University of Glasgow

Roderic Page

The open access taxonomic journal ZooKeys has published a [special
issue](http://pensoftonline.net/zookeys/index.php/journal/issue/view/52)
with four papers, each available in HTML, PDF, and XML, the later being
extensively marked up. Penev et al. (\"Semantic tagging of and semantic
enhancements to systematics papers: ZooKeys working examples\",
[doi:10.3897/zookeys.50.538](http://dx.doi.org/10.3897/zookeys.50.538))
describes the process involved in creating these XML files. Two papers
([doi:10.3897/zookeys.50.506](http://dx.doi.org/10.3897/zookeys.50.506)
and
[doi:10.3897/zookeys.50.505](http://dx.doi.org/10.3897/zookeys.50.505))
were created using authoring tools available in
[Scratchpads](http://scratchpads.eu/), as outlined by Blagoderov et al.
(\"Streamlining taxonomic publication: a working example with
Scratchpads and ZooKeys\",
[doi:10.3897/zookeys.50.539](http://dx.doi.org/10.3897/zookeys.50.539)).
When you view the HTMl for these articles you can toggle on or off the
highlighting citations, taxonomic names, and geographic co-ordinates.
Mousing over a taxonomic name, for example, a popup appears with links
to GBIF, NCBI, EOL, BHL, Wikipedia, etc.):  
  
![brake.png](http://lh3.ggpht.com/_Gct8lVAxKqQ/TDM00dj-j7I/AAAAAAAAAsc/2vzET-1XTaE/brake.png?imgmax=800){style="display:block; margin-left:auto; margin-right:auto;"
border="0" width="400" height="168"}  
  
I think these papers represent one view of the future of scientific
publishing (\"article 2.0\"), and I\'m flattered that Penev et al. cite
my Elsevier challenge work
([doi:10.1016/j.websem.2010.03.004](http://dx.doi.org/10.1016/j.websem.2010.03.004),
preprint at
[hdl:10101/npre.2009.3173.1](http://hdl.handle.net/10101/npre.2009.3173.1))
as one of the sources of inspiration (along with the landmark Shotton et
al. \"Adventures in Semantic Publishing: Exemplar Semantic Enhancements
of a Research Article\"
[doi:10.1371/journal.pcbi.1000361](http://dx.doi.org/10.1371/journal.pcbi.1000361),
which I\'ve [discussed
previously](http://iphylo.blogspot.com/2009/04/semantic-publishing-towards-real.html)).
It is also good to see the
[TaxPub](http://sourceforge.net/projects/taxpub/) XML schema used by a
publisher, and Scratchpads being a part of the process of publishing
taxonomic information.  
  
**Deep linking**  
  
My initial impression is that there is huge of potential here, although
I think there is still lots to do. I\'m not totally convinced that
popups are they way to go (although I\'ve dabbled with them as well),
and we need to move beyond simply linking to other sites to a deeper
form of integration. For example, a Zookeys article might link to BHL
via a taxonomic name, but how about deeper linking? For example, the
paper by Brake and von Tschirnhaus
([doi:10.3897/zookeys.50.505](http://dx.doi.org/10.3897/zookeys.50.505))
contains the following citations:  
  

> Biró L (1899) Commensalismus bei Fliegen. Természetrajzi füzetek 22:
> 198--204.  
>   
> Kertész K (1899) Verzeichnis einiger, von L. Biró in Neu-Guinea und am
> Malayischen Archipel gesammelten Dipteren. Természetrajzi füzetek 22:
> 173--19

  
Neither reference has any links in the HTML, so the user is under the
impression that they aren\'t available online, but both references have
been scanned by BHL. You can see full text for these articles in BioStor
(references [52005](http://biostor.org/reference/52005) and
[52004](http://biostor.org/reference/52004), respectively \-- note that
the pagination for Biró 1899 is given incorrectly in the paper). This is
one area where BHL has a lot to offer publishers, and it would be great
to see BHL provide the services publishers need to add these links to
their articles.  
  
This integration should go both ways. It\'s odd that the paper by Brake
and von Tschirnhaus contains LSID used by the ZooBank for this paper
(urn:lsid:zoobank.org:pub:DABB03F4-A128-43BB-990C-02F25D656B00, see the
tag in the XML), but ZooBank doesn\'t know about the DOI for the paper,
hence the ZooBank [page for this
article](http://zoobank.org:80/?lsid=urn:lsid:zoobank.org:pub:DABB03F4-A128-43BB-990C-02F25D656B00)
has no link to the article itself. It\'s time to join this stuff
together.  
  
**What\'s next?**  
  
What I\'d really like to see is article XML repurposed as, say, RDF, and
used to populate a database so that we can query it. In this way we can
start to atomise the article into useful parts, and recombine them in
new and interesting ways. Might be something to play with over the
summer.  
  
On a practical level, I\'m somewhat bemused by the variety of XML
formats being used by open access publishers. PLoS use version 2.0 of
the [NLM Journal Archiving and Interchange Tag
Suite](http://dtd.nlm.nih.gov/), and I wrote a XSLT style sheet to
[transform PLoS articles for viewing on an
iPad](http://iphylo.blogspot.com/2010/06/plos-doesn-ipad-or-web.html).
TaxPub is based on version 3.0 of the NLM DTD, which breaks quite a bit
of my code relating to citations, so I\'ll have to tweak this to get it
to display Zookeys articles correctly. Handling TaxPub itself will also
require some additional work. Then there are the BMC journals, which
have their own flavour of XML (based on something called the \"KETON
DTD\"). It\'s all a bit messy. But I guess it\'d be no fun if it was
*too* easy\...  
  
  


The open access taxonomic journal ZooKeys has published a special issue with four papers, each available in HTML, PDF, and XML, the later being extensively marked up. Penev et al. ("Semantic tagging of and semantic enhancements to systematics papers: ZooKeys working examples", doi:10.3897/zookeys.50.538) describes the process involved in creating these XML files.

Messaggi di Rogue Scholar

ZooKeys publishes articles of the future