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ChemSpider: How an online resource of chemical compounds, reaction syntheses, and property data can support green chemistry
A Pragmatic Vision <ul><ul><li>“ Build a Structure Centric Community to </li></ul></ul><ul><ul><li>Serve Chemists” </li></...
Answer Questions <ul><li>Questions a chemist might ask… </li></ul><ul><ul><li>What is the melting point of n-heptanol?  </...
Resourcing structure-based info
Resourcing structure-based info
What is Levulinic Acid?
Basic Info
Wikipedia and External Links
External Links to Data
SureChem Patent Integration
Google Patent Integration
Access to Articles <ul><li>RSC Journals </li></ul><ul><li>RSC Books </li></ul><ul><li>PubMed </li></ul><ul><li>Google Scho...
Access to Articles
Google Scholar
RSC Databases <ul><li>Direct links into six Royal Society of Chemistry databases </li></ul><ul><ul><li>Mass Spectrometry B...
Experimental and Predicted Properties
Experimental and Predicted Properties
Experimental and Predicted Properties
Data Slices <ul><li>Data Segregation tags will shortly be introduced so that chemicals can be segregated: </li></ul><ul><u...
Reactions on the Internet <ul><li>ChemSpider intends to be a high-quality source of structure-based information </li></ul>...
Reactions on the Internet <ul><li>ChemSpider intends to be a high-quality source of structure-based information </li></ul>...
 
Org Prep Daily  (Blog)
ChemSpider SyntheticPages
ChemSpider SyntheticPages
Submission process <ul><li>Register as a user </li></ul><ul><li>Use the Submit button and fill in the fields… </li></ul>
Submission Process <ul><li>Submissions reviewed by editorial board </li></ul><ul><li>Published as is or comments sent to a...
Entity-Extraction, Mark-up, Annotate
Semantic Markup: Project Prospect
Success Depends on Dictionaries Link to a Structure or the Right Structure?
Name-Structure Pairs
Semantic Linking of Structures <ul><li>What would you want to link off a structure? </li></ul><ul><ul><li>Chemical supplie...
Can I Submit My Reactions? <ul><li>Most chemistry is  UN published and all attempted reactions can be valid additions - “J...
Editorial Team  <ul><li>Peter Scott, Kevin Booker-Milburn, Steve Caddick (original team) and Martin Walker and Jean-Claude...
ChemSpider for Green Chemistry <ul><li>ChemSpider is presently building “sliced environments” </li></ul><ul><ul><li>“ Chem...
ChemSpider Green Chemistry <ul><li>Green chemistry  is a data slice and a subset of functionality initially.  </li></ul><u...
Chemistry on the Internet FUTURE <ul><li>The semantic web for chemistry is in place </li></ul><ul><li>Crowdsourced contrib...
ChemSpider demos and training <ul><li>ChemSpider demos at booth 301: Royal Society of Chemistry </li></ul><ul><li>Hands-on...
Thank you [email_address] Twitter: ChemSpiderman www.chemspider.com/blog SLIDES: www.slideshare.net/AntonyWilliams
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How An Online Resource Of Chemical Compounds Reaction Syntheses And Property Data Can Support Green Chemistry

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ChemSpider is an online database containing in excess of 20 million chemical compounds and associated experimental and predicted physicochemical data, reaction synthesis details and analytical data. A significant amount of the data contained within the database has been harvested and collated from a number of inventory systems and integrated to provide a centralized resource for the community. The ChemSpider database has the added benefit of being available for community deposition, annotation and curation. As a result it offers the potential for researchers to share their latest research with the public and participate in the creation of a rich resource of chemistry related information for the Green Chemistry community. This presentation will provide an overview of present capabilities and discuss the future vision for the platform.

