ZooKeys publishes articles of the future

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On the eve of its second year’s birthday (4th of July 2008), ZooKeys published its jubilee issue No 50 (http://pensoftonline.net/zookeys/index.php/journal/issue/view/52). This special editition demonstrates how integrating the traditional part of publication with the research and dissemination processes can deliver dramatic benefits by using semantic tagging and semantic enhancements (http://pensoftonline.net/zookeys/index.php/journal/article/view/538/469). Several novelties are described in the two forum papers and demonstrated in four exemplar papers:

The papers are published in four different formats: (1) high-resolution, full-colour print version, to satisfy the current requirements of the ICZN, as well as the readers who prefer hardcopy, and for the purposes of paper archiving; (2) PDF to provide an electronic version identical to the printed one, to be archived in BHL and PubMedCentral; (3) HTML to provide links to external resources and semantic enhancements to published texts for interactive reading, and (4) XML version based on the TaxPub extension to the National Library of Medicine’s DTD (http://sourceforge.net/projects/taxpub/) to provide archiving document format for PubMedCentral and a machine-readable copy of the contents to facilitate future data mining (e.g., by EOL, GBIF, Plazi and others).

An XML-based editorial, publication and dissemination workflow was implemented, which permits acceptance of manuscripts generated either from databases (Scratchpads websites and Proctotrupoidea website) or as standard MS Word file. The XML manuscripts generated “by pushing the button” from Scratchpads are linked to the online dynamic versions of the same after publication.

A dynamic web-page for any taxonomic name mentioned in a publication is being created and explored online through the so-called Pensoft Taxon Profile tool, just by clicking on the name during the reading process.  The dynamically generated taxon profile gathers and displays information from several leading biodiversity websites, e.g., GBIF, NCBI (GenBank, PubMed and PubMedCentral), EOL, BOLD, BHL, IUCN, ZooBank, Morphbank, Wikipedia, Wikimedia and others.  An example can be a plant species, i.e., the cork oak (Quercus suber):  http://pmt.pensoft.eu/resources/articles/external_details.php?query=Quercus+suber, mentioned in a zoological paper (http://pensoftonline.net/zookeys/index.php/journal/article/view/504/448).  

The tool offers an option to “Create your own taxon profile” for any taxonomic name of interest.

A number of additional semantic enhancements are used in the HTML versions: (i) internal cross-linking between paper sections, citations, references, tables, figures; (ii) vizualisation of main tag elements within the text (e.g., taxon names, taxon treatments, citations); (iii) mapping of georeferenced localities listed in the whole paper or within separate taxon treatments; (iv) enlarging figures and visualization of literature references by pointing on citations within the text; (v) external  linking to GenBank and BOLD accession numbers, Morphbank, online maps, literature references, museum collections, and some more.
The partnering organisations are listed in: http://pensoftonline.net/Parnering%20organisations-special%20issue-ZooKeys-50.pdf

It is anticipated that the workflow will be soon implemented also in the forthcoming PhytoKeys, a partner journal of ZooKeys.  Needless to say, the editors and authors involved in the current issue are thrilled by this development and would like to receive comments and critisim for further developing of the proposed workflow.

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