Recommendations for use of annotations and persistent identifiers in taxonomy and biodiversity publishing

Abstract

The paper summarises many years of discussions and experience of biodiversity publishers, organisations, research projects and individual researchers, and proposes recommendations for implementation of persistent identifiers for article metadata, structural elements (sections, subsections, figures, tables, references, supplementary materials and others) and data specific to biodiversity (taxonomic treatments, treatment citations, taxon names, material citations, gene sequences, specimens, scientific collections) in taxonomy and biodiversity publishing. The paper proposes best practices on how identifiers should be used in the different cases and on how they can be minted, cited, and expressed in the backend article XML to facilitate conversion to and further re-use of the article content as FAIR data. The paper also discusses several specific routes for post-publication re-use of semantically enhanced content through large biodiversity data aggregators such as the Global Biodiversity Information Facility (GBIF), the International Nucleotide Sequence Database Collaboration (INSDC) and others, and proposes specifications of both identifiers and XML tags to be used for that purpose. A summary table provides an account and overview of the recommendations. The guidelines are supported with examples from the existing publishing practices.

L'herbier Daniel Pellé (DP) – La collection d'un botaniste amateur de l'Aube (France)

“…L'attribution d'identifiants pérennes à l'herbier a constitué l'un des buts de notre démarche (voir Agosti et al 2022). Ainsi, L'herbier DP a été enregistré en 2010 dans l'« Interface de gestion des collections en ligne; COEL», proposée par Tela Botanica (identifiant: urn:lsid:tela-botanica.org:coel:col1405).…”

“…L'enregistrement d'un jeu de données sur Zenodo (https://doi.org/10.5281/zenodo.4443430), couplée à l'utilisation des identifiants des planches, permet de définir des URL sous la forme https://zenodo.org/record/4443430/files/DP0684.jpg, et donc de maintenir dans le temps les liens vers ces fichiers. Des QR-codes collés sur les planches physiques de l'herbier permettent d'afficher facilement la page correspondante en ligne (sur les identifiants numériques, voir Chester et al 2019; voir aussi Agosti et al 2022). Autres identifiants.…”

Joint statement on best practices for the citation of authorities of scientific names in taxonomy by CETAF, SPNHC and BHL

“…Either way, the various inconsistent practices related to the citation of taxon authorships lead to inconsistencies and ultimately confusion (Fig. 2, from Bénichou et al 2018). Such inconsistencies lead to inconsistent linking in the article, with some authorities linked to their bibliographic reference while others for which the reference is not provided are left unlinked (Fig.…”

“…Such inconsistencies lead to inconsistent linking in the article, with some authorities linked to their bibliographic reference while others for which the reference is not provided are left unlinked (Fig. 3, from Bénichou et al 2018). In this example, the bibliographic citation is in yellow, the bibliographic reference in red and the taxon name with its authority in green.…”

“…Figure 2.In this article published in 2016 in Malacologia, the mentions highlighted in orange are only cited as authorship and yet listed under the references section; the references in yellow are unambiguous bibliographic references (as they also are followed by a page number for instance), thus they are listed under the references section; the blue references should have been listed in the bibliography list but are not (Waite and Allmon 2016, cited inBénichou et al (2018)). …”