building a Structure Centric Community for Chemists

19. How do people generally use
ChemSpider?
Searching for chemical structures, in rank order, via:
Registry numbers, trade names and synonyms.
Structure identifiers such as SMILES or InChI
Intrinsic properties: commonly mass-based searches executed
by mass spectrometrists
Systematic names: IUPAC or CAS Index name
Generation of physicochemical properties
Text-based searching of Open Access articles
Structure-based searching of Patents
Building a Structure Centric Community for Chemists

20. Some Initial Feedback
“I must say that this site is excellent because it is the only place I
can drop the name of a published molecule like a bile acid or
steroid metabolite and actually get a hit.” Department of Animal
Sciences, University of Wisconsin-Madison
“I saw the ChemSpider release today - looks like an awesome
service!” Stanford University
“We encourage our students to use the chemspider services for
looking up chemical structures and their properties. My
collaborators use it to find company information. Your services
are very valuable for us.” Faculty of Pharmaceutical Sciences,
University of Leuven (Belgium)
Building a Structure Centric Community for Chemists

21. Curators - An Active Community
Building a Structure Centric Community for Chemists

22. The ChemSpider Platform
ChemSpider is developed using a series of components
and programming languages.
The core is C/C++
The database engine is Microsoft SQL Server
Web interface is ASP.NET and C#
Server-side scripting is Perl.
ChemSpider is hosted on x86 PCs on Windows 2003
Server
Building a Structure Centric Community for Chemists

23. The ChemSpider Platform
Building a Structure Centric Community for Chemists

24. ChemSpider – The Entity
The team consists of five people including 3 developers
The team has almost 40 years of experience in
developing modern cheminformatics software
applications for the desktop and the enterprise
ChemSpider has been built in off-hours only and with
personal funding
ChemSpider has an active Advisory Group
Building a Structure Centric Community for Chemists

25. The Advisory Group
The Advisory Group has been built from industry experts in the
fields of:
Pharmaceutical sciences
Analytical Sciences
Academia and Public Chemistry Efforts
Forensic Sciences
Open Standards
Open Source/Open Access Spectroscopy
Software Development
Chemistry Databases
Natural Products
Chemical Informatics and Statistics
Media, web skills and public relations
Building a Structure Centric Community for Chemists

26. Targets for 2007
End of year intentions for ChemSpider include
Adding more databases to the index to expand database to 20
million unique structures
Enhance integrations to other structure drawing packages
Include additional property prediction algorithms as provided
Extend integrations to synergistic software offerings
Expand the Public Domain analytical data handling
Enhance the Patent integration
Expand the Open Access article index to >100,000 articles
Building a Structure Centric Community for Chemists

27. ChemSpider in the Landscape
Common questions include:
How does ChemSpider compare with PubChem?
Is ChemSpider a competitor to eMolecules?
PubChem and CAS collided. Do ChemSpider and CAS
collide?
Building a Structure Centric Community for Chemists

28. ChemSpider and PubChem
Pubchem was built to support the National Screening Libraries
Initiative. The system is delivering very well on managing and
providing access to associated data
ChemSpider HAS taken advantage of the PubChem data sets –
PubChem data is only a subset of ChemSpider
Aspects of PubChem’s approach to manage and display structure
data are worth emulating – so ChemSpider does
ChemSpider is in the process of curating data and submitting
back to PubChem
ChemSpider will make submissions to the PubChem dataset and
provide input, guidance and feedback
The relationship is synergistic
Building a Structure Centric Community for Chemists

29. ChemSpider and eMolecules
ChemSpider and eMolecules are similar efforts to deliver
access to structure-related information
Both groups are developing new cheminformatic
technologies to facilitate their systems
ChemSpider is actively delivering on a wiki-like
environment for expansion and curation of the database
Building a Structure Centric Community for Chemists

30. ChemSpider and CAS
CAS is the gold standard in many domains – the Registry is a
highly curated and controlled assembly of chemical structures
and related information connected to publications, patents and
vendors.
ChemSpider is primarily an algorithmically curated database with
manual curation enabled. ChemSpider is a system facilitating the
deposition and association of chemical structures and related
information including, but not limited to public and commercial
databases, chemical vendor catalogs, patents and individual
chemists
CAS is not yet concerned with providing capabilities to manage
chemistry depositions submitted by individual scientists, research
groups, with the management of analytical data and the provision
of APIs to provide integration to other Open Access systems
Building a Structure Centric Community for Chemists

31. Conclusion
ChemSpider is successfully building a structure centric
community for chemists
Over 1000 chemists per day utilize ChemSpider to help
answer questions and solve their problems
A well-defined path forward to enhance the service has
been defined
Building a Structure Centric Community for Chemists

32. Acknowledgments
Thousands of users for their feedback and ongoing
encouragement
The “naysayers” – criticism, when taken constructively,
can drive creative actions
Our advisory group of scientists, specialists and friends
The bloggers coming to the ChemSpider Blog and
ChemSpider News
Building a Structure Centric Community for Chemists