Pre-Publication Data Linking in Taxonomy and Biodiversity: The ARPHA and Metotaxa-Metostem Publishing Systems

• Published in: Biodiversity Information Science and Standards 2023-08, Vol.7, p.1
• Main Authors: Benichou, Laurence, Salaün, Marianne, Boyadzhieva, Iva, Demirov, Seyhan, Georgiev, Teodor, Penev, Lyubomir
• Format: Article
• Language: English
• Subjects: Automation; Biodiversity; Citations; Scholarly publishing; Semantics; Taxonomy
• ISSN: 2535-0897; 2535-0897
• DOI: 10.3897/biss.7.110919

The traditional way of publishing in PDF makes it difficult to retrospectively convert the legacy literature into data. This presentation will discuss pre-publication tagging as an alternative solution for publishing FAIR (Findable, Accessible, Interoperable, Resuable) biodiversity data. The Metotaxa-Metostem workflow Тhe MetoTaxa project aims to create a new digital production chain for the European Journal of Taxonomy , which enables the pre-publication semantic structuring of text, automatic tagging and semantic enrichment (annotation). The system is based on a single-source publishing model, where the development of an XML file enables technical editors to automatically enrich text and produce multiple digital outputs. This makes it possible to structure generic or domain-specific sections of articles (e.g., Introduction; Material and methods; Taxon names or Мaterial examined). Thanks to the GoldenGate API developed by Plazi, the Text Encoding Intiative (TEI) XML source file is automatically annotated with JATS TaxPub tags: taxon names are labeled and each authorship can be checked via Catalogue of Life, each element of the material examined is parsed thanks to the preformatting of the text (Chester et al. 2019). Also, each bibliographic reference is parsed into Journal Article Tag Suite (JATS) elements (author names, title, journal, etc.), which automatically links references to their in-text citations. Pre-publication tagging will be carried out by the technical editors and then checked by the authors before publication, and will be sent to databases such as Global Biodiversity Information Facility (GBIF) or Biodiversity Literature Repository (BLR) as soon as the article is published. We will also briefly present MetoStem, which offers a technical solution for the digital transformation of monographs, and particularly floras. The tools and methods developed by this project will enable advanced publication of interoperable structured text and data. ARPHA Publishing Platform Launched in 2010 by Pensoft, ARPHA (Penev et al. 2010) is the first ever scholarly publishing platform to support pre-publication semantic tags and enhancements to entities (e.g., taxon treatments, taxon names, sequences) in the JATS TaxPub XML format developed by Plazi, which are then embedded into the HTML version of the article. Having proved advantageous for biodiversity scientists, Pensoft’s pre-publication tagging workflow has since been adopted by over 30 biodiversity journa