Chem spider introduction spring 2011

An introduction to Chemspider

1. ChemSpider:
A chemistry resource

2. Community Contribution and Innovation
ChemSpider 2010 Bio-IT World Best
Practices Award for contributions to
community chemistry
ChemSpider Innovation Software Award
at the iExpo/KM Forum, June 2010
ChemSpider names as winner for the
2010 ALPSP Award for Publishing
Innovation, September 2010
ChemSpider has won several awards for
innovation since its acquisition by the RSC

3. ChemSpider Agenda
What is ChemSpider?
How to conduct a search
What do you get?
Our Agenda is to look at the content of
ChemSpider and how to approach searching

4. What is ChemSpider?
Building a Structure Centric Community
for Chemists
A deposition and curation platform
A publishing platform for the community
Grows daily – more depositions, more links,
more data sources
ChemSpider SyntheticPages
•An online database of synthetic procedures
ChemSpider is a FREE resource which provides access to
more than 25 M compounds and more than 400 data
sources

5. What is ChemSpider?
Largely small organic molecules
No support, YET, for:
•Polymers
•Minerals
•Markush structures
•Biological Macromolecules
ChemSpider relies upon InChIs
•International Chemical Identifier
Std. InChIKey for the drug Fluconazole is:
RFHAOTPXVQNOHP-UHFFFAOYSA-N
Can be used to search in Google

6. ChemSpider as Chemical Search
Single search across 400 data sources
Text, structure and substructure
search tools
•Simple and very advanced
Validated names for external
search expansion
•Google Scholar
•RSC publications and PubMed
Links to original sources
Mobile version
•cs.m.chemspider
ChemSpider can be accessed at anytime with any Web
browser, including mobile devices and tablets

7. ChemSpider Search
 Chemical Name
 Tradename (Synonym)
 CAS Registry Number or other Identifier (SMILES, InChI)

8. ChemSpider Links
Data Sources
Patents
Literature Sources
•Google Scholar
•RSC Journals
•RSC Databases
•PubMed Articles

9. Search by Chemical Name
The Record View
Expand a literature search in Google Scholar using validated
names from ChemSpider

10. Search by Chemical Name
Chemical Names, Synonyms and other Identifiers
Chemical names are listed in the Identifiers box. Those in
bold are approved as validated names

11. Synonyms give expanded results via Google Scholar
ChemSpider Results

12. ChemSpider Results
Supplier catalogs and links to other data sources
Clicking on any of the tabs will link you to other Internet
resources – mostly free

13. ChemSpider Results
Property Data from ACD/Labs and others
Options to select alternative algorithms for property prediction

14. ChemSpider Results
Find articles on this compound from RSC Journals and Books
Titles link through to full-text articles in RSC Publishing
platform

15. ChemSpider Results
Find articles in RSC Abstract & Indexing Databases
Subject specific articles from all publishers

16. ChemSpider Results
User or publisher recommended articles
Specific articles on this compound added by users or publishers

17. ChemSpider Results
Expanded compound search on PubMed titles and
abstracts

18. ChemSpider Results
Patents from SureChem and Google Patents
SureChem provides access to patents from the USPTO, EPO and
PCT filings, Japanese Abstracts

19. ChemSpider Result Links
Click on a title to view the patent document

20. Search by Structure
Auto-generate structure from chemical
name or SMILES or InChI
To search by structure: click on the search menu from the top
navigation bar and select structure search from the drop down
menu. The structure drawing applet is then activated by clicking
on the structure image

21. Search by Structure
Draw a structure using Java applet
There are several structure drawing applets available. Need
Java enabled

22. Search by Structure
Load a mol file from another drawing package –
such as ChemSketch, ChemDraw or SymyxDraw

23. Search by Structure
LOAD the molfile into the structure drawing applet
When happy with the structure, click Accept

24. Search by Structure
Accept the loaded structure
Choose between an Exact or Substructure search

25. Search by Structure
Expand these links to see more properties, names, identifiers
The Record view for Codeine

26. ChemSpider Results
Embedded spectra
Results can also include spectra. Options to download (if a
registered user and logged in) and print

27. ChemSpider as Wiki
Adds quality and quantity…
Users can comment for others to action
Registered users can curate names, add
links, spectra, data and multimedia
resources
Depositors can load data sets which are
curated on load
Curators and Master Curators approve
additions and decide what is the correct
structure
Anyone can comment on records, but you need to be a
registered user to curate names or deposit structures and
spectra

28. ChemSpider as Wiki
Users can contribute data and use as
a shared resource for research group
Jacqueline Bennett’s group use ChemSpider as a repository of their
research to give easy access, for themselves and other ChemSpider
users

29. ChemSpider as a Resource
Download and reuse structures
Download and reuse search
structure set
2D and 3D images
Embed and link - never draw
a structure again
Spectra, crystal structures
ChemSpider SyntheticPages
Registered users can download the results set from a substructure
search and can embed structures in a blog or wiki

30. ChemSpider – What we’re working on…
Working with our users to give you what you
need to do your job
Adding more pharmacological data (Open
PHACTS project)
Creating an eLearning resource for 16-19 yrs –
to be released later in 2011
Growing the community of data depositors
and curators
Putting ChemSpider at the heart of publicly
accessible chemistry data

31. Thank you for your attention
Twitter: ChemSpider
www.chemspider.com/blog
[email protected]