TaxPub: An Extension of the NLM/NCBI Journal Publishing DTD for Taxonomic Descriptions

TaxPub is an extension of the NLM/NCBI Journal Publishing DTD (Version 3.0) for the encoding of the literature of biological taxonomy. A key feature of this literature is the taxonomic description: publications or sections of publications that name and describe species and other taxonomic information. Given that it is estimated that the majority of all species have yet to be described, and that some 15-20,000 new species are described each year, and that markup might be applied prior to publication at less expense than applying markup to existing publications, TaxPub aims at providing a tagset for the encoding of new taxonomic literature. TaxPub extends the Publishing ("Blue") DTD parsimoniously. A few phrase-level elements are available at the relevant places throughout the entire DTD. Most of the extension, however, occurs in a single section-level element . The development of the extension proceeded smoothly, but several challenges have been encountered: lack of consensus on the components of taxonomic descriptions; relationship and alignment of TaxPub to other related schemas in the field; decisions on creating new elements or using existing NLM DTD elements and how to document and validate the usages; resistance to DTD as the XML schema language; and the efficiency of creating a superset extension rather than utilizing other simpler profiling mechanisms