[tdwg-lit] FW: ZooKeys jubilee issue: New publishing tools to accelerate biodiversity research

Donat Agosti agosti at amnh.org
Fri Jul 2 15:23:06 CEST 2010

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.



-----Original Message-----
From: Lyubomir Penev [mailto:info at 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

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
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, 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): 
mentioned in a zoological paper
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:

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 Penev
ZooKeys Editorial Manager
Pensoft Publishers
Phone +359-888-451668
Fax +359-2-8704282
info at pensoft.net

ZooKeys 50 (2010) Special Issue
Table of Contents

Taxonomy shifts up a gear: New publishing tools to accelerate biodiversity
	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,
Brake,	Simon Ryrcroft,	Ben Scott,	Norman F. Johnson,	Robert A.
Morris,	Guido
Sautter,	Vishwas Chavan,	Tim Robertson,	David Remsen,	Pavel Stoev,
Parr,	Sandra Knapp,	W. John Kress,	F. Christian Thompson,	Terry Erwin

Streamlining taxonomic publication: a working example with Scratchpads and
	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,
Enghoff,	Gregory D. Edgecombe,	Teodor Georgiev,	Lyubomir

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.

ZooKeys - Launched to accelerate biodiversity research

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