Abstract
The European Journal of Taxonomy (EJT) is a decade-old journal dedicated to the taxonomy of living and fossil eukaryotes. Launched in 2011, the EJT published exactly 900 articles (31 778 pages) from 2011 to 2021. The journal has been processed in its entirety by Plazi, liberating the data therein, depositing it into TreatmentBank, Biodiversity Literature Repository and disseminating it to partners, including the Global Biodiversity Information Facility (GBIF) using a combination of a highly automated workflow, quality control tools, and human curation. The dissemination of original research along with the ability to use and reuse data as freely as possible is the key to innovation, opening the corpus of known published biodiversity knowledge, and furthering advances in science. This paper aims to discuss the advantages and limitations of retro-conversion and to showcase the potential analyses of the data published in EJT and made findable, accessible, interoperable and reusable (FAIR) by Plazi. Among others, taxonomic and geographic coverage, geographical distribution of authors, citation of previous works and treatments, timespan between the publication and treatments with their cited works are discussed. Manually counted data were compared with the automated process, the latter being analysed and discussed. Creating FAIR data from a publication results in an average multiplication factor of 166 for additional access through the taxonomic treatments, figures and material citations citing the original publication in TreatmentBank, the Biodiversity Literature Repository and the Global Biodiversity Information Facility. Despite the advances in processing, liberating data remains cumbersome and has its limitations which lead us to conclude that the future of scientific publishing involves semantically enhanced publications.
Highlights
Natural History Institutions (NHIs), including natural history museums, herbaria, botanical gardens, and other research institutions, have traditionally been founded to contribute to the understanding of the natural world and to disseminate this knowledge
The European Journal of Taxonomy (EJT), a journal jointly published by several NHIs in Europe, was created in 2011 by its founding institutions (National Museum of Natural History, Paris; Natural History Museum, London; Royal Belgian Institute of Natural Sciences, Brussels; Royal Museum for Central Africa, Tervuren; Meise Botanic Garden) with the intent to enable its members to collectively tackle the strategic and technical challenges related to the visibility, access, format and financial structure of academic journals, especially publicly-funded titles
The automation is based on the GoldenGate Imagine software program (Sautter et al 2007), creation of a template that describes the layout necessary for machine processing, quality control including error reporting and a user interface for error removal, a gatekeeper that prevents erroneous documents from being uploaded, tools to upload and interlink the figures, treatments and original publications to Biodiversity Literature Repository, and the repackaging of the processed article as a Darwin Core Archive that is retrieved from TreatmentBank by Global Biodiversity Information Facility (GBIF)
Summary
Natural History Institutions (NHIs), including natural history museums, herbaria, botanical gardens, and other research institutions, have traditionally been founded to contribute to the understanding of the natural world and to disseminate this knowledge. The nature of the Internet, allows linking one page to another or a cited publication to its digital copy, and linking a cited specimen to its digital copy, a cited gene sequence to the actual DNA sequence, a trait to the definition of the trait, or a taxonomic name to the taxonomic treatment. This implies that data from within a publication need to be findable, accessible, interoperable, and reusable (FAIR: Wilkinson et al 2016). Machine processing depends on high quality text recognition and decoding of the portable document format (PDF) of the articles, text flows over pages, font sizes, etc. to recognize blocks of texts such as taxonomic treatments
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