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Transcript of "How An Online Resource Of Chemical Compounds Reaction Syntheses And Property Data Can Support Green Chemistry"

  1. 1. ChemSpider: How an online resource of chemical compounds, reaction syntheses, and property data can support green chemistry
  2. 2. A Pragmatic Vision <ul><ul><li>“ Build a Structure Centric Community to </li></ul></ul><ul><ul><li>Serve Chemists” </li></ul></ul><ul><ul><li>Integrate chemical structure data on the web </li></ul></ul><ul><ul><li>Create a “structure-based hub” to information and data </li></ul></ul><ul><ul><li>Provide access to structure-based “algorithms” </li></ul></ul><ul><ul><li>Let chemists contribute their own data </li></ul></ul><ul><ul><li>Allow the community to curate/correct data </li></ul></ul>
  3. 3. Answer Questions <ul><li>Questions a chemist might ask… </li></ul><ul><ul><li>What is the melting point of n-heptanol? </li></ul></ul><ul><ul><li>What is the chemical structure of Xanax? </li></ul></ul><ul><ul><li>Chemically, what is phenolphthalein? </li></ul></ul><ul><ul><li>What are the stereocenters of cholesterol? </li></ul></ul><ul><ul><li>Where can I find publications about xylene? </li></ul></ul><ul><ul><li>What are the different trade names for Ketoconazole? </li></ul></ul><ul><ul><li>What is the NMR spectrum of Aspirin? </li></ul></ul><ul><ul><li>What are the safety handling issues for Thymol Blue? </li></ul></ul>
  4. 4. Resourcing structure-based info
  5. 5. Resourcing structure-based info
  6. 6. What is Levulinic Acid?
  7. 7. Basic Info
  8. 8. Wikipedia and External Links
  9. 9. External Links to Data
  10. 10. SureChem Patent Integration
  11. 11. Google Patent Integration
  12. 12. Access to Articles <ul><li>RSC Journals </li></ul><ul><li>RSC Books </li></ul><ul><li>PubMed </li></ul><ul><li>Google Scholar </li></ul><ul><li>Google Books </li></ul><ul><li>Microsoft Academic Search </li></ul>
  13. 13. Access to Articles
  14. 14. Google Scholar
  15. 15. RSC Databases <ul><li>Direct links into six Royal Society of Chemistry databases </li></ul><ul><ul><li>Mass Spectrometry Bulletin </li></ul></ul><ul><ul><li>Laboratory Hazards Bulletin </li></ul></ul><ul><ul><li>Methods in Organic Synthesis </li></ul></ul><ul><ul><li>Catalysts and Catalyzed Reactions </li></ul></ul><ul><ul><li>Natural Product Updates </li></ul></ul><ul><ul><li>Analytical Abstracts </li></ul></ul>
  16. 16. Experimental and Predicted Properties
  17. 17. Experimental and Predicted Properties
  18. 18. Experimental and Predicted Properties
  19. 19. Data Slices <ul><li>Data Segregation tags will shortly be introduced so that chemicals can be segregated: </li></ul><ul><ul><li>Elements </li></ul></ul><ul><ul><li>Natural Products </li></ul></ul><ul><ul><li>Antibiotics </li></ul></ul><ul><ul><li>Drugs </li></ul></ul><ul><ul><li>Catalysts </li></ul></ul><ul><ul><li>Green chemicals </li></ul></ul><ul><ul><li>Not an ontology but an effective segregation </li></ul></ul>
  20. 20. Reactions on the Internet <ul><li>ChemSpider intends to be a high-quality source of structure-based information </li></ul><ul><li>What of reactions? </li></ul>
  21. 21. Reactions on the Internet <ul><li>ChemSpider intends to be a high-quality source of structure-based information </li></ul><ul><li>What of reactions? </li></ul><ul><li>Reactions on the Internet today include </li></ul><ul><ul><li>Focused websites: e.g : OrgSyn, OrgChem portal </li></ul></ul><ul><ul><li>Wikipedia </li></ul></ul><ul><ul><li>Blogs </li></ul></ul><ul><ul><li>Web-based access to commercial DBs </li></ul></ul>
  22. 23. Org Prep Daily (Blog)
  23. 24. ChemSpider SyntheticPages
  24. 25. ChemSpider SyntheticPages
  25. 26. Submission process <ul><li>Register as a user </li></ul><ul><li>Use the Submit button and fill in the fields… </li></ul>
  26. 27. Submission Process <ul><li>Submissions reviewed by editorial board </li></ul><ul><li>Published as is or comments sent to author </li></ul><ul><li>Online Peer Review process </li></ul><ul><li>Data supported include web movies, images, live spectra etc. </li></ul>
  27. 28. Entity-Extraction, Mark-up, Annotate
  28. 29. Semantic Markup: Project Prospect
  29. 30. Success Depends on Dictionaries Link to a Structure or the Right Structure?
