OMA Visiting Fellowship

• Author: Christophe Dessimoz •

Are you working on a project that could benefit from collaboration with the OMA team? Join us as OMA Visiting Fellow:

Share or comment:

To be informed of future posts, sign up to the low-volume blog mailing-list, subscribe to the blog's RSS feed, or follow us on Twitter. To read old posts, check out the index here.

Topic Pages: a bridge between academia and Wikipedia

• Author: Christophe Dessimoz •

We have published our latest review, on methods to infer horizontal gene transfer, in Wikipedia. It was peer-reviewed and it simultaneously appeared in PLOS Computational Biology. After our review on approximate Bayesian computations published two years ago, this is our second contribution using an exciting new format called “Topic Page”. In this post, I reflect on our motivation and experience as Topic Page authors.

The difficult relationship between academia and Wikipedia

Academia has mixed feelings about Wikipedia. Although many academics—and certainly many students—consult Wikipedia frequently, I’d venture to say that most remain reluctant to cite Wikipedia or admit relying on it otherwise.

As for academics contributing to Wikipedia, things are even worse. As a result, the quality of Wikipedia articles on scientific topics is often quite poor.

I think there are two main reasons for this reluctance to contribute. First, the lack of clear authorship and therefore credit makes it difficult for scientists to get recognition for contributing to Wikipedia. Given the intense competitiveness of contemporary science, this is more than a vanity issue; recognition is tightly coupled with funding and job success—i.e. survival in the profession. But perhaps just as importantly, many scientists are unfamiliar with Wikipedia’s conventions and practices and are thus (rightly!) concerned that their contributions might be “diluted” by further edits by others or even flat out turned down. I know of several disgruntled people who have given up on editing Wikipedia because of such bad experiences.

Simson Garfinkel provides an illuminating account of this sort of tensions in this article:

“I have attempted to retire from directing films in the alternative universe that is the Wikipedia a number of times, but somebody always overrules me,” Lanier wrote. “Every time my Wikipedia entry is corrected, within a day I’m turned into a film director again.”

Since Lanier’s attempted edits to his own Wikipedia entry were based on firsthand knowledge of his own career, he was in direct violation of Wikipedia’s three core policies. He has a point of view; he was writing on the basis of his own original research; and what he wrote couldn’t be verified by following a link to some kind of legitimate, authoritative, and verifiable publication.

For the tertiary source Wikipedia aims to be, these core policies are entirely reasonable but it’s easy to imagine situation where they might frustrate some contributors.

Wikipedia’s tremendous impact

It’s however worth considering the upsides of contributing to Wikipedia. For all the obsessions many of us have about publishing articles in generalist journals with broad readership, the lack of interest in Wikipedia feels like a missed opportunity. Consider the wikipedia page on Phylogenetics. It was consulted over 50,000 in the last 3 months alone. This is over twice as much as the median number of views of papers published in, say, the 17 Oct 2013 issue of Nature in a quarter of the time (as it happens, this particular issue has “impact metrics” as its cover story…).

PLOS Topic Pages

Fortunately, the good folks at PLOS Computational Biology have worked out a great solution to this conundrum: the “Topic Page”. In short, authors contribute Wikipedia-style articles on topics not or only poorly covered in Wikipedia. These get peer-reviewed and published in the journal with attribution, a DOI, and all the bells and whistles that come with journal articles. But in addition, the page gets incorporated into Wikipedia, where it starts a new life.

This format solves the problem discussed above. Authors get credit for their work in a way that fits well to existing structures. There is a permanent record of the contribution, indexed in scholarly databases such as PubMed, Google Scholar, etc. The contribution benefits from additional feedback from the peer-review and editorial process. And, perhaps most importantly, the authors can relinquish control over their work—for better or worse—with the reassurance that an unadulterated version of their work will remain available no matter what.

Our experience publishing Topic Pages

So far, we have published two Topic Pages: one on Approximate Bayesian Computations (paper, peer-reviews, Wikipedia page) and one on inferring horizontal gene transfer (paper, peer-reviews, Wikipedia page).

We’ve been pleasantly surprised by the excellent reception of the ABC article. It has been viewed over 26,000 times on the PLOS site alone. It’s also consulted a few thousand times every month on Wikipedia.

Remarkably, since the article was publicly accessible while we were drafting it on the PLOS Topic Page wiki, it had already accumulated over 10,000 views even before publication (see counter at bottom of this page). It was also picked up by a prominent’s statistician’s blog.

But just as importantly, the editorial process itself was great. Editing the manuscript on the PLOS Topic Page wiki provided a natural environment for collaborative writing. The wiki-based, open peer-review process yielded constructive and timely reviews (we could start addressing referee reports as they rolled in!). Our editor Daniel Mietchen was helpfully hands-on and did a substantial number of edits directly on the manuscript itself.

