XML schemas and mark-up practices of taxonomic literature

By

Penev, Lyubomir
Lyal, Christopher
Weitzman, Anna L.
Morse, David
King, David
Sautter, Guido
Georgiev, Teodor
Morris, Robert
Catapano, Terry
Agosti, Donat

Type

Article

Date of Publication

2011

Original Publication

ZooKeys

Volume

150

Pages

89-116

Subjects

mark-up , taXMLit , taxonomy , TaxonX , TaxPub , XML schema

Contributed by

Pensoft Publishers

Language

English

Published by

Sofia, Bulgaria Pensoft Publishers

Identifiers

DOI: https://doi.org/10.3897/zookeys.150.2213

 

Abstract

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.