Overview
• What is ChemSpider?
• How to conduct a search
• What data ChemSpider records
can contain
• Contributing data
• Sharing reaction protocols
What is ChemSpider?
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Free to use
ChemSpider brings together many different
types of data, from a variety of sources
What sort of data?
2-(Acetyl​oxy)benzo​ic acid
2-(Acetyl​oxy)benzo​lcarbonsä​ure [German]
2-Acetoxy​benzeneca​rboxylic ​acid
2-Acetoxy​benzoesäu​re [German]
2-Acetoxy​benzoic a​cid
2-acetylo​xybenzoic​ acid
50-78-2 [RN]
Acetoxybe​nzoic acid
acetyl sa​licylic a​cid
Acetysali​cylic acid
acide 2-(​acétyloxy​)benzoïque [French]
Acide 2-a​cétoxyben​zoïque [French]
Aspirin [Wiki]
Aspirin (​JP15/USP) (​VAN)
Benzoic a​cid, 2-(a​cetyloxy)Kyselina ​acetylsal​icylova [Czech]
o-(Acetyl​oxy)benzo​ic Acid
Headline facts
• >27 million structures = >27 million records
– from ~400 data sources
• Free – no need to register
• Provides access to chemistry information:
– anyone, any time, anywhere
Desktop PC in the lab, laptop at home, phone/tablet on the move
• Data isn’t perfect – but still has value
• Users can get involved!
– Share your data
– Raise your profile
ChemSpider in more detail
• Key concept:
“all data that is added to the database must be
associated a with discrete chemical structure”
• This sounds easy
... but is actually hard
• Huge advantages to aggregating information
around a chemical structure
What about other chemical species?
•
Polymers
Ph
Ph
•
Organometallics
•
Biological macromolecules:
Proteins, antibodies, DNA
n
Ph
• Gels (& other supramolecular species)
•
Ordered inorganics:
– Minerals etc.
Why are structures so important?
• Fundamental language of chemists
– Concise
– Contain huge amount of data
• How else do we share chemical information?
– Common/trivial names
– Systematic names
– Registry numbers
These are
abstractions/derivatives
What’s in a name?
Spongistatin 1
Systematic Name:
(1S,3S,5R,9R,10R,11R,13R,14S,15R,17S,18R,19R,23Z,25R,27S,29S,31S, ​33S,36
S,37S,38R,41S,43S,49S)-11-[(4S,5E)-7-chloro-4-hydroxy-2-met​hylideneocta5,7-dien-1-yl]-10,14,15,17,27,43-hexahydroxy-31-meth​oxy-18,36,38,43,49pentamethyl-39-methylidene-7,35-dioxo-8,12,4​ 5,46,47,48,50heptaoxaheptacyclo [39.3.1.11,5.19,1​3.115,19.125,29.129,33] pen​tacont-23ene-3,37-diyl diacetate
Getting started
• Quick and easy
•No special software
• No need to register/login to get started
• http://www.chemspider.com
• Or http://cs.m.chemspider.com (mobile)
ChemSpider search
• Chemical name
• Tradename or synonym
• Registry number or other identifiers (SMILES, InChI)
ChemSpider results
• The record view
ChemSpider results
• Systematic names, synonyms and other identifiers
ChemSpider results
 Validated synonyms can be used to query other
services: eg. Google Scholar
ChemSpider results
• Find articles on this compound from RSC
journals and books
• Also link to PubMed
ChemSpider results
• Patent citations provided by:
– SureChem
– Google Patents
ChemSpider results
• User or publisher recommended articles
ChemSpider results
• Supplier catalogues and links to other data sources
ChemSpider results
• Where
Predicted
available
property
wedata
also from
display
ACD/Labs
experimental
and others
data
Search by structure
Search by structure
• The record view for codeine
ChemSpider results
• Embedded spectra
Adding data to ChemSpider
• Users can contribute data and use as
a shared resource for research group
ChemSpider Synthetic Pages - CSSP
• An online database of synthetic reactions
Synthetic Pages - Online publishing
• Deposit synthetic procedures on Synthetic Pages
– Share/Highlight your chemistry
• Emphasis on reliable/robust chemistry
– Not so easy to gauge in traditional publications
– Platform allows users to comment/query protocol
– Share good practice (including safety information)
• Cite the syntheses in your CV (DOIs)
• Contribute quality syntheses to a growing database of
reactions
ChemSpider Synthetic Pages
ChemSpider as a resource
• Download and reuse
structures
• 2D and 3D images
• Spectra, crystal structures
• Synthetic procedures
Summary
• Aggregate, integrate and link data from across the
internet
• Over 27 million structures from ~400 data sources
• Linked to vendors, literature, online databases (Open
& Private), Open Notebook Science, patents
• Providing access to types of data that traditional
databases don’t link to: Podcasts, Blogs, Videos
Summary
• Access to chemistry information any time, anywhere
• Free – no need to register
• Data isn’t perfect (this reflects the datasources that
we cover) – but still lots of value
• Machine processing and crowdsourced curation
improves quality
• Users can share data, raise their profile, get more
value from their data
ChemSpider needs you
• What can I do in ChemSpider?
– Curate and Verify names
– Deposit data
– Add links to your publications
– Tell your colleagues
– Use the site and submit feedback
Thank you
Email: [email protected]
Twitter: ChemSpider
http://www.chemspider.com
http://cssp.chemspider.com/
ChemSpider Questions
• Can I search for reactions/synthetic transformations?
– Not currently
• Why would I use this rather than SciFinder®, ReAxys®
or similar?
–
–
–
–
ChemSpider is not a free replacement for such tools
Overlap on some areas covered by such tools
Different users will get different things out of ChemSpider
Pick the right tool for the job
• Do you have X, Y, Z data?
– All the data we have is in the record
– Look for links to relevant datasources
Common ChemSpider Questions
• There are no spectra on record X, Why?
– We don’t have a lab or spectrometers: We need users to help
make the data richer
• How can I trust the data in ChemSpider?
– It is healthy to always assess the data that you use
– Ensure that you examine the provenance
– The data in ChemSpider is constantly open to scrutiny, criticism
and revision by anyone (10’s of thousands of scientists: experts
in their fields)
– We are actively trying to improve the quality of the data all of
the time
– We have built-in mechanisms for facilitating quality assurance