PLoS Computational Biology goes wiki

Today saw an important step forward towards a wikification of scholarly workflows: PLoS Computational Biology published an article that did not only follow the journal’s own author guidelines but also those for writing articles on the English Wikipedia, where a copy of the journal article has been pasted into [[Circular Permutation in Proteins]], where it shall live on in the hands of the wiki community.



The article is the first in a new manuscript track – Topic pages – that adds a dynamic component to articles published in the journal, as explained in the accompanying editorial:

This month, we have published our first Topic Page on “Circular Permutations in Proteins” by Spencer Bliven and Andreas Prlić [6] as part of our Education section. Topic Pages are the version of record of a page to be posted to (the English version of) Wikipedia. In other words, PLoS Computational Biology publishes a version that is static, includes author attributions, and is indexed in PubMed. In addition, we intend to make the reviews and reviewer identities of Topic Pages available to our readership. Our hope is that the Wikipedia pages subsequently become living documents that will be updated and enhanced by the Wikipedia community, assuming they are in keeping with Wikipedia’s guidelines and policies, either by individuals, or, perhaps as is already happening in medicine and molecular and cell biology, by something more organized, or with a more formal review structure. We also hope this will lead to improved scholarship in a changing medium of learning, in this case made possible by the Creative Commons Attribution License that we use.


The editorial also discusses the issue of reward for scholars to contribute to endeavours like Wikipedia, for which Topic Pages provide a novel mechanism.

Like the quoted section, the paper contains direct links to Wikipedia pages for background, which dramatically reduces the need to rehash what is already known, while still allowing for a minimum of context.

The reviews that have been produced as a result of the journal’s peer review process have since been posted to the talk page of the Wikipedia entry, along with some further procedural explanations.

Through this manuscript track, PLoS Computational Biology joins the so far very small circle of journals that have experimented with dynamic features (which, by the way, form a core aspect of the Criteria for the journal of the future). Most closely related is the effort at RNA Biology (interestingly, not an Open Access journal), where a dedicated manuscript track established in 2008 requires that a manuscript on a new family of RNA be accompanied by the draft for a corresponding entry on the English Wikipedia. This effort is part of the Rfam project whose scope now includes over 900 articles on the English Wikipedia that are integrated with Rfam, a database dedicated to RNA families. Ideas for a similar project have been put forward in relation to the journal Gene and the Gene Wiki project.

Much older efforts to render publications more dynamic are the Living Reviews series of physics-related journals (established in 1998) and Scholarpedia (2005), which is implemented on a highly customized version of MediaWiki, the same software that Wikipedias run on. Both platforms, however, employ licensing schemes that are incompatible with reuse on Wikipedias.

While the workflow for Topic Pages is a bit convoluted (as described by Andreas Prlić), automated journal-to-wiki export has been routine practice for about a year now with several Pensoft journals. In both cases, the workflows involve dedicated wikis, for reasons that have to do with licensing (Wikipedias are more restrictively licensed than Open-Access journals) or with policies (taxonomic treatments are considered original research and thus not allowed on Wikipedias).

It can thus be expected that the workflows for Topic Pages at PLoS Computational Biology will be streamlined. Of note, other journals are invited to take advantage of that by using the dedicated Topic Pages wiki for preparing articles in their wiki track. In addition to that, Wikimedia Germany has approved funds to help journals integrate their workflows with those of Wikimedia projects. The support will be limited to the first journal per integration step, but any resulting software will be made openly available for reuse, so that other journals can build on these efforts. The funds can also be used to cover up to 50% of author-side publication fees for the first paper in such wiki tracks in up to five journals.

More general support on matters of Open Access on Wikimedia projects is also available via WikiProject Open Access.

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17 Responses to PLoS Computational Biology goes wiki

  1. Gaurav says:

    This is ridiculously cool, Daniel! I had never thought of the possibility of journals changing to be more like Wikipedia as a way of improving content transfers between them. Thanks for sharing this, and for your work in making this happen!

    In both cases, the workflows involve dedicated wikis, for reasons that have to do with licensing (Wikipedias are more restrictively licensed than Open-Access journals)

    That’s interesting! Is that because Wikipedia content is ShareAlike? What about dual-licensing individually licensing some content: say, a PDF under CC-BY and CC-BY-SA on the Wikimedia Commons or on Wikisource? Or am I misunderstanding how the licensing is more restrictive?

    or with policies (taxonomic treatments are considered original research and thus not allowed on Wikipedias).

    Taxonomic treatments might be problematic on Wikipedia, but they’re probably fine on Wikisource as long as they’re CC-BY-SA or better. In fact, unpublished open-access taxonomic treatments should now be allowed on Wikisource, as long as the writer meets Wikipedia’s Notability criteria.

    • Ad 1: Yes, the Share-Alike clause in use at Wikimedia causes the problems here. Dual-licensing is only a theoretical solution, since (then it is unlikely to be site-wide soon, and there will thus always remain some (then rather confusing) statements (e.g. in edit mode) that only shows the default license.

      Ad 2: Treatments would make sense on Wikispecies rather than Wikisource, and it is on my radar, but I have yet to see any treatments there.

      • Gaurav says:

        Thanks for your reply! I mentioned Wikisource because there are already some treatments there (and the possibility of getting more content there, from providers like Pensoft and the BHL). I’m really excited about getting more treatments into the Wikiworld, so if I can help in any way, please let me know!

        • I am generally interested in uploading OA materials to Wikisource but find it odd to open yet another venue for taxonomic information by adding treatments to Wikisource rather than Wikispecies (or Wikipedia, for that matter). I signed up on your page there and remain open to discuss the merits of having treatments on Wikisource, though.

          • Gaurav says:

            Sounds great, and thanks so much for signing up! I think Wikisource is the right place for treatments because it can be used to keep a raw, text-searchable, unedited copy of the original taxonomic treatment, (hopefully) permanently. But there’s definitely good reasons to put it up on Wikipedia (more eyeballs), Wikispecies (although I don’t really know what Wikispecies is for?), and especially the Commons. I’m not playing around with taxonomic treatments at the moment, but I’d like to work on them later this year. Drop me an e-mail if you want to discuss this in more detail!

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  3. Good news, Daniel!

    Thanks for mentioning our journal-to-wiki export in your blog. The very positive experience we had so far with wiki environments (Wikimedia Commons, Species-Id, Wikispecies, etc.) convinces me to speed up establishing a routine workflow at Pensoft for writing Wikipedia articles related to the published papers.


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  7. Gregor Hagedorn says:

    The pointer to is very interesting. This is an important step. However, presently notability criteria for scholars exclude the vast majority of academics, since only popular and widespread newspaper or magazine coverage of the person is acceptable, not scientific merits. I have been personally involved in deletion discussion about the articles on widely publishing researchers that academically are doubtlessly notable. 30 publications in renowned journals are irrelevant under present rules if the person is not also published in the popular press with a personal story. I hope this will be fixed in the future on Wikipedia, and then the specification of wikisource is truly a big step forward!

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