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XML schemas and mark-up practices of taxonomic literature

Penev, Lyubomir; Lyal, Christopher H. C.; Weitzman, Anna; Morse, David R.; King, David; Sautter, Guido; Georgiev, Teodor; Morris, Robert A.; Catapano, Terry and Agosti, Donat (2011). XML schemas and mark-up practices of taxonomic literature. ZooKeys, 150 pp. 89–116.

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We review the three most widely used XML schemas used to mark-up taxonomic texts, TaxonX, TaxPub and taXMLit. These are described from the viewpoint of their development history, current status, implementation, and use cases. The concept of “taxon treatment” from the viewpoint of taxonomy mark-up into XML is discussed. TaxonX and taXMLit are primarily designed for legacy literature, the former being more lightweight and with a focus on recovery of taxon treatments, the latter providing a much more detailed set of tags to facilitate data extraction and analysis. TaxPub is an extension of the National Library of Medicine Document Type Definition (NLM DTD) for taxonomy focussed on layout and recovery and, as such, is best suited for mark-up of new publications and their archiving in PubMedCentral. All three schemas have their advantages and shortcomings and can be used for different purposes.

Item Type: Journal Item
Copyright Holders: 2011 Authors retain copyright and grant the journal right of first publication with the work simultaneously licensed under a Creative Commons Attribution License 3.0.
ISSN: 1313-2970
Project Funding Details:
Funded Project NameProject IDFunding Body
ViBRANT (Virtual Biodiversity Research and Access Network for Taxonomy, FP7 projectNot SetEU
Keywords: mark-up; XML schema; taxonomy; TaxonX; TaxPub; taXMLit
Academic Unit/School: Faculty of Science, Technology, Engineering and Mathematics (STEM) > Computing and Communications
Faculty of Science, Technology, Engineering and Mathematics (STEM)
Research Group: Centre for Research in Computing (CRC)
Item ID: 30401
Depositing User: David Morse
Date Deposited: 05 Jan 2012 12:41
Last Modified: 07 Dec 2018 09:57
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