Nothing in (taxonomic) publishing makes sense

Donat Agosti will provide the lecture Nothing in (taxonomic) publishing makes sense except in the light of treatments at the conference of the Society for the Preservation of Natural History Collections (SPNHC).

The goal of taxonomic literature is to describe taxonomic diversity as a result of charting the Earth’s biological diversity. As research adds to our knowledge, our understanding of taxa increases with additional published results. This is how it has happened since the standard publications by Linnaeus in 1753 and 1758 in the format of taxonomic treatments, clearly delimited sections of text about a particular taxon. Later, material citations were added, providing an explicit link to the material that led to the published research result. Each treatment has a nomenclatural section including the referenced taxonomic name representing the usage of a specific citable name. Thus, the taxonomic name Apis mellifera L, 1758 refers to the taxonomic treatment published by Linnaeus 1758 on page 576. Later usage of the name cites this treatment thereby adding new research to the scientific corpus.

From a semantic point of view, a treatment and a material citation provide context to the content. For example, a geo-coordinate or specimen code in a material citation are references to a specimen which is a reference to the taxon of the treatment in which the material citation is in the text of a publication.

While this can be easily perceived by a human, machines depend on the treatment, treatment citation, material citation and taxonomic name annotations for recognizing this relationship.

These elements are in most cases distinct entities discoverable and annotatable by machines, can support human curation, but even better, the annotations can be embedded in prospective publications like those championed by Pensoft and the European Journal of Taxonomy.

Over the last 15 years, Plazi has been spearheading efforts to develop TaxPub, a schema modeling the taxonomic treatments, as well as material citations. Plazi has developed a processing workflow to discover these elements, make them open and citable using TreatmentBank and the Biodiversity Literature Repository and reused in collaboration with the Global Biodiversity Information Facility. Currently 730,000 treatments and over 1M material citations have been liberated from 51,000 publications. They have also been made reusable by GBIF, including over 80,000 taxa that are in GBIF only because of Plazi-provided treatments.