EJT editorial standard for the semantic enhancement of specimen data in taxonomy literature

Abstract

This paper describes a set of guidelines for the citation of zoological and botanical specimens in the European Journal of Taxonomy. The guidelines stipulate controlled vocabularies and precise formats for presenting the specimens examined within a taxonomic publication, which allow for the rich data associated with the primary research material to be harvested, distributed and interlinked online via international biodiversity data aggregators. Herein we explain how the EJT editorial standard was defined and how this initiative fits into the journal’s project to semantically enhance its publications using the Plazi TaxPub DTD extension. By establishing a standardised format for the citation of taxonomic specimens, the journal intends to widen the distribution of and improve accessibility to the data it publishes. Authors who conform to these guidelines will benefit from higher visibility and new ways of visualising their work. In a wider context, we hope that other taxonomy journals will adopt this approach to their publications, adapting their working methods to enable domain-specific text mining to take place. If specimen data can be efficiently cited, harvested and linked to wider resources, we propose that there is also the potential to develop alternative metrics for assessing impact and productivity within the natural sciences.

Mining data from legacy taxonomic literature and application for sampling spiders of the Teutamus group (Araneae; Liocranidae) in Southeast Asia

“…Data extraction from taxonomic literature can proceed along two major pathways: (1) prospective, where data is mobilized and shared with GBIF as part of the routine publication process, as has been implemented some journals like EJT 13 and ZooKeys 2,8 and some revisionary studies 51 ; and (2) retrospective, where data is mined from legacy taxonomic data 11,12 . This retrospective approach was tested in our study by semantically enhancing records from more than 50 legacy taxonomic documents.…”

“…Recently developed tools allow text in PDF documents to be interpreted and categorized in XML format (mark-up) allowing information to be mobilized, aggregated and reanalyzed 9 – 12 . Plazi Treatment Bank 8 , 13 , 14 , is a project dedicated to creating a comprehensive compendium of taxonomic and biological data extracted from primary literature 15 . This platform permits mined treatment data to be accessed, queried, compared, and reused in a customized way.…”

“…This platform permits mined treatment data to be accessed, queried, compared, and reused in a customized way. The strategy for data extraction can be prospective: where journals generate new data in XML format that can be uploaded directly to repositories (as has been implemented by Zookeys 2 and EJT 8 , 13 ). or retrospective: where data is mined from legacy taxonomic literature 3 , 11 – 13 through a process called semantic enhancement 9 , 13 .…”

“…The strategy for data extraction can be prospective: where journals generate new data in XML format that can be uploaded directly to repositories (as has been implemented by Zookeys 2 and EJT 8 , 13 ). or retrospective: where data is mined from legacy taxonomic literature 3 , 11 – 13 through a process called semantic enhancement 9 , 13 . This retrospective approach is more complicated and time consuming since the semi-automatic process of text recognition and tagging needs to be checked by a human operator 3 , 15 .…”

An illustrated catalogue of Rudolf Sturany’s type specimens in the Naturhistorisches Museum Wien, Austria (NHMW): more Red Sea species

“…Any citation to the International Code of Zoological Nomenclature (ICZN 1999) should be considered to its online version, which includes all recent amendments. We follow the guidelines for the citation of specimen data by Chester et al (2019). Photos were shot with a Nikon SMZ25 microscope; larger shells were photographed with a Nikon D7200 camera and a Nikon Micro-Nikkor 60 mm lens.…”