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Chemistry and Web 2.0<br />Martin A. Walker<br />Dept. of Chemistry, SUNY Potsdam<br />Member of the Wikipedia Chemistry P...
Overview<br />Chemistry information in 2010<br />The “lay of the land”<br />Chemistry Web 1.0<br />Chemistry Web 2.0<br />...
CHEMISTRY: The Lay of the Land<br />
The lay of the land<br />Chemistry has long had superb information resources<br />Beilstein, Chemical Abstracts, etc<br />...
The lay of the land<br />Chemistry has long had superb information resources<br />Beilstein, Chemical Abstracts, etc<br />...
The lay of the land<br />Chemistry has long had superb information resources<br />Beilstein, Chemical Abstracts, etc<br />...
Chemistry on the Web (Version 1.0)<br />
Web 1.0<br />The Web has already transformed <br />chemical information<br />Picture by azure elixir, on Flickr.  CC licen...
Chemistry Web 1.0<br />We can read articles without leaving our desks<br />
Chemistry Web 1.0<br />We can search, find and read patents:<br />
Chemistry Web 1.0<br />Google Scholar can also help us find recent articles by Lavoisier…<br />
One of the oldest sites is still one of the best<br />
Organic Chemistry Portal<br />
Web 1.0<br />
Chemistry on the web(Version 2.0)<br />
Chemistry Web 2.0<br />Picture by Mighty Mighty Big Mac, Flickr , CC License<br />
Chemistry Web 2.0<br />Scientists already depend on their own social networks to learn, share ideas<br />The Web offers us...
Some Chemistry Web 2.0 initiatives<br />Wikipedia chemistry and other wikis<br />ChemSpider<br />NMRShiftDB<br />RSC Proje...
Wikipedia Chemicals Project<br />~60 members (~20 active)<br />Collaborated on writing quality articles and standards for:...
Wikipedia Chemicals Project<br />
Traffic can be very high….<br />
Even for specialized topics<br />
And people too!<br />
References for sodium sulfate<br />
Content validation<br />In 2008 a data validation drive was initiated for basic chemical identifiers<br />Led to a collabo...
CommonChemistry<br /><ul><li> Launched in April 2009
Came about as a result of a collaboration between CAS & Wikipedia
Offered as a free service for CAS RNs for members of the public.</li></li></ul><li>Pfizerpedia<br />Thanks to Antony Willi...
Wikis for IUPAC<br />One IUPAC workgroup recently used a wiki to reach consensus on Mass Spectrometry terms.<br />
ChemSpider<br />Started by Antony Williams, March 2007. Acquired by the Royal Society of Chemistry in May 2009.<br />Now t...
ChemSpider<br />
ChemSpider<br />
ChemSpider<br />
ChemSpider<br />The goal of ChemSpider is to build a “community of chemists”<br />Not trying to be “Facebook for chemists”...
New this week – ChemSpider Synthetic Pages!<br />
NMRShiftDB<br />
Blue Obelisk group<br />An informal international group of chemists committed to open science and open source software for...
Project Prospect<br />
Blogs<br />
Nature Island in Second Life<br />“I think that being able to walk around a molecule can add valuable new insight<br /> to...
Ionicviper.org<br />
WikiEducator<br />
Open Access<br />
Open Access<br />Web 2.0 methods depend on sharing data, to produce a network of information.  The data need to be freely ...
Open Access<br />
Open Access<br />
Open Science <br />
Open Notebook Science<br />
SOME Concerns<br />
Is it reliable?<br />Traditional peer review vs community controls<br />Current review system is flawed<br />Community con...
Peer review: How will publications be evaluated in the Web 2.0 world?<br />Traditional<br />Critical review by subject exp...
Judge the quality of the output, not the perceived quality of the process<br />
The future?<br />
The Future?<br />“Grey” questions can be answered<br />Data shared openly – a web of all information<br />Chemistry “socia...
