ZooKeys 50 (2010) Special Issue

Taxonomy shifts up a gear: New publishing tools to accelerate biodiversity research by Lyubomir Penev, et. al.

From the editorial:

The 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 significant 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 difficult to find. 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. The 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 different 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). The latter two were submitted as XML-tagged manuscript. These examples demonstrate the suitability of the workflow to a range of possibilities that should encompass most current taxonomic efforts. To implement the aforementioned routes for XML mark up in prospective taxonomic publishing, a special software tool (Pensoft Mark Up Tool, PMT) was developed and its features were demonstrated in the current issue. The XML schema used was version #123 of TaxPub, an extension to the Document Type Definitions (DTD) of the US National Library of Medicine (NLM) (http://sourceforge.net/projects/taxpub/).

A second forum paper from Blagoderov et al. (doi: 10.3897/zookeys.50.539) sets out a workflow that describes the assembly of elements from a Scratchpad taxon page (http://scratchpads.eu) to export a structured XML file. The publisher receives the submission, automatically renders the file into the journal‘s layout style as a PDF and transmits it to a selection of referees, based on the key words in the manuscript and the publisher’s database. Several steps, from the author’s decision to submit the manuscript to final publication and dissemination, are automatic. A journal editor first spends time on the submission when the referees’ reports are received, making the decision to publish, modify or reject the manuscript. If the decision is to publish, then PDF proofs are sent back to the author and, when verified, the paper is published both on paper and on-line, in PDF, HTML and XML formats. The original information is also preserved on the original Scratchpad where it may, in due course, be updated. A visitor arriving at the web site by tracing the original publication will be able to jump forward to the current version of the taxon page.
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This sounds like the promise of SGML/XML made real doesn’t it?

See the rest of the editorial or ZooKeys 50 for a very good example of XML and semantics in action.

This is a long way from the “related” or “recent” article citations in most publisher interfaces. Thoughts on how to make that change?

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