Thursday, March 29, 2012

PLoS comp biol goes Wikipedia

Wikipedia  has become a primary resource of information for many students when looking up basic information. However there is an interesting gap between the scientific community and the people who are regularly contributing to wikipedia articles. There are only few prominent scientists who are regulars, such as the Pfam authors who recently integrated wikipedia into the Xfam series of databases. Another major science related project on wikipedia with about ten thousand articles describing various genes is GeneWiki, lead by Andrew Su. A possible reason for this difference in communities might be the lack of acceptance as academic publishing for wikipedia articles. As of today PLoS comp biol tries to resolve this disparity by publishing a new type of manuscripts, Topic Pages.

Topic Pages are designed to provide review style articles. These articles serve as a copy of reference, that can be cited and will show up in Pubmed. It will also be released at wikipedia where a living copy of the document can be edited and updated by the wider public. This is done in collaboration with the wikiproject computational biology.

How does this work? In short, an article is first submitted to PLoS where it is peer reviewed and upon acceptance it will be published by PLoS comp biol as well as uploaded to wikipedia. While this sounds rather straightforward, one of the issues with this approach is around licensing.

PLoS is publishing all articles under a very liberal license, the Creative Commons Attribution License.  This means, you can do with the article what you want, even change the license, as long as you credit the original sources. This license is in fact more liberal than the wikipedia license, which is Creative Commons Attribution Share Alike. This means we can take a PLoS comp biol article and publish it on wikipedia, as long as we cite the original source of the text, but we can not do this in the opposite direction.

In order to avoid any licensing conflicts, Spencer Bliven set up a custom Mediawiki instance with the liberal PLoS style license. It can be found at  By drafting the manuscript there we are able to transfer the content easily over to both PLoS and wikipedia, once it has passed the PLoS review process. Besides this, also the review process is transparent and you can see what the referees commented on our article at the talk page of the article (both at wikipedia and the topicpages sites)

Our  latest paper is the first such Topic Page. It provides a review on Circular Permutations in proteins, a type of relationship in proteins, whereby the proteins have a changed order of amino acids in their protein sequence while their 3D shape remains very similar.

For more information read the full article at plos ( doi:10.1371/journal.pcbi.1002445 ) or take a look at the latest version of this at wikipedia. Also read the PLoS comp biol editorial, announcing the Topic Pages