University of Glasgow

Roderic Page

As part of a project to build a tool to navigate through taxonomic names
and classifications I\'ve become interested in quick ways to compare
classifications. For example, [EOL](http://eol.org) has multiple
classifications for the same taxon, and I\'d like to quickly discover
what the similarities and differences are.  
  
One promising approach is to use \"cluster maps\", a technique described
by Fluit et al. (see [Aduna Cluster
Map](http://www.aduna-software.com/technology/clustermap) for an
implementation):  
  
Fluit, C., Sabou, M., & Harmelen, F. (2006). Visualizing the Semantic
Web. (V. Geroimenko & C. Chen, Eds.) (pp. 45--58). Springer Science +
Business Media.
[doi:10.1007/1-84628-290-X_3](http://dx.doi.org/10.1007/1-84628-290-X_3)
(see also <http://www.cs.vu.nl/~frankh/abstracts/VSW05.html>)  
  
![Cluster map
details](http://lh6.ggpht.com/-40TNwnPVXuU/T9jEbCMx2BI/AAAAAAAABac/uv-JsgnfZNs/cluster-map-details.png?imgmax=800 "cluster-map-details.png"){style="display:block; margin-left:auto; margin-right:auto;"
border="0" width="550" height="440"}  
  
Cluster maps can be thought of as fancy Venn Diagrams, in that they can
be used to depict the overlap between sets of objects. The diagram is a
graph with two kinds of nodes. One represents categories (in the example
above, file formats and search terms), the other represents sets of
objects that occur in one or more categories (in the example above,
these are files that match the search terms \"rdf\" and \"aperture\").  
  
I\'ve cobbled together a crude version of cluster maps. For a given
taxon (e.g., a genus) I list all the immediate sub-taxa (e.g., species)
in each classification in EOL, and then find the sets of sub-taxa that
are shared across the classification sources (e.g., ITIS, NCBI, etc.)
and those that are unique to one source. I then create the cluster map
using [Graphviz](http://www.graphviz.org/). Inspired by the hexagonal
packing used by Aduna, I\'ve done something similar to display the taxa
in each set. Adding these to the output of Graphviz required a little
fussing with. First I get Graphviz to output the graph in SVG, then I
load the SVG into a program that locates each node in the graph and
inserts SVG for the packed circles (given that SVG is XML this is fairly
straightforward).  
  
As an example, consider the genus *Demansia*
(<http://eol.org/pages/34967/overview>). EOL reports [four
classifications](http://eol.org/pages/34967/names) for this genus. Below
is a cluster map for this genus:  
  
![34967](http://lh4.ggpht.com/-m5NwOLObgAs/T9jEcH5Pl6I/AAAAAAAABak/-NsI_lMWqx8/34967.png?imgmax=800 "34967.png"){style="display:block; margin-left:auto; margin-right:auto;"
border="0" width="550" height="536"}  
  
This diagram show that, for example, the Catalogue of Life (CoL) and
Reptile databases share 4 names, these databases share three other names
with ITIS. All databases have names unique to themselves, one database
(NCBI) is completely disconnected from the other three databases.  
  
One important caveat here is that I\'m mapping the scientific names **as
returned by EOL**, and in many cases these contain the taxonomic
authority. This is a major headache, prompting this outburst:  
  

> Argh, taxonomic databases that don\'t provide canonical names (i.e.,
> with authority names REMOVED) will be first against the wall
> @[eol](https://twitter.com/eol)
>
> --- Roderic Page (@rdmpage) [June 13,
> 2012](https://twitter.com/rdmpage/status/212932316341866497){data-datetime="2012-06-13T15:39:54+00:00"}

  
If we clean the names by removing the taxonomic authority the clusters
overlap rather more:  
![Demansia](http://lh6.ggpht.com/-taX3oLOFo3U/T9jEdsSL3xI/AAAAAAAABas/uLQoblMNpz0/Demansia.png?imgmax=800 "Demansia.png"){style="display:block; margin-left:auto; margin-right:auto;"
border="0" width="550" height="519"}  
Now we see that only ITIS and the Reptile Database have unique names.
This is one reason why I get stroppy when taxonomists start saying
databases shouldn\'t have to supply cleaned \"canonical\" names. If the
names have authorities then I have to clean them, because in many cases
the authorities (while useful to know) are inconsistent across
databases. For example:  
  

- *Demansia olivacea* GRAY 1842 versus *Demansia olivacea* (Gray, 1842)
- *Demansia torquata* GÜNTHER 1862 versus *Demansia torquata* (Günther,
  1862)

  
Taxonomic authorities are frequently misspelt, and people seem confused
about when to use parentheses or not. Databases should spare the user
some pain and provide clean names (and authority strings separately
where they have them).  
  
The visualisation is still incomplete (I need to make it interactive),
but it shows promise. The names that are unique to one database are
usually worth investigating. In some cases they are names other
databases regard as synonyms, in other cases they represent spelling
variations. The goal of this visualisation is to highlight the names
that the user might want to investigate further.  
  


As part of a project to build a tool to navigate through taxonomic names and classifications I've become interested in quick ways to compare classifications. For example, EOL has multiple classifications for the same taxon, and I'd like to quickly discover what the similarities and differences are.

Messaggi di Rogue Scholar

Visualising differences between classifications using cluster maps