15.01.2020 21:32

Science Magazine: Why not be more open? Liberated biodiversity data as a win-win case

[https://www.lemonde.fr/sciences/article/2020/01/15/cinq-nouvelles-especes-d-oiseaux-decouvertes-en-indonesie_6025894_1650684.html Monday Jan 15, 2020 via Le Monde App]

This morning news had two headlines covering conservation and biodiversity and, in fact pointing out its dire state and what ought to be done. For example, in Le Monde one reported on the UN 2030 goal to protecting 30% of the Earth’ surface, and another covered targeted expeditions to chart the unknown biodiversity before it vanishes respectively. Both call for action from everybody. But this becomes only obvious with a newspaper subscription at hand.

Now that I have such a subscription I can dive right into it.  It takes a moment to find the cited UN document, but at least it is accessible. The link to the cited paper including the description of the five new species from Indonesia seems to be straight forwards. But then I am stuck, because I am hitting a paywall. I know, I am not the only one being frustrated for not having access to this scientifically intriguing story. But even more so that the scientist’s call for action is in vain, and in fact Science Magazine’s related perspective article’s too.

Being an active scientist in the northern hemisphere though, I have options to find out - discover known biodiversity, even if it of comes with great pain. To make clear, Science Magazine is not alone helping to raise the challenge to not to be left in the dark. A nuisance we at Plazi together with Zenodo, Pensoft, the European Journal of Taxonomy (EJT), and the Arcadia Fund try to mitigate. So, what have I discovered?

Behind the paywall, there is the expected article plus a second “perspective” that, as the name expresses, put’s the main article into a wider context, and an editor’s comment. The article itself describes the montane archipelagic avifauna, but not the subject of the news article, the new species. These are referred to in the Supplementary Materials, of which there are four, including 3 tables, but all behind paywall and not visible otherwise.

The Download Supplement link leads to a PDF file of some 104 pages with very detailed descriptions of the species and subspecies. It is not formatted at all but in a manuscript style with each line numbered and including 15 figures. The new names have been registered at Zoobank, but the only way to cite the supplement is indirectly via the DOI of the parent article (which in fact at the moment does not resolve). In the respective taxonomic treatments, only the holotype is cited, and a reference is given to the supplement where the materials examined is provided. There are in fact two, one including the over 300 specimen codes of materials examined in collections, and a second with observation records, including bio-acoustic data. The third supplement is a list of the new bird species discovered from 2000 to 2016 used to put the present discovery into perspective.

Quite rightly, this is a great discovery, at least in the bird world. With an expected ca 17,000 new species discovered every year, this can be looked at differently. But this is not the point here.

The point is, that we don’t know what we know, and we keep adding what we could know. Practically, we don’t know how many species we know and might loose, and what we know about them, because we do not have access to the data in our scholarly published record.

The current article, and I would argue this for a high profile Science Magazine specifically, is a good example why our biodiversity is largely unknown and stays so: not to the few specialists around each taxon with their own networks, but to all of us at large, and especially those where the biodiversity is. So, how can we talk seriously about loss of species if we can’t know even what we know, because career and financial aspects prevail, over understanding the data in an article and building a global biodiversity knowledge base?

What we at Plazi suggest is that such discoveries should only make it into the news, if they are an integral part of the Global Biodiversity Information Facility (GBIF) complementing the over 1 billion occurrence records. Wouldn't it be helpful for science and conservation if all the data about species is immediately accessible through at least one place with a robust infrastructure such as GBIF like in the present case?

To make it clear, tools are in place to make this happen, as the presence of taxonomic treatments from over 27,000 articles in GBIF demonstrate, including the Biodiversity Literature Repository (BLR) at Zenodo allowing depositing all the data in the article as FAIR data.

New Taxa

BLR (Zenodo)
(DataCite DOI)

TreatmentBank / Plazi
(http URI)

(species ID)

(name registration)

Rhipidura habibiei





Locustella portenta





Myzomela wahe





Phylloscopus suaramerdu





Phylloscopus emilsalimi





Phyllergates cucullatus subsp. sulanus





Phyllergates cucullatus subsp. relictus





Cyornis omissus subsp. omississimus





Turdus poliocephalus subsp. sukahujan





Ficedula hyperythra subsp. betinabiru





In this case, each taxonomic treatment can be cited using a recommended Digital Object Identifier (DOI), persistent http URI from Treatmentbank or linked to the respective deposit on GBIF, which is using the data from TreatmentBank. Zoobank as official registry of zoological nomenclature provides a persistent ID for the taxonomic name.

Supporting such a policy by Science Magazine (and others) would mean that journals make a commitment to conserve global biodiversity.

In fact, the win-win is that this set up enhances the visibility of the adopting journals, because the deposits of their data in BLR and GBIF produce many links leading back to the original articles and thus ways to discover the article that do not exist otherwise. This in fact is a novel index to journal articles based on the accumulation of all the liberated data.