Nature Blog Network

Wednesday, May 28, 2008

PLoS ONE Publishes First Taxonomic Paper

PLoS ONE has heeded the call of the systematic wild and made open access history with an excellent paper by Fisher and Smith on the ants of Malagasy region with an evaluation of the role of DNA barcoding in species identification and description. What makes this particular article so special? It is the first time a species description has been published in a PLoS journal! I applaud PLoS ONE at taking the initiative and contributing to advancing the science of systematics and biodiversity research. Maybe it was my call to PLoS to publish taxonomy open access or maybe it was just destiny. I will talk about the ant paper in a separate post. First, I would like discuss further the role of open access publishing in taxonomy.

Why should one support open access publishing of taxonomic papers?
Visibility is important to the field of systematics, where the relevance is often lost amidst the taxonomic jargon. By removing the subscription barrier, taxonomists make their work accessible and noticeable to researchers all over the world. Increasingly, the need has never been greater for high quality taxonomy. The treatment of neglected tropical diseases relies on proper identification a the pathogen or parasite. Species form the fundamental unit of much of evolution and ecology. Sound knowledge of species and their attributes is basic to all other fields of biology ranging from the molecular to the metacommunity. While scientists might not agree on what a species is, there is no doubt about their importance and the necessity to identify and describe them.

The time is now for taxonomy and taxonomists to enter the digital age. New web technologies can prove effective at linking papers, potentially increasing readership and bringing disparate fields together. For instance, a paper describing a new species of pathogenic nematode can have hyperlinked keywords that summarize the findings, i.e. "Nematoda" "Genus species sp.nov." "Genus species (of host)" "Pathogenesis" "Endoparasite" "Locality Information", etc. Other articles of interest with hyperlinked keywords can be linked together for researchers to uncover. Species names themselves can be linked to the original paper, so one can find basic information about that species. This will make it easier to ground-truth simple observations about a species that can affect interpretations in other research, such as where it has been described from, variation in characteristics between sexes and sites, behavioral and diet observations and life history traits.

Why should one care if PLoS ONE publishes taxonomy?
PLoS ONE is an innovative publishing model that is part of the PLoS (Public Library of Science) network. PLoS is already established as a leader in online, open access publishing of high quality research in biology and the health sciences. The importance of the papers published in PLoS journals is well-recognized by academics and funding agencies. PLoS ONE, being relatively new, has yet to acquire the same metrics as the other 6 journals. Seeing the diversity and quality of papers being published, there is little doubt the initial metrics will reflect positively on the mission of PLoS. The visibility and reputation that articles published in PLoS journals gain will benefit taxonomy.

PLoS ONE's model allows for post-publication tools such as annotating and commenting on articles. Instead of articles being the final word on an experiment or hypothesis, they become the beginning of a conversation. For taxonomy, one can comment on new observations or developments in that species. You can drop a link on the comments of that paper to a revision you did or another paper investigating that species physiology. In short, the PLoS ONE model lets a paper, or species description, have a permanent home on the web where it be used as a record of its existence and any discussion of that species.

Some barriers exist to publication in a journal like PLoS ONE. Taxonomy is not a rich science despite its unsung significance. In the open access model, the author pays a publication fee to offset the journal making the paper freely available in perpetuity. Its a trade-off and it prevents publishing houses from double dipping into funds by charging institutions for access to content and charging authors page fees. Libraries and institutions worldwide can openly access content irrespective of their financial status, as can members of the public whose tax dollars pay for a good chunk of research. One obvious solution is for more funding to taxonomy and systematic research. Publication fees can be written into new grants or possibly creation of special grants from money saved from journal subscriptions can be used to pay open access fees. PLoS journals also make sure that the ability of authors to pay publication charges is not a consideration in the decision whether to publish. They can provide fee waivers for authors without grants or other financial resources.

This may encourage more papers being published to include a synthesis of many taxa or to be written in monographic style encompassing the fauna of a region per se. Putting more taxa into the paper may increase the bang for the buck. You pay less in fees (per page charges are eliminated in online publishing) and perhaps make the paper more citable. I am not suggesting this works in all cases, more information in a paper certainly doesn't make a better paper. Certainly there are situations where grouping taxa into a single article may make sense, i.e. The Crustacea of Coastal Norway instead of a 2 papers on shrimp and a paper on crabs.

Another barrier deals with requirements by the International Code of Zoological Nomenclature, which promotes "stability and universality in the scientific names of animals and to ensure that the name of each taxon is unique and distinct". One requirement (Chapter 3, Article 8.6) for articles published online is for deposition of the printed article in "at least 5 major publicly accessible libraries which are identified by name in the work itself". PLoS ONE went out of their way to work with leading institutions in 5 countries to ensure the proper cataloging of their first taxonomic paper. This willingness to do what it takes to get quality publications published irrespective of their discipline highlights their commitment to their core principles, in particular those of Breadth, Cooperation, Internationalism, and Science as a Public Resource.

Should taxonomists forego traditional publishing outlets?
The better option would be for those outlets to go online and open access! If there is some success to PLoS ONE in their venture to publish papers of a taxonomic nature, hopefully it will inspire established journals to follow suit. If you believe strongly in the force of the digital age to implement positive change in science, support open access initiatives by publishing your articles there. One may posit that hybrid journals, where authors may elect to pay an additional fee to make their article accessible online for free, is a step forward in the right direction. Noted open access proponent Peter Suber notes one should proceed with caution when electing to publish in a hybrid journal for several reasons. In particular, hybrid journal options do not free up subscription money from libraries. Because it is a risk-free strategy for journals, there is not an incentive to get rid of subscriptions fees all together, since most authors do not elect the free-access option. Many publishers still do not make their publishing model or data on the efficacy of the hybrid option available. This makes it difficult to police whether they are reducing subscription fees in relation to author uptake of the free-access option, where high fees are paid to offset subscription fees.

In conclusion, I applaud PLoS ONE for working hard to pave the way for publications with a taxonomic nature to be published truly open access and online. I would like to see more web tools being utilized in online scientific publishing. The tools exist and the potential is great for weaving together the threads of science. I look forward to submitting my next paper to a PLoS journal!


  1. That's excellent news!
    I love that PLoS went to that effort, but what a pain. That sounds like a rule that needs revision in the digital access world.

  2. Quite on the contrary. An online paper requires direct maintenance of its availability, while archived copies are more durable. What happens if the site goes down, for instance? My own experience is that it can be difficult to find online material from more than a few years ago. The ICZN requirements make more of a guarantee of long-term availability.

  3. Ok, I can definitely see that. Thank you or the clarification.

  4. An interesting and thought-provoking post, Kevin. For one, I had not thought of that drawback to publishing hybrid papers before... thanks for highlighting this important development on both of your blogs.


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