How community crowdsourcing and social networking is helping to build a quality online resource for chemists
A Pragmatic Vision <ul><ul><li>“ Build a Structure Centric Community to </li></ul></ul><ul><ul><li>Serve Chemists” </li></...
www.chemspider.com
We’re Out to Answer Questions <ul><li>Questions a chemist might ask… </li></ul><ul><ul><li>What is the melting point of n-...
Search for a Chemical…by name
Available Information… <ul><li>Linked to vendors, safety data, toxicity, metabolism </li></ul>
Available Information….
Search for a chemical…by structure Substructure search coming…
Crowdsourcing – Wikipedia definition <ul><li>“ Crowdsourcing is a distributed problem-solving and production model.  </li>...
Annotating, Cleaning and Growing... <ul><li>Almost 25 million chemicals from 400 diverse data sources </li></ul><ul><li>“ ...
ChemSpider Searching <ul><li>Most chemists perform text-based searches first </li></ul><ul><li>To get the correct structur...
Search “Vitamin H”
Search “Vitamin H”
“ Curate” Identifiers
“ Curate” Identifiers
“ Curate” Identifiers
“ Curate” Identifiers <ul><li>General curation activities </li></ul><ul><ul><li>Remove incorrect names </li></ul></ul><ul>...
Crowdsourced “Annotations” <ul><li>Registered Users can add  </li></ul><ul><ul><li>Descriptions/Syntheses/Commentaries </l...
 
Spectra Linked
Spectra Linked
Web Services
www.SpectralGame.com http://www.jcheminf.com/content/1/1/9
Spectral Game
Increasing Complexity
Reactions and ChemSpider <ul><li>ChemSpider intends to be a high-quality source of structure-based information </li></ul><...
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...
Community crowdsourcing and social networking <ul><li>Community crowdsourcing and social networking  is  helping to build ...
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 Community Crowdsourcing and Social Networking is Helping to Build a Quality Online Resource for Chemists

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With an intention to provide a free internet resource of chemistry related data for the community, ChemSpider provides an online database of chemical compounds, reaction syntheses and related data. Members of the community can contribute to the database via the deposition of chemical structures, synthesis procedures and analytical data. Data are also aggregated from many other depositors, at present over 400 data sources. The aggregation of data associated with over 25 million chemical compounds does not come without data quality issues. By engaging the community to curate the data the quality continues to improve on a daily basis. The presentation will provide an overview of our ongoing efforts to expand and curate the database. Using a combination of game-based and recognition systems as well as our dependence on societal giveaway by the community ChemSpider continues its path to become a high quality resource and foundation for the semantic web for chemistry.

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How Community Crowdsourcing and Social Networking is Helping to Build a Quality Online Resource for Chemists

  1. 1. How community crowdsourcing and social networking is helping to build a quality online resource for chemists
  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. www.chemspider.com
  4. 4. We’re Out to 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>
  5. 5. Search for a Chemical…by name
  6. 6. Available Information… <ul><li>Linked to vendors, safety data, toxicity, metabolism </li></ul>
  7. 7. Available Information….
  8. 8. Search for a chemical…by structure Substructure search coming…
  9. 9. Crowdsourcing – Wikipedia definition <ul><li>“ Crowdsourcing is a distributed problem-solving and production model. </li></ul><ul><li>Problems are broadcast to an unknown group of solvers in the form of an open call for solutions. Users—also known as the crowd—typically form into online communities, and the crowd submits solutions. </li></ul><ul><li>The crowd also sorts through the solutions, finding the best ones.” </li></ul>
  10. 10. Annotating, Cleaning and Growing... <ul><li>Almost 25 million chemicals from 400 diverse data sources </li></ul><ul><li>“ Diverse” data sources… </li></ul><ul><ul><li>High Quality through questionable to wrong </li></ul></ul><ul><ul><li>Rich content of Wikipedia links, YouTube videos and photographs to “Stub Records” containing “just a structure” </li></ul></ul><ul><ul><li>All records can be further enhanced…25 million compounds need annotation by the masses </li></ul></ul>
  11. 11. ChemSpider Searching <ul><li>Most chemists perform text-based searches first </li></ul><ul><li>To get the correct structure from a text-based search the name-structure association needs to be “correct” – should Viagra return sildenafil or sildenafil citrate? </li></ul>
  12. 12. Search “Vitamin H”
  13. 13. Search “Vitamin H”
  14. 14. “ Curate” Identifiers
  15. 15. “ Curate” Identifiers
  16. 16. “ Curate” Identifiers
  17. 17. “ Curate” Identifiers <ul><li>General curation activities </li></ul><ul><ul><li>Remove incorrect names </li></ul></ul><ul><ul><li>Correct spellings </li></ul></ul><ul><ul><li>Remove names with/without stereo compared to the structure </li></ul></ul><ul><ul><li>Correct registry numbers and other numeric identifiers (Beilstein, EINECS etc) </li></ul></ul><ul><ul><li>Add multilingual names </li></ul></ul><ul><ul><li>Add alternative names </li></ul></ul>
  18. 18. Crowdsourced “Annotations” <ul><li>Registered Users can add </li></ul><ul><ul><li>Descriptions/Syntheses/Commentaries </li></ul></ul><ul><ul><li>Links to PubMed articles </li></ul></ul><ul><ul><li>Links to articles via DOIs </li></ul></ul><ul><ul><li>Add spectral data </li></ul></ul><ul><ul><li>Add Crystallographic Information Files </li></ul></ul><ul><ul><li>Add photos </li></ul></ul><ul><ul><li>Add MP3 files </li></ul></ul><ul><ul><li>Add Videos </li></ul></ul>
  19. 20. Spectra Linked
  20. 21. Spectra Linked
  21. 22. Web Services
  22. 23. www.SpectralGame.com http://www.jcheminf.com/content/1/1/9
  23. 24. Spectral Game
  24. 25. Increasing Complexity
  25. 26. Reactions and ChemSpider <ul><li>ChemSpider intends to be a high-quality source of structure-based information </li></ul><ul><li>What about chemical reactions? </li></ul>
  26. 27. ChemSpider SyntheticPages
  27. 28. ChemSpider SyntheticPages
  28. 29. Submission process <ul><li>Register as a user </li></ul><ul><li>Use the Submit button and fill in the fields… </li></ul>
  29. 30. 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>
  30. 31. Community crowdsourcing and social networking <ul><li>Community crowdsourcing and social networking is helping to build a quality online resource for chemists </li></ul><ul><ul><li>Community provides and/or deposits data </li></ul></ul><ul><ul><li>Community curation, feedback, annotation </li></ul></ul><ul><ul><li>Social networking tools keep the community engaged and connected – the latest web design was voted for on a blog </li></ul></ul><ul><ul><li>The path is working and we will continue to optimize </li></ul></ul>
  31. 32. 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:   Room 102B </li></ul><ul><li>Location:   Boston Convention Center </li></ul><ul><li>Date:   Tuesday 24 th August   </li></ul><ul><li>Time:   3:30-6pm </li></ul>
  32. 33. Thank you [email_address] Twitter: ChemSpiderman www.chemspider.com/blog SLIDES: www.slideshare.net/AntonyWilliams

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