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RSC ChemSpider as an environment for teaching and sharing chemistry


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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

  1. 1. RSC|ChemSpider as an environment for teaching and sharing chemistry Antony Williams ACS Anaheim March 28 th 2011
  2. 2. A Conversational Inquiry… <ul><li>“ What would you want from an online chemistry database?” </li></ul><ul><ul><li>Nothing but the facts – give us facts and they must be right! </li></ul></ul><ul><ul><ul><li>Chemical structures, properties, spectra and other data </li></ul></ul></ul><ul><ul><li>Data to teach analysis – specifically spectral data </li></ul></ul><ul><ul><li>“ Pictures” – structure images </li></ul></ul><ul><ul><li>An environment to teach searching databases </li></ul></ul><ul><ul><li>A place to put some of our own data </li></ul></ul><ul><ul><li>A wiki for our students to contribute </li></ul></ul><ul><ul><li>Can we help with “ChemSpider”? </li></ul></ul>
  3. 3. What is ChemSpider? <ul><li>ChemSpider (and its offshoots )… </li></ul><ul><ul><li>An online database of >25 million unique chemical compounds </li></ul></ul><ul><ul><li>A repository of data, both experimental and predicted: physicochemical and analytical </li></ul></ul><ul><ul><li>A search engine for the web of chemistry </li></ul></ul><ul><ul><li>An environment to learn about searching for (and validating) data </li></ul></ul><ul><ul><li>A platform for programming against (use the resources for other purposes) </li></ul></ul><ul><ul><li>Lots more besides… </li></ul></ul>
  4. 4. Search for a Chemical…by name
  5. 5. Available Information… <ul><li>Linked to vendors, safety data, toxicity, metabolism </li></ul>
  6. 6. Available Information….
  7. 8. Spectra
  8. 9. Searching:text, structure, substructure, similar structure… (GGA)
  9. 10. “ Nothing but the Facts” <ul><li>ChemSpider has lots of data! </li></ul><ul><li>Data are harvested, deposited, curated and annotated from various sources. </li></ul><ul><li>Always be cautious of data QUALITY! </li></ul><ul><li>Data quality is good, not perfect (what is?!) </li></ul>
  10. 11. Where does ChemSpider get data? <ul><li>Data are sourced from collaborators, the community and across the internet </li></ul><ul><li>Data quality on the internet is heterogeneous </li></ul><ul><li>Data have been validated and curated by the community and ChemSpider team for >4 years </li></ul><ul><li>Jean-Claude Bradley “There are no facts, only measurements embedded within assumptions” </li></ul>
  11. 12. Chemical Information Validation JC Bradley:
  12. 13. Data to Teach Analysis - Spectra <ul><li>Over 2500 spectra. Most are “Open Data” from the community. Download and reuse in lessons </li></ul><ul><li>H1, C13, X and 2D NMR, Infrared and Raman data, Mass Spec data </li></ul><ul><li>Open Data with full web services interface. Allows for game-based curation and validation! </li></ul>
  13. 15. Spectral Game
  14. 16. Increasing Complexity
  15. 17. Spectral Game
  16. 18. Reversed Spectrum
  17. 19. True Curation of Data
  18. 20. Not Just NMR Data
  19. 21. Spectral Uploading <ul><li>Database expanded by community contributions </li></ul>
  20. 22. Multiple Spectra/One Structure
  21. 23. CSID 24528095 : H1 NMR
  22. 24. CSID 24528095 : C13 NMR
  23. 25. CSID 24528095 : HHCOSY
  24. 26. CSID 24528095 : HSQC
  25. 27. CSID 24528095 : HMBC
  26. 28. Full C13 assignment
  27. 29. Spectra for new structure <ul><li>If a NEW compound has spectral data then deposit the structure onto ChemSpider first </li></ul>
  28. 30. ChemSpider SyntheticPages <ul><li>Many syntheses are not published but are of value </li></ul><ul><li>A database of synthesis procedures built for the community, by the community. Peer-reviewed by the community </li></ul><ul><li>Each contribution has a DOI. Students can build an online reputation in a time of “micro-publications” </li></ul><ul><li>Integrates semantic mark-up, interactive experimental data (spectra), movies etc. </li></ul>
  29. 32. ChemSpider SyntheticPages
  30. 33. Supporting “Mobile Chemistry”
  31. 34. Reaction Database Look-up
  32. 35. Reaction Database Look-up
  33. 36. NEXT UP: RSC eLearning <ul><li>The Initial Vision of RSC eLearning </li></ul><ul><ul><li>From last two years of secondary school to end of undergraduate </li></ul></ul><ul><ul><li>Integrated to a small slice of ChemSpider </li></ul></ul><ul><ul><li>Introduction of more educational “games”: Chemistry quizzes – e.g reactions </li></ul></ul><ul><ul><li>Hosting training/educational resources </li></ul></ul><ul><ul><li>Integrate to existing RSC websites </li></ul></ul><ul><ul><li>An environment of participation. It’s a WIKI! </li></ul></ul>
  34. 37. RSC eLearning
  35. 38. 2DNMR Spectral Game
  36. 40. Conclusion <ul><li>ChemSpider as an educational resource </li></ul><ul><ul><li>Provides access to reference data – identifiers, structures, physicochemical data, spectra </li></ul></ul><ul><ul><li>Can teach skills in information retrieval, validation and basic cheminformatics </li></ul></ul><ul><ul><li>Is a crowdsourcing platform for curation, validation and data sharing </li></ul></ul><ul><ul><li>Is a platform for integration to other systems such as RSC eLearning, Wikipedia, Wikipathways… </li></ul></ul>
  37. 41. Acknowledgments <ul><li>RSC|ChemSpider team </li></ul><ul><li>RSC e-Learning: Martin Walker and Lorna Thomson </li></ul><ul><li>SpectralGame: Jean-Claude Bradley, Andrew Lang and Robert Lancashire and iChemLabs (ChemDoodle Components) </li></ul><ul><li>GGA Software Services LLC: Bingo and Ketcher </li></ul>
  38. 42. ChemSpider Training Session <ul><li>ChemSpider: </li></ul><ul><li>A Community Resource for Chemical Data </li></ul><ul><li>Wednesday, March 30th </li></ul><ul><li>8:30-11:00 AM </li></ul><ul><li>Anaheim Convention Center, Room 211 A </li></ul>
  39. 43. Thank you Email: Twitter: ChemConnector Personal Blog: SLIDES: