Wikimedia Blog/Drafts/PLOS Computational Biology's Topic Pages

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Title[edit]

  • Making Open Access publications dynamic

Illustrations[edit]

Alternate text by Carlos Monterrey[edit]

There are a growing number of English Wikipedia articles that are incorporating text and media from peer-reviewed scholarly publications available under a Wikimedia-compatible license. Several important examples of this are the Topic Pages published in the journal PLOS Computational Biology as part of its Topic Pages collection, which is produced in collaboration with Wikipedia:WikiProject Computational Biology and aims to improve Wikipedias coverage of topics related to Computational Biology.

The Topic Pages also expand on earlier attempts to add a dynamic component to scholarly publishing. They provide the English Wikipedia with expert-written and expert-reviewed content, and allow authors to get credit for their work. The goal is to write new articles or replace those that have not made use of these new resources and hopefully expand on them to create a more comprehensive resource.

Take for example the article for cooperative binding. The source article was published in PLOS Computational Biology. Cooperative binding was the fifth such Topic Page, following in the footsteps of Viral phylodynamics (new), Evolving digital ecological networks (new), Approximate Bayesian computation (rewrite) and the pilot, Circular permutation in proteins (rewrite).. Since then Flow cytometry bioinformatics has been added to the list.

Of the three rewrites so far, cooperative binding was longest before the rewrite (5.5 kB), and the idea so far was to mainly write new articles or to replace ones that have not moved beyond stub status. However, expert involvement could also be interesting for higher-level articles, many of which have already reached impressive lengths.

PLOS Computational Biology uses a Creative Commons Attribution License (CC BY), which is more liberal than the Creative Commons Attribution Share-Alike License (CC BY-SA) in use at Wikimedia projects. For this reason, the Topic Pages are being drafted in a separate CC BY wiki and do not make use of existing materials that are licensed more restrictively.

Publication of topic pages on Wikipedia has provided significant incentive for young researches that see publication as an opportunity to provide much needed exposure. The idea of seeding a dynamically updatable review article on a topic central to their work is also an attractive concept to senior researchers. It has been a relatively seamless transition for many authors to contribute via MediaWiki, since many of them are already accustomed to working in different software environments.

The main barrier to increasing the quantity of Topic Pages is lack of time, and writing for Wikipedia is not a high priority for most active researchers these days. That said, the Topic Pages scheme appears to be attractive for researchers early in their careers, when any good publication helps to differentiate them from the crowd. The idea of seeding a dynamically updatable review article on a topic central to their work is attractive to senior researchers as well.

    • Conclusion discussing the future of Topic Pages? Are there more in the process?

Text[edit]

In April, the New York Times reported on a study of commuters in the New York City Subway:

Similar patterns have been observed amongst passengers on London buses. In contrast, oxygen molecules traveling though our blood vessels are more social and prefer the last remaining seat on a hemoglobin molecule over having the choice between multiple empty ones. This phenomenon is known as cooperative binding. The cooperativity can be negative as in the case of the New York or London commuters trying to keep distance from each other, or positive, as in the case of the oxygens on the hemoglobin line.

The English Wikipedia's cooperative binding entry is one of a growing number of articles that incorporate text or media from peer-reviewed scholarly publications available under a Wikimedia-compatible license. In this case, the source article was published in the journal PLOS Computational Biology as part of its Topic Pages collection that is produced in collaboration with Wikipedia:WikiProject Computational Biology and aims to improve Wikipedias coverage of topics related to Computational Biology. The concept can be summed up as follows:

Cooperative binding was the fifth such Topic Page, following in the footsteps of Viral phylodynamics (new), Evolving digital ecological networks (new), Approximate Bayesian computation (rewrite) and the pilot, Circular permutation in proteins (rewrite). It has since been followed by Flow cytometry bioinformatics (new). Of the three rewrites so far, Cooperative binding was longest before the rewrite (5.5 kB), and the idea so far was to mainly write new articles or to replace ones that have not moved beyond stub status. However, expert involvement could also be interesting for higher-level articles, many of which have already reached impressive lengths.

PLOS Computational Biology uses a Creative Commons Attribution License (CC BY), which is more liberal than the Creative Commons Attribution Share-Alike License (CC BY-SA) in use at Wikimedia projects. For this reason, the Topic Pages are being drafted in a separate CC BY wiki and do not make use of existing materials that are licensed more restrictively.


Text quarrel[edit]

  • links to Wikipedia throughout
  • In final paragraph, return to cooperative binding and apply to Wikipedia articles

Now if we replace the seats with binding sites of a macromolecule, and the commuters with molecules that could potentially bind to those sites, then the phenomenon of occupied seats not increasing proportionally with the number of passengers even has a name: cooperative binding. The cooperativity can be negative as in the case of the subway passengers avoiding the last empty seats, or positive. For instance, the more oxygen molecules are bound to a hemoglobin molecule, the easier it is for other oxygen molecules to bind to that same hemoglobin molecule, until all its binding sites are occupied.

Questions[edit]

The content of this section has informed a blog post at Jisc.

  • How much software development/customisation has it taken to set up the topic pages wiki? Has any money been spent on software?
    The Topic Pages wiki uses MediaWiki, which is open-source software available for free under a GNU Public License. Customization was very light-weight in comparison to most Wikipedias or Wiktionaries, which all run on MediaWiki.
  • Was there a cultural barrier to be overcome to get authors working on Topic Pages?
    The main barrier is lack of time, and writing for Wikipedia is certainly not a high priority for active researchers these days.
  • Did the Topic Pages' publication on Wikipedia provide a significant incentive for authors? Or even a disincentive?
    I am not aware of any disincentives here. The Topic Pages scheme appears to be attractive for researchers early in their careers, when any good publication helps to differentiate them from the crowd. The idea of seeding a dynamically updatable review article on a topic central to their work is attractive to senior researchers as well.
  • Was it a barrier for authors to learn wikicode and Wikipedia formatting conventions? What help was available to them?
    Most computational biologists are accustomed to working in different software environment and have seen code worse than what we have in MediaWiki. Topic Pages authors tend to struggle, though, with some of Wikipedia's editorial policies, e.g. regarding the lead section and the neutral point of view as well as its ramifications. Help is available from WikiProject Computational Biology and from the journal end as well as from the authoring guidelines.
  • Was there any element of "stage fright" for authors creating drafts on a wiki that can be read by the public?
    Perhaps, but I didn't notice any. Most of the authors involved so far have had experience with open-source software and database projects, though, which provided them with similar opportunities for "stage fright" and learning how to deal with it, probably limiting the extent to which their on-wiki ventures might create feelings of that kind.
  • The wiki has been used for pre-publication review and feedback (e.g. on Talk pages). To most researchers, this is novel format for feedback: has it been difficult for authors to adapt?
    Again, collaborative software or database projects provide a similar environment in this regard, and many research groups or projects are using wikis, so that sort of communication isn't as alien to them as it may seem. Finally, arXiv has been around for two decades, and in recent years, many open-access publishers - e.g. Copernicus, Frontiers, BMC, F1000 Research, eLife, PeerJ - have established peer review workflows that are more open than in traditional journals, with similar efforts underway at PLOS, Pensoft and elsewhere.
  • Has it taken much effort to adapt a topic paper for Wikipedia once it is suitable for the journal?
    We keep an eye on the Wikipedia Manual of Style throughout the drafting and reviewing process, and we invite feedback from WikiProject Computational Biology members early on, so most issues arising from that dual-target drafting process are usually solved by the time the article is accepted for the journal, and since we are drafting in a MediaWiki environment, most of the effort of moving the accepted version onto Wikipedia amounts to copypasting, with some find-and-replace in between (e.g. for wikilinks) and some spice added by things like categorization and attribution of the journal article as the source.
  • Has there been any reaction from the Wikipedia community, positive or negative, to the introduction of these pages?
    I am not aware of negative reactions to the initiative as a whole, and the most negative reaction to individual articles was that several of them have been tagged for deletion by a user (typically a bot) that found the PLOS version and was not aware of its open license. One of the articles actually remained deleted for a few weeks. There have been a good number of positive reactions from the communities around the WikiProjects on Computational Biology, Molecular and Cell Biology and Open Access.
  • Is the Topic Pages model one that other journals are likely to take up?
  • Do you think that Wikipedia and similar sites will change academic publishing in the long term?
  • You've shown that review papers, images and video can be shared through Wikimedia sites. What about other research outputs, such as data sets or presentations?
  • Some academics are very attached to traditional, closed models of scholarly publishing, saying that they are necessary for the scholarly record to be credible and authoritative. Do they have anything to fear if Wikipedia and similar sites become part of the process?

References[edit]

Notes[edit]