XML schemas and mark-up practices of taxonomic literature.

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.

Towards the bibliography of life.

This paper discusses how we intend to take forward the vision of a Bibliography of Life in the ViBRANT project. The underlying principle of the Bibliography is to provide taxonomists and others with a freely accessible bibliography covering the whole of life. Such a bibliography has been achieved for specific study areas within taxonomy, but not for "life" as a whole.The creation of such a comprehensive tool has been hindered by various social and technical issues. The social concerns focus on the willingness of users to contribute to the Bibliography. The technical concerns relate to the architecture required to deliver the Bibliography. These issues are discussed in the paper and approaches to addressing them within the ViBRANT project are described, to demonstrate how we can now seriously consider building a Bibliography of Life. We are particularly interested in the potential of the resulting tool to improve the quality of bibliographic references. Through analysing the large number of references in the Bibliography we will be able to add metadata by resolving known issues such as geographical name variations. This should result in a tool that will assist taxonomists in two ways. Firstly, it will be easier for them to discover relevant literature, especially pre-digital literature; and secondly, it will be easier for them to identify the canonical form for a citationThe paper also covers related issues relevant to building the tool in ViBRANT, including implementation and copyright, with suggestions as to how we could address them.