The future?<br />
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  1. 1. Chemistry and Web 2.0<br />Martin A. Walker<br />Dept. of Chemistry, SUNY Potsdam<br />Member of the Wikipedia Chemistry Project<br />
  2. 2. Overview<br />Chemistry information in 2010<br />The “lay of the land”<br />Chemistry Web 1.0<br />Chemistry Web 2.0<br />Wikipedia<br />ChemSpider<br />Project Prospect<br />Educational resources<br />Open Access and Open Notebook Science<br />Concerns<br />The future?<br />Discussion<br />
  3. 3. CHEMISTRY: The Lay of the Land<br />
  4. 4. The lay of the land<br />Chemistry has long had superb information resources<br />Beilstein, Chemical Abstracts, etc<br />Picture by JOE M500<br />from Flickr, CC licence<br />
  5. 5. The lay of the land<br />Chemistry has long had superb information resources<br />Beilstein, Chemical Abstracts, etc<br />Traditional ties with the chemical and pharmaceutical industries have fostered a “for-profit” environment e.g., for publication<br />A chemistry book is typically $200, and many journals cost >$1 per page<br />Picture by JOE M500<br />from Flickr, CC licence<br />
  6. 6. The lay of the land<br />Chemistry has long had superb information resources<br />Beilstein, Chemical Abstracts, etc<br />Traditional ties with the chemical and pharmaceutical industries have fostered a “for-profit” environment e.g., for publication<br />A chemistry book is typically $200, and many journals cost >$1 per page<br />As a result, chemistry has been slower to adapt to “Web 2.0”<br />Picture by JOE M500<br />from Flickr, CC license<br />
  7. 7. Chemistry on the Web (Version 1.0)<br />
  8. 8. Web 1.0<br />The Web has already transformed <br />chemical information<br />Picture by azure elixir, on Flickr. CC license.<br />
  9. 9. Chemistry Web 1.0<br />We can read articles without leaving our desks<br />
  10. 10. Chemistry Web 1.0<br />We can search, find and read patents:<br />
  11. 11. Chemistry Web 1.0<br />Google Scholar can also help us find recent articles by Lavoisier…<br />
  12. 12. One of the oldest sites is still one of the best<br />
  13. 13. Organic Chemistry Portal<br />
  14. 14. Web 1.0<br />
  15. 15. Chemistry on the web(Version 2.0)<br />
  16. 16. Chemistry Web 2.0<br />Picture by Mighty Mighty Big Mac, Flickr , CC License<br />
  17. 17. Chemistry Web 2.0<br />Scientists already depend on their own social networks to learn, share ideas<br />The Web offers us the chance to share the sum of human knowledge – including the deep knowledge of specialists such as scientists.<br />Mashups can allow seamless sharing of data between sites<br />Picture courtesy of<br />Jim Hendrickson, Brandeis<br />
  18. 18. Some Chemistry Web 2.0 initiatives<br />Wikipedia chemistry and other wikis<br />ChemSpider<br />NMRShiftDB<br />RSC Project Prospect<br />Blue Obelisk, Jmol and the open source movement<br />Educational initiatives<br />
  19. 19.
  20. 20. Wikipedia Chemicals Project<br />~60 members (~20 active)<br />Collaborated on writing quality articles and standards for:<br />developing data boxes for articles<br />chemical naming, structure drawing<br />article assessment<br />Data validation<br />New collaboration with CAS<br />Wim Van Dorst, a Dutch member of WP:Chem since March 2005.<br />
  21. 21. Wikipedia Chemicals Project<br />
  22. 22. Traffic can be very high….<br />
  23. 23. Even for specialized topics<br />
  24. 24. And people too!<br />
  25. 25.
