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Wikipedia and the Molecular Sciences

File:BLW.svgA talk given by Henry Rzepa, sharing his thoughts[1] about Wikipedia and its use on the occasion of the London Wikipedia Academy launch

I venture to suggest that ... the general development of the human race to be well and effectually completed when all men, in all places, without any loss of time, at a low rate of charge, are cognizant through their senses, of all that they desire to be cognizant of in all other places. ... This is the grand annihilation of time and place which we are all striving for, and which in one small part we have been permitted to see actually realised" (Samuel Butler, 1863, [2])

A brief history of Molecularpedias

  1. Chemistry is mostly about molecules. Hence it is one of the molecular sciences
    • The process was started around 1881 by Friedrich Konrad Beilstein.
    • His handbook was the (molecular) Wikipedia of his day!
    • And it introduced many modern concepts, such as the information triple: Molecule|Property|Citation
    • as well as the concept of assiduously citing your sources! No citation, no entry!!
  2. As of today, there are 58,303,485 molecules known
    • For each of which between 10 - 50 well-defined properties (sometimes more) are recorded (or calculated).
    • Augmented with virtual molecules (which could, in principle exist if people wished them to)
  3. You will see from the below, that collecting and curating information about molecules has historically been done by just a small number of (commercial) organisations:
    • CAS (closed)
    • REAXYS (closed)
    • CCDC (closed)
    • PubChem (Open!)
    • These organisations harvest data from the original sources (just like Wikipedia)
  4. Academic promotion still (in part) depends on your citations in CAS (= gold-plated standard)
  5. But, accessing citations from these sources is Expensive and only available to rich(er) organisations.

The era of Egalitarian Communities

Rzepa CIT1.jpg
  1. 1860: Our department was one of the first to use 3D models of molecules in teaching
  2. The idea in 1994 to put molecules on the Web for all.[3],[4]
  3. In 1997, Henry Rzepa decided to teach a course on how students might retrieve (chemical) information.
    • The course was presented as conventional Web pages (they are still up, as a historical document!)
    • And we got students to express what they had learnt by each writing a small project about an interesting molecule
    • In those days, students were keen to learn how to write HTML
    • But as the years went by, they started to query the usefulness of this skill!
  4. In 2001, Wikipedia was launched.
  5. From 2004, Chemists spotted that molecules map beautifully onto Wiki(pedia) pages!

The Wikipedia Chemistry Projects era

Virtuous Circle.svg
  1. Chemistry WikiProject (for general topics on chemistry)
    • Chemical concepts
    • Chemical reactions and processes
    • Chemists
  2. Chemicals WikiProject (for articles on specific chemical compounds)
    • Currently ~20 active members, who write articles
    • develop boxes
    • validate data
  3. Elements WikiProject (chemical elements).
  4. Pharmacology WikiProject (mainly drugs),
  5. Molecular and Cellular Biology WikiProject (much biochemistry)
  6. Geology WikiProject (which oversees minerals)
  7. Physics WikiProject (covering some chemical physics).
  8. The Virtuous circle
    1. WikiTrust in FireFox

Thinking (about molecules) inside the Box

Rzepa drugbox aspirin.jpg
  1. The ChemBox, the ElementBox, DrugBox (and DOI) templates.
    1. Example of a drugbox for Aspirin
    2. Example of a chembox for ethanol
    3. Example of a Infobox element for carbon
  2. Curation: ChemSpider and ChemAxon
  3. CommonChemistry, ~3500 molecules
  4. CheMoBot This bot is used to monitor changes to infoboxes in mainspace
  5. Where did I get this information from?
    1. Martin Walker[5] has written a splendid article on Wikipedia and the chemistry in it.

What happened at Imperial College ?

Rzepa jmol.jpg
  1. In 2008, the decision was taken to move from an HTML to a Wiki authoring environment @Wiki
    • A Modelling course now expresses the Molecule Project
      • and the students describe their project using (Media)Wiki markup instead of HTML.
      • this is much more to their liking!
    • The original course that spawned it all is now a Wiki!
  2. A key feature of our Wiki is the molecule renderer (Jmol).
    • Following our 3D models of molecules in 1860
    • We build them on computer
    • which means anyone can play with them
    • or look at how molecules vibrate
    • and how the electrons are distributed around them
    • and they feature extensively in blogs
  3. There is much current discussion on how to best incorporate Jmol into Wikipedia itself
    • You can see for example that I am not able to install Jmol on this Wiki!

What else molecular or chemical is happening on Wikipedia itself?

  1. Jmol: a discussion in progress on whether and how Jmol can be absorbed into Wikipedia.
  2. New formats for content: Books, Mobile devices
  3. Offline
  4. More validation
  5. Mashups
  6. Integration with lab instruments

References and citations

  1. Henry Rzepa, Podcast of talk. URL: Feed or direct liink to .m4a file
  2. Quoted in George Dyson, "Darwin amongst the Machines, The Evolution of Global Intelligence", Addison-Wesley, N.Y., 1997. ISBN 0-201-400649-7
  3. H. S. Rzepa, B. J. Whitaker and M. J. Winter, "Chemical applications of the World-Wide-Web system", J. Chem. Soc., Chem. Commun., 1994, 1907-1910. doi:10.1039/C39940001907
  4. O. Casher, G. Chandramohan, M. Hargreaves, C. Leach, P. Murray-Rust, R. Sayle, H. S. Rzepa and B. J. Whitaker, "Hyperactive Molecules and the World-Wide-Web Information System", J. Chem. Soc., Perkin Trans 2, 1995, 7-11. doi:10.1039/P29950000007
  5. M. Walker, Enhancing Learning with Online Resources, Social Networking, and Digital Libraries, Chapter 5, pp 79–92, ACS Symposium Series, 2010, Vol. 1060, ISBN13: 9780841226005, eISBN: 9780841226012. doi:10.1021/bk-2010-1060.ch005