This document discusses ChemSpider, a free chemical structure database that aggregates and connects chemistry data from across the internet. ChemSpider aims to be a central hub for chemical data by standardizing structures, connecting related data and services, and enhancing data through predictions. It provides access to data on millions of compounds, including properties of the herbicide Roundup. While useful, ChemSpider has limitations from errors in source data and issues with standardizing complex molecules. Future work includes improving data quality, developing a validation platform, and adding predictive capabilities and repository functions.

1. Connecting Chemistry Across the
Internet Using ChemSpider
Antony J Williams and Valery Tkachenko
SERMACS, November 15th 2012

2. Chemistry Data and the Weeds

3. Tell me about Roundup

4. So what is Round Up?

5. The World’s Encyclopedia

6. Roundup

7. Where do we Round Up data?
 Where can I find the molfile for Roundup?
 Papers/Patents about Roundup?
 What are the side effects of Roundup?
 Where can I order Roundup?
 What are the physicochemical properties?
 Metabolic pathways?
 Different synonyms of Roundup?
 Synthesis of Roundup?
 Side effects of Roundup?
 Etc….

8. Where do I Round Up Data?

10. In an increasing LinkedData map….

11. But I want to aggregate data? So…

12. ChemSpider
 Takes on the role of a structure centric hub:
 Connecting, validating, qualifying data
 Enhancing data with connections to services
 Provides access to data and services for others
to use (Thermo, Agilent, Bruker, Waters,
ACD/Labs, Accelrys, etc.)
 Uses available services to integrate, connect
and enhance the offering

13. Roundup on ChemSpider

14. What will ChemSpider give us??

15. What will ChemSpider give us??

16. What will ChemSpider give us??

17. What will ChemSpider give us??

18. What will ChemSpider give us??

19. What will ChemSpider give us??

20. ChemSpider is Collapsing Data???

21. What will ChemSpider give us??

22. For Glyphosate itself

23. How did we build it?
 We deal in Molfiles or SDF files – with coordinates
 Deposit anything that has an InChI – we support
what InChI can handle, good and bad
 Standardization based on “InChI standardization”
 InChIs aggregate (certain) tautomers
 How much of ChemSpider is “on ChemSpider”?

24. Connecting Chemistry across the web
 So much of what is seen on ChemSpider is
retrieved in real time using services

25. Connecting Chemistry across the web

26. Online Predictions

27. A Comment on Quality
 For >28 million chemical compounds there are
some errors:
 “Incorrect” structure representations
 Mismatched name-structure relationships
 Experimental properties (the values, the units)
 Real vs. virtual compounds – text-mining and
conversion
 We have deprecated a LOT of data…

28. Downsides of InChI
 Good for small molecules – but no polymers,
issues with inorganics, organometallics, imperfect
stereochemistry. ChemSpider is “small molecules”
 InChI used as the “deduplicator” – FIRST version
of a compound into the database becomes THE
structure to deduplicate against…

29. Side Effects of InChI Usage

30. SMILES by comparison…

31. Side Effects of InChI Usage

32. Standardization Issues
Depiction based on molfile

33. Downsides of Overall Approach
 Meshing data together based on InChIs worked
for simple molecules
 2D layout errors inherited or limited by algorithm
 Complex molecules that are meant to be the
same thing were NOT deduplicated. Compounds
differing by one stereocenter, named the same,
meant to be the same, are not the same

34. So much data online is “erroneous”

35. The confusion of name-structures

36. Collapsing Data – Standardization

37. What needs to happen?
 If we could validate
 Catch errors in databases (and clean)
 Proactively catch errors in publications/patents
 Reduce junk in the ether – improve QUALITY!
 If we collectively standardized
 Interlinking between databases should improve
 CVSP – a separate presentation….stick around

38. Crowdsourcing ChemSpider
 ChemSpider is crowdsourced
 Community deposition, annotation
and curation
 Anyone can “Leave Feedback”
 Registered users can add data

39. ChemSpider and Global Chemistry Hub
Internet Data
Small organic molecules Commercial Software
Undefined materials Pre-competitive Data
Organometallics Open Science
Nanomaterials Open Data
Polymers Publishers
Minerals Educators
Particle bound Open Databases
Links to Biologicals Chemical Vendors

40. Delivering a Prediction Platform
 Experimental data will be used as the basis of
model generation – a predictive platform…

41. The Future of ChemSpider
 Continued focus on quality over quantity –
but more data is good too!
 ChemSpider Reactions – work in progress
and includes >300,000 reactions
 Plugging in a validation and standardization
platform
 Delivering personal and institutional
repository capabilities

42. Thank you
Email: williamsa@rsc.org
Twitter: ChemConnector
Personal Blog: www.chemconnector.com
SLIDES: www.slideshare.net/AntonyWilliams