Thursday, July 24, 2008

WikiPathways

Find a website with a correct citric acid cycle and win $1,000,000 or equivalent!NatureNews has an article on the growth of biological Wikis as a way of involving the molecular biology community in annotating genes, proteins, etc. [Molecular biology gets wikified]. I strongly support the work of Huss et al. (2008) as I described in a previous posting [A Gene Wiki].

Now Pico et al. (2008) have tried to do for metabolic pathways what Huss et al. did for genes. Unfortunately, WikiPathways isn't going to be successful for a number of reasons.

The idea is to create a Wiki for various pathways and allow the biological community to update and comment on the various entries. However, whereas Gene Wiki did the right thing by adding the human genes to Wikipedia, WikiPathways creates its own separate database. This makes it much less accessible since not only do you have to make an effort to find the Wiki, you also have to create an account to make changes.


That's not the only problem. Let's look at a familiar metabolic pathway on WikiPathways, the citric acid cycle. Right away you can see that there are no visible chemical reactions. Instead, you just see a pathway created by lines between boxes with the names of molecules. You don't even see that CO2 and reducing equivalents are produced by this pathway! That's not going to be very useful.

Contrast the WikiPathways entry with the existing entry on Wikipedia [citric acdi cycle]. The Wikipedia entry is much more useful and, as it turns out, reasonably accurate. I'd be tempted to correct the Wikipedia entry but I'm not interested in doing all the work required to make the WikiPathways entry useful.

Speaking of corrections, when I teach my biochemistry course in the winter I challenge my students to find a single website that shows the citric acid cycle correctly. By that I mean a website where every single reaction is correctly balanced and all reactants and products are shown. The Wikipedia reactions are not correct and the sum of all reactions is incorrect, although in this case the only errors are in balancing the number of hydrogen atoms. Can anyone find the mistakes? Can anyone find a website that's correct? (You can't count any website that shows a figure from my textbook and you can't count the IUBMB website (e.g., citrate synthase). (The most serious error is in getting the products of the succinate dehydrogenase reaction wrong.)

The prize for finding a correct website is seeing your name in print on Sandwalk or $1,000,000 (one million dollars), whichever I think is the most valuable.


Huss III, J.W., Orozco, C., Goodale, J., Wu, C., Batalov, S., Vickers, T.J., Valafar, F., and Su, A.I. (2008) A Gene Wiki for Community Annotation of Gene Function. PLoS Biol 6(7): e175 [doi:10.1371/journal.pbio.0060175]

Pico, A.R., Kelder, T., van Iersel, M.P., Hanspers, K., Conklin, B.R., and Evelo, C. (2008) WikiPathways: Pathway Editing for the People. PLoS Biology, 6(7), e184. [DOI: 10.1371/journal.pbio.0060184]

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