RSC ChemSpider as an environment for teaching and sharing chemistry

RSC|ChemSpider as an environment for teaching and sharing chemistry Antony Williams ACS Anaheim March 28 th 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 Validation JC 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

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

2DNMR Spectral Game

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: ChemConnector Personal Blog: www.chemconnector.com SLIDES: www.slideshare.net/AntonyWilliams

http://www.chemconnector.com	24
http://www.chemspider.com	6
url_unknown	3
http://paper.li	1

RSC ChemSpider as an environment for teaching and sharing chemistry

by Antony Williams, ChemConnector on Mar 29, 2011

Accessibility

Categories

Tags

Upload Details

Usage Rights

4 Embeds 34

Statistics

RSC ChemSpider as an environment for teaching and sharing chemistry — Presentation Transcript