University of Glasgow

Roderic Page

One of goals of [BioNames](http://bionames.org) is to be more than
simply another taxonomic database. In particular, I\'m interested in the
idea of having a platform for viewing taxonomic publications. One way to
think about this is to consider the experience of viewing Wikipedia. For
any given page in Wikipedia there will be links to other, related
content in Wikipedia. Reading an article about a city, you can go and
read about the country the city occurs in. Reading about a battle, you
can discover more about the generals who fought it. The ability to
discover all this interconnected information in one place is
compelling.  
  
I\'d like something similar for taxonomy. Given that a taxonomic
database is in essence a collection of taxonomic names and publications,
and a taxonomic publication is in essence a collection of names and
citations of taxonomic publications, why not embed the publication
within the database and have the names and citations link to the
corresponding entries in the database?  
  
Based on some earlier efforts (e.g., [Towards an interactive taxonomic
article: displaying an article from
ZooKeys](http://iphylo.blogspot.co.uk/2011/12/towards-interactive-taxonomic-article.html))
and inspired by the [eLife Lens](http://www.elifesciences.org/lens)
project, I\'ve created a live demo of a way to view articles from the
journal *ZooKeys*. Below is a screencast:  
  

::: {style="text-align:center"}
::: {.iframe src="http://player.vimeo.com/video/68721604"}
:::
:::

  
  
If you want to try this out, here are some live examples:  

- <http://bionames.org/labs/zookeys-viewer/?doi=10.3897/zookeys.183.3073>
  Description of Alpheus cedrici sp. n., a strikingly coloured snapping
  shrimp (Crustacea, Decapoda, Alpheidae) from Ascension Island, central
  Atlantic Ocean
- <http://bionames.org/labs/zookeys-viewer/?doi=10.3897/zookeys.99.723>
  The spider family Selenopidae (Arachnida, Araneae) in Australasia and
  the Oriental Region
- <http://bionames.org/labs/zookeys-viewer/?doi=10.3897/zookeys.154.1963>
  At the lower size limit for tetrapods, two new species of the
  miniaturized frog genus Paedophryne (Anura, Microhylidae)

  
Note the pattern in the URL, just append the DOI for an article to
http://bionames.org/labs/zookeys-viewer/?doi=  
  
Everything is a bit rough, but it\'s working well enough for you to get
the basic idea. Code is in
[github](https://github.com/rdmpage/zookeys-viewer) Essentially the
viewer grabs the ZooKeys HTML, extracts the URL for the XML file,
fetches that, then uses some XSLT style sheets to convert the XML into
something viewable. There\'s a sprinkling of Javascript to call the
BioNames API. Much of the code could be tweaked to accepted other NLM
XML-based articles, such as content from PLoS and the BMC journals.  
  
One direction this could go in is to make a viewer like this the default
viewer in BioNames for ZooKeys articles, so that instead of being
restricted to a PDF you can interactively navigate between the article
and the cited literature. Indeed, the very action of locating cited
references in BioNames builds citation links. We could imagine extending
the approach to content that isn\'t in NLM XML, such as Zootaxa PDFs, or
content from BHL. Eventually I\'d like to have the taxonomic literature
fully embedded in the database, not as PDF or image silos, but as
documents linked to names and literature. The journal becomes a
database.


One of goals of BioNames is to be more than simply another taxonomic database. In particular, I'm interested in the idea of having a platform for viewing taxonomic publications. One way to think about this is to consider the experience of viewing Wikipedia. For any given page in Wikipedia there will be links to other, related content in Wikipedia.

Rogue Scholar Beiträge

A new way to view taxonomic publications