PLoS ONE and botanical pioneer helps to bring open-access taxonomy a step closer

This post was written by PLoS Biology’s Senior Editor, Catriona MacCallum.  Catriona also acts as a Consulting Editor for PLoS ONE.

There are several thousand new plant species described every year, published in a range of plant taxonomy journals and other venues. Publishing another description might not be seen as a particularly earth-shattering event but we are enormously proud to be able to publish Sandra Knapp’s new paper on four new vining species in PLOS ONE today as it represents a turning point for PLoS and for botanical nomenclature. The paper is a botanical pioneer: it is the first to be published in an online-only journal whilst adhering to the strict botanical code that sets out how new species can be named.

So what’s special about publishing an online-only paper, I hear you mutter. And this is where it gets interesting. The naming of new taxa in plants is governed by the International Code of Botanical Nomenclature (ICBN), which has traditionally been thought to not allow publication of new names in anything other than print on paper. The Code also states that print copies must be distributed to specific museums and organisations on the same day of publication. If this doesn’t happen, the new name is not formally recognised. Although such rules might seem arcane to those outside this field, especially with the increasing digitisation of scientific information, complying with the code is hugely important. As Sandy said for our press release about the paper:

“Without such codes governing naming, there would be chaos; numerous different names could exist for the same species and numerous different species would potentially be referred to by the same name. This would impact all branches of life sciences as the name of a species – be it a pathogen or a crop – represents a fundamental part of communicating knowledge about the natural world.”

Solanum sanchez-vegae

This photo is of Solanum sanchez-vegae which is Figure 4 of PLoS ONE article e10502. Photo courtesy of A. Cano, USM

The PLoS ONE article provides a solution to this conundrum by separating the printing process from the publisher and enabling the author to print their own copies on the day of publication and distribute them to relevant museums and institutions. As such, it is the first to effectively publish new plant names in an online-only journal while complying with the rules and recommendations of the ICBN.

Sandy, who is a leading plant taxonomist, author of numerous books and a world authority on Solanaceae (the nightshade family, which is the topic of the PLoS ONE paper), was the driving force in trying to develop guidelines with us that could be published at the same time as her paper. These new guidelines are presented within our ‘discipline specific’ author guidelines – scroll down to the section “Information and guidelines for PLoS authors submitting a new taxon name – botanical nomenclature only”.  She is well acquainted with the Codes of Nomenclature, of which the ICBN is one (the others govern cultivated plant, animals and bacterial names). Her publication therefore acts as the ‘type’ specimen for other plant taxonomists should they want to publish in an online-only journal such as those published by PLoS. In the paper, she explicitly states that it is “a test case for the electronic publication of new names in flowering plants”. What is also crucial – and of long-term significance – is that there are now far fewer barriers to other taxonomists who want to make their articles fully open access. Most open access journals, such as those run by PLoS or BMC, are online only.

This is not the first time that PLoS has come up against this issue. More than two years ago we started discussions with the International Commission of Zoological  Nomenclature (ICZN) about how we could publish new descriptions of animal species in PLoS journals without violating their code on nomenclature (which is different to the botanical code mentioned above). Some of the papers in PLoS ONE had been criticized for not complying with the ICZN however we were able to agree some guidelines that would ensure the names were effectively published in line with the ICZN Code. Ellinor Michel, the Executive Secretary of the International Commission on Zoological Nomenclature, and Rich Pyle, one of the ICZN commissioners, were enormously helpful and absolutely key in helping us agree these guidelines (which can also be found in our ’discipline specific’ author guidelines, this time scroll down to “Information and guidelines for PLoS authors submitting a new taxon name – zoological nomenclature only”). There is also a proposed amendment to the zoological Code, which would allow for online-only publication although this still has to be approved and is provoking a huge amount of discussion.

It’s taken about two years for PLoS to become ‘Code Compliant’ in this way, but compliance is important. All the Codes of Nomenclature rely on the community of scientists adhering to the standards set out by generations of taxonomists. As Kevin Zelnio, a marine biologist and taxonomist, noted about the ICZN on his blog (which is well worth exploring if you want to dig into these issues more deeply):

While the Code is voluntary, I do not know of any taxonomist who would risk being totally out of touch and ignoring the system. It is set up to facilitate species naming to avoid confusion further down the line or with previously named animals. In other words, it is there to make life easier to us, not as an Orwellian agency bent on subversion of all zoological taxonomists to its agenda:

As publishing changes, so the Codes themselves will change, but the rate of change in publishing is currently outstripping that of the Codes. The botanical code, for example, is amended every 6 years through the deliberations of a Nomenclature Section at the International Botanical Congresses, the last was in Vienna in 2005, and the next in Melbourne in 2011. Sandy Knapp will preside as President of the 2011 Nomenclature Section in Melbourne, and the issue of electronic publishing of new names will be part of the debates about changes to the Code that will help taxonomists keep pace with the rapidly changing nature of scholarly communication.

With the help of Sandy, Ellinor, Rich, and other progressive taxonomists, we’re glad to be able to help facilitate this process at PLoS.

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3 Responses to PLoS ONE and botanical pioneer helps to bring open-access taxonomy a step closer

  1. rdmpage says:

    Catriona, PLoS ONE is doing great things for taxonomy, but unfortunately Sandy’s paper (http://dx.doi.org/10.1371/journal.pone.0010502) is let down by broken links. The LSIDs (Life Science Identifiers) assigned to each new plant name return essentially empty data, and the stated method for resolving these LSIDs doesn’t work (see my blog post http://iphylo.blogspot.com/2010/05/linnaeus-meets-internet-plos-botany.html for details).

    Now, this is to some extent outside PLoS’s control, but if you are going to publish a paper with links to a database, and those links are an integral part of the process, then surely it would be nice if those links actually worked. In other words, PLoS ONE, the author, and IPNI, should have done their best to ensure that everything was in place in time for publication. Given that there will be lots of discussion about paper copies, codes, etc. It’s a tad ironic that it’s the informatics side of this electronic publication that is broken.

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  2. cmaccallum says:

    Hi Rod, Thanks for the post. The links are now working but normally IPNI LSIDs are not available until some time after publication. It’s not a formal registration system (e.g. in the way that ZooBank is proposed to be) and currently functions purely as an index. Also, Sandy mentions in her paper that the IPNI LSID numbers will be made available but doesn’t specify when. I think in an online-only world, it would be ideal to coincide the availability of the LSIDs with the e-publication. IPNI have already been a great help to us – Alan Paton and Katherine Challis at Kew kindly provided the IPNI LSID numbers in advance which is also unusual, and they helped to develop the guidelines. As this is a test case, I hope all of these issues can be captured and incorporated into future discussions to improve the process. Our guidelines will change accordingly. There is already a healthy discussion about these issues on your blog and we should try to capture some of this on the comments to the actual paper.

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