Taxonomy shifts up a gear: New publishing tools to accelerate biodiversity research

Abstract

Biodiversity is under severe threat. It is estimated that there are untold millions of species on the planet and we have, in the past 250 years and recently with a decreasing number of specialists, described only about 2 million of them.Th ough this happens with an agonizing low description rate of an estimated number of 20,000 new species per year (Polaszek et al. 2005), digital and genomic resources now are allowing discovery of new and identifi cation of existing species at a never before seen pace. Th e principles of Open Access greatly facilitate dissemination of information through the Web where it is freely accessed, shared and updated in a form that is accessible to indexing and data mining engines using Web 2.0 technologies. Web 2.0 turns the taxonomic information into a global resource well beyond the taxonomic community. A signifi cant bottleneck in naming species is the requirement by the current Codes of biological nomenclature ruling that new names and their associated descriptions must be published on paper, which can be slow, costly and render the new information diffi cult to fi nd. In order to make progress in documenting the diversity of life, we must remove the publishing impediment in order to move taxonomy “from a cottage industry into a production line” (Lane et al. 2008), and to make best use of new technologies warranting the fastest and widest distribution of these new results. In this special edition of ZooKeys we present a practical demonstration of such a process. Th e issue opens with a forum paper from Penev et al. (doi: 10.3897/zookeys.50.538) that presents the landscape of semantic tagging and text enhancements in taxonomy. It describes how the content of the manuscript is enriched by semantic tagging and marking up of four exemplar papers submitted to the publisher in three diff erent ways: (i) written in Microsoft Word and submitted as non-tagged manuscript (Stoev et al., doi: 10.3897/zookeys.50.504); (ii) generated from Scratchpads (Blagoderov et al., doi: 10.3897/zookeys.50.506 and Brake and Tschirnhaus, doi: 10.3897/ zookeys.50.505); (iii) generated from an author’s database (Taekul et al., doi: 10.3897/ zookeys.50.485). Th e latter two were submitted as XML-tagged manuscript. Th ese examples demonstrate the suitability of the workfl ow to a range of possibilities that should encompass most current taxonomic eff orts. To implement the aforementioned routes for XML mark up in prospective taxonomic publishing, a special software tool ZooKeys 50: i-iv (2010)