  30. 31. Name-Structure Pairs
  31. 32. Semantic Linking of Structures <ul><li>What would you want to link off a structure? </li></ul><ul><ul><li>Chemical suppliers </li></ul></ul><ul><ul><li>Other publications </li></ul></ul><ul><ul><li>Analytical Data </li></ul></ul><ul><ul><li>Related Reactions </li></ul></ul><ul><ul><li>Wikipedia </li></ul></ul><ul><ul><li>Patents </li></ul></ul><ul><ul><li>“ Everything” </li></ul></ul>
  32. 33. Can I Submit My Reactions? <ul><li>Most chemistry is UN published and all attempted reactions can be valid additions - “Journal of Attempted Reactions” </li></ul><ul><li>Commercial databases host abstracted reactions </li></ul><ul><li>Are published reactions copyrighted? RSC does not consider a simple reaction as copyrighted and adding to CSP is not infringement. </li></ul><ul><li>The depositor is responsible for </li></ul>
  33. 34. Editorial Team <ul><li>Peter Scott, Kevin Booker-Milburn, Steve Caddick (original team) and Martin Walker and Jean-Claude Bradley – five synthetic organic chemists </li></ul><ul><li>Presently accepting submissions </li></ul><ul><li>Segregation/tagging for various subsets of chemistry under design. “Green Chemistry” reactions makes sense </li></ul>
  34. 35. ChemSpider for Green Chemistry <ul><li>ChemSpider is presently building “sliced environments” </li></ul><ul><ul><li>“ ChemSpider Elements” </li></ul></ul><ul><ul><li>“ ChemSpider Education” </li></ul></ul><ul><ul><li>“ ChemSpider Environmental Science” </li></ul></ul><ul><li>Green chemistry is a data slice and a subset of functionality initially. </li></ul><ul><ul><li>Needs the community to identify/tag chemicals of interest </li></ul></ul><ul><ul><li>Needs the community to help define functionality </li></ul></ul>
  35. 36. ChemSpider Green Chemistry <ul><li>Green chemistry is a data slice and a subset of functionality initially. </li></ul><ul><ul><li>Needs the community to identify/tag chemicals of interest </li></ul></ul><ul><ul><li>Needs the community to help define functionality </li></ul></ul><ul><li>Compound tagging will be exposed shortly. A simple user interface for tagging/segregating </li></ul><ul><li>Anybody interested in helping to set the vision for ChemSpider Green Chemistry? </li></ul>
  36. 37. Chemistry on the Internet FUTURE <ul><li>The semantic web for chemistry is in place </li></ul><ul><li>Crowdsourced contributions are commonplace </li></ul><ul><li>Chemists will search by structure/substructure </li></ul><ul><li>Chemistry articles indexed and searchable </li></ul><ul><li>Reduced number of searches to find data </li></ul><ul><li>Data are integrated – compounds, vendors, syntheses, data, publications and patents </li></ul><ul><li>A world of Open Access and Open Data </li></ul>
  37. 38. ChemSpider demos and training <ul><li>ChemSpider demos at booth 301: Royal Society of Chemistry </li></ul><ul><li>Hands-on ChemSpider Training </li></ul><ul><li>Room:  110  </li></ul><ul><li>Location:   Moscone Center </li></ul><ul><li>Date:   Monday 22 nd March   </li></ul><ul><li>Time:   4:00 PM - 6:00 PM </li></ul>
  38. 39. Thank you [email_address] Twitter: ChemSpiderman www.chemspider.com/blog SLIDES: www.slideshare.net/AntonyWilliams
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