Below the announcement of the launch of Zookeys revamp to become a XML based taxonomic journal. I believe this is not only timely, but it allows to study and discuss the use for marked-up and enhanced literature. As far as I know, taxpub, the underlying DTD is the first NLM publishing and archiving DTD that has been enhanced for a specific domain.
Lyubo and we at Plazi are interested to hear your opinions and suggestions.
Cheers
Donat
-----Original Message----- From: Lyubomir Penev [mailto:info@pensoft.net] Sent: Thursday, July 01, 2010 7:44 PM To: Donat Agosti Subject: ZooKeys jubilee issue: New publishing tools to accelerate biodiversity research
Dear ZooKeys readers,
I have certainly good news to share (apologies to Taxacom subscribers for cross-posting!)
On the eve of its two-years birthday (4th of July 2008), ZooKeys published its jubilee issue No 50 (http://pensoftonline.net/zookeys/index.php/journal/issue/view/52). This special edition 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 Medicines 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, http://www.sciaroidea.info and http://milichiidae.info and Proctotrupoidea website, http://www.vsyslab.osu.edu) 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, Barcode of Life, BHL, IUCN, ZooBank, Morphbank, Wikipedia, Wikimedia and others. An example can be a plant species, e.g., 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 Barcode of Life 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-5 0.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 criticism for further developing of the proposed workflow.
Once again, many thanks to all ZooKeys friends for their valuable support!
Lyubomir
Lyubomir Penev ZooKeys Editorial Manager Pensoft Publishers Phone +359-888-451668 Fax +359-2-8704282 info@pensoft.net
ZooKeys ZooKeys 50 (2010) Special Issue Table of Contents http://pensoftonline.net/zookeys/index.php/journal/issue/view/52
Editorial -------- Taxonomy shifts up a gear: New publishing tools to accelerate biodiversity research Lyubomir Penev, David Roberts, Vincent Smith, Donat Agosti, Terry Erwin
Forum Paper -------- Semantic tagging of and semantic enhancements to systematics papers: ZooKeys working examples Lyubomir Penev, Donat Agosti, Teodor Georgiev, Terry Catapano, Jeremy Miller, Vladimir Blagoderov, David Roberts, Vincent S. Smith, Irina Brake, Simon Ryrcroft, Ben Scott, Norman F. Johnson, Robert A. Morris, Guido Sautter, Vishwas Chavan, Tim Robertson, David Remsen, Pavel Stoev, Cynthia Parr, Sandra Knapp, W. John Kress, F. Christian Thompson, Terry Erwin
Streamlining taxonomic publication: a working example with Scratchpads and ZooKeys Vladimir Blagoderov, Irina Brake, Teodor Georgiev, Lyubomir Penev, David Roberts, Simon Ryrcroft, Ben Scott, Donat Agosti, Terrence Catapano, Vincent S. Smith
Research Articles -------- The centipede genus Eupolybothrus Verhoeff, 1907 (Chilopoda: Lithobiomorpha: Lithobiidae) in North Africa, a cybertaxonomic revision, with a key to all species in the genus and the first use of DNA barcoding for the group Pavel Stoev, Nesrine Akkari, Marzio Zapparoli, David Porco, Henrik Enghoff, Gregory D. Edgecombe, Teodor Georgiev, Lyubomir Penev
Parisognoriste, a new genus of Lygistorrhinidae (Diptera: Sciaroidea) from the Oise amber with redescription of Palaeognoriste Meunier Vladimir Blagoderov, Heikki Hippa, Andre Nel
Stomosis arachnophila sp. n., a new kleptoparasitic species of freeloader flies (Diptera, Milichiidae) Irina Brake, Michael von Tschirnhaus
World species of the genus Platyscelio Kieffer (Hymenoptera: Platygastridae) Charuwat Taekul, Norman F. Johnson, Lubomír Masner, Andrew Polaszek, Rajmohana K.