Forward to wikipedia – topic pages in computational biology

By Grant Jacobs 04/04/2012

The PLoS (Public Library of Science) journal Computational Biology has offered it’s first Topic Page, Circular permutations in proteins,* along with a short editorial introducing the Topic Page concept.

Basically, authors write a wikipedia-style review of a topic that is reviewed and accepted by the journal, then forwarded to wikipedia to become a ‘living’ version of the Topic Page. Initial versions are developed on the PLoS Computational Biology Topic Page wiki site.**

There has been on-going commentary that some types of work is not easily recognised under the current journal publication formats and hence not rewarded as academic credit – part of the aim is to allow work on wikipedia topics to be created as publications, cited via DOIs, included in CVs, publication lists, etc., by having them first presented as submissions to PLoS Computational Biology.

So, opinions? (Feel free to share your own in the comments below.)

PLoS Computational Biology explicitly wish to target topics not covered well in wikipedia. A potential catch might be if credit is only given for the initial Topic Page and later work is not credited. It’s certainly better than no credit at all, but it strikes me that the quality of pages on wikipedia might eventually deteriorate as there will less incentive to update these ‘living’ counterparts to the Topic Pages. I suppose at some point major updates could be accepted as ‘replacement’ Topic Pages to those already existing, although this would not seem possible under current policy as they only target content poorly covered in wikipedia.

Perhaps this might lead to an initial lolly scramble of researchers covering topics, followed by a lull as areas get filled? It looks as interesting short- to medium-term endeavour, but it’s less clear to me how this will work in the longer term and in an on-going fashion.

They are calling for topic ideas, but I don’t–yet–see a page listing ideas that have been offered.

A different, but related effort, might be to develop topic pages covering the topics set in nascent efforts to develop a bioinformatics teaching curriculum.


* I recall encountering these as a student learning about proteins from my own reading. They’re interesting things – related proteins where the sequence, or the order of the domains, have been shuffled, but as a circular permutation. Think of counting in modulo fashion, like the hours on a clock. Domains A, B, C, D circularly permuted by ‘one forward’ might become B, C, D, A. These circularly permuted proteins may retain the same overall fold (three-dimensional architecture).

** The first author of the initial Topic Page is the coordinator of the Topic Page wiki.

Other articles on Code for life:

Teaching bioinformatics at high school

Online lecture series on genomics and bioinformatics

The world in DNA sequencers

The software developer’s generalisation dilemma

0 Responses to “Forward to wikipedia – topic pages in computational biology”

  • I think this is a very interesting effort. PLoS CB take our earlier efforts with RNA Biology to merge the Wiki & publishing formats to an entirely new level.

    I generally avoid reading review articles if I can. I’ve been burned a few times where the reviews will gloss over important details that are covered well in the primary literature. Review articles can also date VERY quickly. I’m certain these PLoS CB/WP articles wont entirely solve these issues, however, the fact that these are just summaries of the knowledge to date will be much more explicit (especially for gullible people like me). They shouldn’t date too rapidly either (hopefully).

    The one issue I do have is thinking of good topics to write about. This is probably a total failure of imagination on my part. It might be fun to start a public brainstorm on WP (maybe on the MCB/Comp. Bio. wikiproject talk pages) of good subjects for expansion.