06.06.2016 09:31

Naiveté or obstructionism in biological systematics publishing?


Taxonomists are very finicky about saving their legacy, such as publications, into the far future, certainly doubling the current shelf life of publications starting 1756. A recent publication by Ward & Fisher in one of the top taxonomic journals, Systematic Entomology by the Royal Entomological Society, one of the world’s oldest entomological societies, and published by Wiley et al., one of the world’s leading STM publishers, is a remarkable case of either naiveté, obstructionism or an out of touch with the state of the art of publishing.

How else can a publishing policy be understood that results in nomenclatural changes be cited as narrative, is completely unstructured in the article, but full detail being provided in supplementary material that exists of a Word (!) document? An article, furthermore, that is closed access and costs USD38 to purchase, and at the same time has implications for all the downstream users?

Interestingly, the supplementary material is not available in Antcat, and thus the first step to loose this material has already been taken. 

The authors refer for nomenclatural detail to Antcat which takes several mouse-clicks to get there. Through this they do not cite the bibliographic references of any of the taxa they mention. This way they break the system that allows measuring the impact of taxonomist by counting how often they are cited.  The low citation indexes is one of the most often heard complaint in taxonomy, that dispite the very long citation life of early work, taxonomic works have a very low impact in citation metrics. 

For any automated machine extraction of data from taxonomic work – Plazi’s contribution to opening up taxonomic data - such publications are not suited. 

This completely unstructured article shows very clearly why the current publishing is pretty anachronistic, and indicates that neither the publisher, the editor or the authors have an understanding of what publishing in the digital age means.

A taxonomic article is not independent but part of an ongoing discovery process to chart the world’s biodiversity. Furthermore, the goal is to provide a stable naming system for the world’s taxa. As a scientific process, the understanding of what a taxon is might change which is reflected in a dynamic naming system. The scientific process includes also the citation of sources, and with increasing movement towards linked open data, citable references and statements that are defined by ontologies.

Without moving the entire publishing process into semantically enhanced publishing workflows available through JATS-Taxpub and implemented by Pensoft, traditional publishers might consider the following steps to ease machine processing of the documents.

1. Be explicit. For any cited reference, e.g. Mann, 1919, even as authority of a taxon, the bibliographic reference should be provided, including a DOI to allows access to a digital representation  of the document. Mann, W. M. 1919. The ants of the British Solomon Islands. Bulletin of the Museum of Comparative Zoology 63: 273-391. doi:10.5281/zenodo.25890 

2. Be explicit. For any name changes, provide the original combination. The author is the expert and knows what he cites. The machine does not.

3. Prefer technical language over narrative. A synonymy should be provided as list or in tabular form, not verbatim in a paragraph. The latter is extremely difficult to parse.

4. Avoid supporting material. Supporting material has a tendency to be lost. Either do not make use of it, or then provide it in a non-proprietory (e.g. NOT MS Word) format and mint a DOI so it can be cited. There are plenty of archives that offer such services.

5. Consider using terminology for nomenclatural or taxonomic changes that are part of an ontology, such as the taxonomic nomenclatural status terms.

6. Use Open Access, semantically enhanced publications. The cost of a slightly higher citation index and closed access keeps taxonomy in the dark ages.

An example.

Instead of 

Fulakora Mann, 1919 stat.r., stat.n.

= Ericapelta Kusnezov, 1955 syn.n.

= Paraprionopelta Kusnezov, 1955 syn.n.

Species transferred from Paraprionopelta (minima) and Stigmatomma (others) to Fulakora:

agostii (Lacau & Delabie, 2002) comb.n.


this way

Fulakora Mann, 1919 stat.r., stat.n.

= Ericapelta Kusnezov, 1955 syn.n.

= Paraprionopelta Kusnezov, 1955 syn.n.


Species transferred from Paraprionopelta (minima) and Stigmatomma (others) to Fulakora:

agostii (Lacau & Delabie, 2002) comb.n.

= Amblyopone agostii Lacau & Delabie, 2002: 36.

= Stigmatomma agostii, Yoshimura & Fisher, 2012: 19. Generic transfer

 

and add the references


Kusnezov, N. 1955. Zwei neue Ameisengattungen aus Tucuman (Argentinien). Zoologischer Anzeiger, 154: 268-277. doi: 10.5281/zenodo.26127

Lacau, S., Delabie, C.H.. 2002. Description de trois nouvelles espèces d'Amblyopone avec quelques notes biogéographiques sur le genre au Brésil (Formicidae, Ponerinae). Bulletin de la Société Entomologique de France, 107: 33-41. doi: 10.5281/zenodo.54865

Mann, W.M.. 1919. The ants of the British Solomon Islands. Bulletin of the Museum of Comparative Zoology, 63: 273-391. doi: 10.5281/zenodo.25890

Yoshimura, M., Fisher, B.L.. 2012. A revision of male ants of the Malagasy Amblyoponinae (Hymenoptera: Formicidae) with resurrections of the genera Stigmatomma and Xymmer. PLoS ONE, 7(3): 1-23. doi: 10.1371/journal.pone.0033325


Since there is neither a reference name nor a bibliography server, it is better to be more explicit by including all the citations and references in full. For example, from the provided text, it is not clear what the original combination of agostii is, and it needs extra steps to find out.

This is strongly recommended so we finally will be able to provide metrics on the usage of our literature, especially the taxonomic, and eventually can update the catalogue and bibliography of life by machine, if not fill in the many gaps.