Chemistryand web2 ma walker 2 5 10

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