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ChemSpider is an online database of almost 25 million chemical compounds linked out to over 400 different internet resources. Together with its partner site, ChemSpider SyntheticPages, a crowdsourced database of reaction syntheses, these two resources provide an environment where chemists can deposit, share, source and use the data as the basis of lesson plans, games and developing deeper understanding in chemistry. This presentation will provide an overview of how ChemSpider is fast becoming the central online portal for sourcing chemistry data, how the ability for students to engage in the hosting of their own data and the curation and annotation of already existing data can engage students in a social networking environment. These efforts can become the basis of training students in spectroscopy, online data validation and the provision of supporting information for their own experiments.
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RSC|ChemSpider as an environment for teaching and sharing chemistry
Antony WilliamsACS Anaheim March 28th 2011
A Conversational Inquiry…
“What would you want from an online chemistry database?” Nothing but the facts – give us facts and they must
be right! Chemical structures, properties, spectra and other data
Data to teach analysis – specifically spectral data “Pictures” – structure images An environment to teach searching databases A place to put some of our own data A wiki for our students to contribute Can we help with “ChemSpider”?
What is ChemSpider?
ChemSpider (and its offshoots)… An online database of >25 million unique
chemical compounds A repository of data, both experimental and
predicted: physicochemical and analytical A search engine for the web of chemistry An environment to learn about searching for
(and validating) data A platform for programming against (use the
resources for other purposes) Lots more besides…
Search for a Chemical…by name
Available Information…
Linked to vendors, safety data, toxicity, metabolism
Available Information….
Spectra
Searching:text, structure, substructure, similar structure… (GGA)
“Nothing but the Facts”
ChemSpider has lots of data!
Data are harvested, deposited, curated and annotated from various sources.
Always be cautious of data QUALITY!
Data quality is good, not perfect (what is?!)
Where does ChemSpider get data?
Data are sourced from collaborators, the community and across the internet
Data quality on the internet is heterogeneous
Data have been validated and curated by the community and ChemSpider team for >4 years
Jean-Claude Bradley “There are no facts, only measurements embedded within assumptions”
Chemical Information ValidationJC Bradley: http://tinyurl.com/5voxkyb
Data to Teach Analysis - Spectra
Over 2500 spectra. Most are “Open Data” from the community. Download and reuse in lessons
H1, C13, X and 2D NMR, Infrared and Raman data, Mass Spec data
Open Data with full web services interface. Allows for game-based curation and validation!
Spectral Game
Increasing Complexity
Spectral Game
Reversed Spectrum
True Curation of Data
Not Just NMR Data
Spectral Uploading
Database expanded by community contributions
Multiple Spectra/One Structure
CSID 24528095 : H1 NMR
CSID 24528095 : C13 NMR
CSID 24528095 : HHCOSY
CSID 24528095 : HSQC
CSID 24528095 : HMBC
Full C13 assignment
Spectra for new structure
If a NEW compound has spectral data then deposit the structure onto ChemSpider first
ChemSpider SyntheticPages
Many syntheses are not published but are of value
A database of synthesis procedures built for the community, by the community. Peer-reviewed by the community
Each contribution has a DOI. Students can build an online reputation in a time of “micro-publications”
Integrates semantic mark-up, interactive experimental data (spectra), movies etc.
ChemSpider SyntheticPages
Supporting “Mobile Chemistry”
Reaction Database Look-up
Reaction Database Look-up
NEXT UP: RSC eLearning The Initial Vision of RSC eLearning
From last two years of secondary school to end of undergraduate
Integrated to a small slice of ChemSpider Introduction of more educational “games”:
Chemistry quizzes – e.g reactions Hosting training/educational resources Integrate to existing RSC websites An environment of participation. It’s a WIKI!
RSC eLearning
Conclusion
ChemSpider as an educational resource Provides access to reference data – identifiers,
structures, physicochemical data, spectra Can teach skills in information retrieval, validation
and basic cheminformatics Is a crowdsourcing platform for curation,
validation and data sharing Is a platform for integration to other systems such
as RSC eLearning, Wikipedia, Wikipathways…
Acknowledgments
RSC|ChemSpider team
RSC e-Learning: Martin Walker and Lorna Thomson
SpectralGame: Jean-Claude Bradley, Andrew Lang and Robert Lancashire and iChemLabs (ChemDoodle Components)
GGA Software Services LLC: Bingo and Ketcher
ChemSpider Training Session
ChemSpider: A Community Resource for Chemical Data
Wednesday, March 30th
8:30-11:00 AM
Anaheim Convention Center, Room 211 A
Thank you
Email: williamsa@rsc.org Twitter: ChemConnectorPersonal Blog: www.chemconnector.comSLIDES: www.slideshare.net/AntonyWilliams
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