[Taxacom] ZooKeys jubilee issue: New publishing tools to accelerate biodiversity research

Vladimir Blagoderov vblago at gmail.com
Fri Jul 2 03:20:18 CDT 2010

Dear all,

I would like to elaborate a little on Lyubo’s message. It was not an
advertisement of one more issue of a journal, but rather invitation
for discussion. We were working very hard trying to demonstrate how
modern computer technologies can change taxonomy.

For example, with the two papers generated from Scratchpaddata
published in the current issue of ZooKeys
we are presenting an example that combines the advantages of online
publication and semantic web with the perpetuity of traditional
paper-based printed media. The manuscript is prepared online, from the
elements already present on Scratchpad, and these data are made
available to public on the day when the paper is printed.

This workflow may represent a shift in the way taxonomist work. At the
moment our work is paper-oriented, because for many of us the number
and quality of our papers is a key performance indicator. But do we
have to spend so much time on the preparation of the manuscript? Would
it not be better to concentrate on the content of the paper rather
than it's presentation? Most of the elements of a taxonomic paper can
be re-purposed, leaving us time to think on descriptions and
discussion. Few taxonomists can afford to devote their time entirely
to producing a monographic revision, neglecting other duties. But many
have a few spare moments between lectures or meetings to check a
description or upload a new picture - social networks are very good
examples on how people can be productive in between main activities.
If the information is kept organised, small incremental steps will
lead to a major work naturally. One may choose to publish small
descriptive papers or assemble a revisionary work - without
duplication of information.

Whether we like it or not, paper-based publications will disappear as
the major means of dissemination of information, and it will happen
sooner than we expect. Our system demonstrates one of the possible
ways of transition. It brings the best of both worlds: permanent
paper-based publication and access to the most current information
about the taxon on the Scratchpad. Check, for example, species page
Scratchpad publication (http://milichiidae.info/node/15295), and
journal publication
about the new milichiid species.

But, of course, I realise, that it is nowhere as interesting as a
spelling error made 140 yeas ago :)



On Thu, Jul 1, 2010 at 16:38, L Penev <lyubo.penev at gmail.com> wrote:
> Dear Taxacomers,
> 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 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):
> 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-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 criticism for further
> developing of the proposed workflow.
> Lyubomir
> Dr Lyubomir Penev
> ZooKeys Managing Editor
> Pensoft Publishers
> 13a Geo Milev Street
> 1111 Sofia, Bulgaria
> Fax +359-2-8704282
> www.pensoftonline.net/zookeys
> info at pensoft.net
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Dr. Vladimir Blagoderov
Department of Entomology
The Natural History Museum
Cromwell Road, London
Tel: +44 (0) 207 942 6629 (office)
Tel: +44 (0) 207 942 6895 (SBIL)
Fax: +44 (0) 207 942 5229

vlab at nhm.ac.uk
vblago at gmail.com

Fungus Gnats Online:

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