The only caveat I can think of is that the neutral, factual, impersonal, intemporal style of Wikipedia articles is quite different from the type of review articles I am otherwise used to. This is definitely not the right outlet for opinion-type pieces!

On the other hand, this format is great for student work. In fact, both of our Topic Pages started as student assignment in my course Reviews in Computational Biology. That being said, although the course gave the initial impetus, in both cases extensive additional work (and the involvement of additional co-authors) was required to get them published.

What happened since?

As it’s been two years since we published the ABC review, we can start to discern some outcomes.

The Wikipedia version underwent 46 changes, all minor modifications or additions (typo corrections, additional links and “Wikifications”, additional entries in the list of relevant software packages, attempts to sneak in one’s own contributions, … the usual stuff).

It is also gratifying to see our work appearing as first hit in Google. Since the publication in early 2013, it’s already been cited over 50 times.

Way of the future

In conclusion, the Topic Page is a great format. I am surprised that only eight Topic Pages have been published thus far, but perhaps there is still a lack of awareness about the format. I hope that this blog post will inspire some readers to improve Wikipedia by contributing a Topic Page. We are certainly thinking of our Topic Page number three…


Ravenhall M, Škunca N, Lassalle F, & Dessimoz C (2015). Inferring horizontal gene transfer. PLoS computational biology, 11 (5) PMID: 26020646 doi:10.1371/journal.pcbi.1004095 link to Wikipedia page.

Sunnåker M, Busetto AG, Numminen E, Corander J, Foll M, & Dessimoz C (2013). Approximate Bayesian computation. PLoS computational biology, 9 (1) PMID: 23341757 doi:10.1371/journal.pcbi.1002803 link to Wikipedia page

If you enjoyed this post, you might want to check the other entries of our series “story behind the paper”.

Share or comment:

To be informed of future posts, sign up to the low-volume blog mailing-list, subscribe to the blog's RSS feed, or follow us on Twitter. To read old posts, check out the index here.

Quest for Orthologs 4

• Authors: Ed Chalstrey, Jan Koch, Clement Train & Lucas Wittwer •

On 25-27 May 2015, the lab attended the 4th international ‘Quest for Orthologs’ conference held at Center for Genomic Regulation (CRG) in Barcelona, Spain. The following blog entry is a summary of the experiences had at the conference by Ed Chalstrey, Jan Koch, Clement Train, and Lucas Wittwer, who are interns and master’s students in the Dessimoz lab.


Quest for Orthologs (QfO) is a meeting of groups working on orthology detection and phylogenomic databases, with an aim to improve and standardise orthology predictions. This meeting was part of a series of conferences beginning in 2009, which have successfully brought together a community of researchers with shared goals. These goals included collaboration on benchmarking and the sharing of reference datasets.

As short project students in the group, QfO gave an excellent opportunity for those of us based at UCL to meet some of our colleagues from ETH (in Zurich) and Bayer CropScience (in Ghent) in person for the first time and to make contact with other scientists working in the field of ortholog prediction.

QFO picture 1QFO picture 2

As young scientists, some of the most important questions we face are: Will I be able to explain my project to established scientists and discuss it with them? Will I be able to understand the work of other scientists, even if their research topic falls outside my area of expertise? How can I have new ideas and be inspired to contribute to an area of research I’m new to? For us, most of whom had not attended a conference before, QfO was the perfect place to begin answering these questions.

The conference involved talks from each of the research groups and a poster session for students to display their contributions. Each of the postdocs and PhD students in the Dessimoz lab gave a short talk to introduce their posters, as well as one of us (Clement).

Clement: “The talk and the poster were the great practice for us to increase our communication skills by presenting to an audience composed of experts in related topics. This enabled us to adapt our talks depending of the kind of people we had in front of us and exchange ideas with other people during a constructive conversation. Also, attending talks on the many fields related to our work (orthology) was an amazing experience as interns, both in discovering new things and helping us in our own project with new ideas and other ways of thinking.”

QfO was a great opportunity for us to meet scientists that have worked in the field for many years and from all over the world. We were able to benefit from their experience and the advice they gave us after talking with them about our own research projects, gaining a different perspective to that of our usual supervisors and colleagues. One of the discussions had by Jan with two researchers from Switzerland may even lead to a potential future collaboration; they were interested in DLIGHT, a program that was developed by our group.

As well as discussing our current work, the conference also gave us the chance to think about future work opportunities and network with established scientists. One of the highlights for us was meeting Eugene Koonin and Sergei Mekhedov from the NCBI at the conference dinner. We had an amusing chat (about topics not necessarily related to orthology!) and an enjoyable evening. They even invited us to visit them at the NCBI!

All in all, we greatly benefited from our participation in the QfO conference.

Share or comment:

To be informed of future posts, sign up to the low-volume blog mailing-list, subscribe to the blog's RSS feed, or follow us on Twitter. To read old posts, check out the index here.

Creative Commons
                    License The Dessimoz Lab blog is licensed under a Creative Commons Attribution 4.0 International License.