  26. 26. References for sodium sulfate<br />
  27. 27. Content validation<br />In 2008 a data validation drive was initiated for basic chemical identifiers<br />Led to a collaboration with CAS, to ensure Wikipedia CAS registry nos. are correct<br />Now around 3500 substances have been validated against CAS Common Chemistry, as having correct name, structure & CAS RN<br />Validated content indicated with a check mark<br />
  28. 28. CommonChemistry<br /><ul><li> Launched in April 2009
  29. 29. Came about as a result of a collaboration between CAS & Wikipedia
  30. 30. Offered as a free service for CAS RNs for members of the public.</li></li></ul><li>Pfizerpedia<br />Thanks to Antony Williams<br />
  31. 31. Wikis for IUPAC<br />One IUPAC workgroup recently used a wiki to reach consensus on Mass Spectrometry terms.<br />
  32. 32. ChemSpider<br />Started by Antony Williams, March 2007. Acquired by the Royal Society of Chemistry in May 2009.<br />Now the world’s largest open chemical database (over 20 million substances).<br />Open access, all content is free.<br />Brings together data from many different sources, with links out to those sources. Search for structural information, physical properties, etc..<br />Data uploads and curation by volunteers.<br />
  33. 33. ChemSpider<br />
  34. 34. ChemSpider<br />
  35. 35. ChemSpider<br />
  36. 36.
  37. 37. ChemSpider<br />The goal of ChemSpider is to build a “community of chemists”<br />Not trying to be “Facebook for chemists”, instead it offers useful chemical information, FREE.<br />Chemists can share their own data<br />
  38. 38. New this week – ChemSpider Synthetic Pages!<br />
  39. 39. NMRShiftDB<br />
  40. 40. Blue Obelisk group<br />An informal international group of chemists committed to open science and open source software for chemistry, e.g. Jmol for visualizing molecules in 3D<br />Picture courtesy of Wikipedia/NicoV, GFDL license<br />
  41. 41. Project Prospect<br />
  42. 42.
  43. 43.
  44. 44. Blogs<br />
  45. 45. Nature Island in Second Life<br />“I think that being able to walk around a molecule can add valuable new insight<br /> to thinking about and doing chemistry.” Jean-Claude Bradley, April 5, 2007.<br />
  46. 46. Ionicviper.org<br />
  47. 47. WikiEducator<br />
  48. 48. Open Access<br />
  49. 49. Open Access<br />Web 2.0 methods depend on sharing data, to produce a network of information. The data need to be freely available and accessible.<br />For information to be found (e.g., by Google), it needs to be open.<br />“3Bs” (Budapest, Bethesda, Berlin) – agreements that define OA.<br />Groups that keep data behind a subscription firewall may lose market share.<br />
  50. 50. Open Access<br />
  51. 51. Open Access<br />
  52. 52. Open Science <br />
  53. 53. Open Notebook Science<br />
  54. 54. SOME Concerns<br />
  55. 55. Is it reliable?<br />Traditional peer review vs community controls<br />Current review system is flawed<br />Community controls are highly variable<br />Look for validation<br />Confirmation may be just a click away!<br />On Wikipedia, high traffic => more reliable <br />
  56. 56. Peer review: How will publications be evaluated in the Web 2.0 world?<br />Traditional<br />Critical review by subject experts within months<br />Reviews may be cursory, or worse – “Did you even read the paper???!”<br />Review process is not very transparent<br />Hard to update<br />Valued in tenure & promotion<br />Web 2.0<br />Review often by non-experts, and the main point may be overlooked or misunderstood<br />Review may be fast – or may not occur at all?!<br />Potential for “many eyeballs”<br />Transparent, updateable<br />Not considered at all in tenure and promotion<br />Both approaches can lead to very bad – and very good - reviews<br />
  57. 57. Judge the quality of the output, not the perceived quality of the process<br />
  58. 58. The future?<br />
  59. 59. The Future?<br />“Grey” questions can be answered<br />Data shared openly – a web of all information<br />Chemistry “social networks”?<br />Free, fully open sites will thrive; closed sites may end up “closed” forever….?<br />Open sites that can get ordinary chemists to share their data will reallythrive!<br />Simple semantic searches<br />Lab results open & uploaded in real time?<br />
  60. 60. The future?<br />
  61. 61. What do you think?<br />How does this apply to my field?<br />Is open access a dead end? Who will pay for everything?<br />How will the tenure process work under the new paradigm? <br />I don’t want my rivals to steal my data and get the credit!<br />What about peer review?<br />
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