University of Glasgow

Roderic Page

I keep returning to the problem of viewing large graphs and trees, which
means my hard drive has accumulated lots of failed prototypes. Inspired
by some recent discussions on comparing taxonomic classifications I
decided to package one of these (wildly incomplete) prototypes up so
that I can document the idea and put the code somewhere safe.

> Very cool, thanks for sharing this\-- the tree diff is similar to what
> J Rees has been cooking up lately with his \'cl diff\' tool. I\'ll tag
> [@beckettws](https://twitter.com/beckettws?ref_src=twsrc%5Etfw) in
> here too so he can see potential crossover. The goal is autogenerate
> diffs like this as 1st step to mapping taxo name-to concept
>
> --- Nate Upham (@n8_upham) [December 28,
> 2021](https://twitter.com/n8_upham/status/1475834371131289608?ref_src=twsrc%5Etfw)

## Google Maps-like viewer

::: {.separator style="clear: both;"}
[![](https://blogger.googleusercontent.com/img/a/AVvXsEiGDVVKGmwRi0gn-kEtpxBCUEdK-WCLBSpmkALAUDHGeTPkTSICSYVgnsj5N7zUeUfQALfFFHJJCsfeFvRULKbmqxLz51rW5hp_11dVXh-FHrnlRA7RJTA7I82l7sERF5jAjlah0LyEheVayO9nAfHTGZDuw5rnCe9iEO3dHQmA8_5AFIlJJg=s400){border="0"
width="400" original-height="448"
original-width="500"}](https://blogger.googleusercontent.com/img/a/AVvXsEiGDVVKGmwRi0gn-kEtpxBCUEdK-WCLBSpmkALAUDHGeTPkTSICSYVgnsj5N7zUeUfQALfFFHJJCsfeFvRULKbmqxLz51rW5hp_11dVXh-FHrnlRA7RJTA7I82l7sERF5jAjlah0LyEheVayO9nAfHTGZDuw5rnCe9iEO3dHQmA8_5AFIlJJg=s500){style="display: block; padding: 1em 0; text-align: center; "}
:::

I\'ve created a simple viewer that uses a tiled map viewer (like Google
Maps) to display a large graph. The idea is to draw the entire graph
scaled to a 256 x 256 pixel tile. The graph is stored in a database that
supports geospatial queries, which means the queries to retrieve the
individual tiles need to display the graph at different levels of
resolution are simply bounding box queries to a database. I realise that
this description is cryptic at best. The GitHub repository
<https://github.com/rdmpage/gml-viewer> has more details and the code
itself. There\'s a lot to do, especially adding support for labels(!)
which presents some interesting challenges ([levels of
detail](https://en.wikipedia.org/wiki/Level_of_detail_(computer_graphics))
and
[generalization](https://en.wikipedia.org/wiki/Cartographic_generalization)).
The code doesn\'t do any layout of the graph itself, instead I\'ve used
the [yEd](https://www.yworks.com/products/yed) tool to compute the x,y
coordinates of the graph.

Since this exercise was inspired by a discussion of the [ASM Mammal
Diversity Database](https://www.mammaldiversity.org), the graph I\'ve
used for the demonstration above is the ASM classification of extant
mammals. I guess I need to solve the labelling issue fairly quickly!


I keep returning to the problem of viewing large graphs and trees, which means my hard drive has accumulated lots of failed prototypes. Inspired by some recent discussions on comparing taxonomic classifications I decided to package one of these (wildly incomplete) prototypes up so that I can document the idea and put the code somewhere safe.

Large graph viewer experiments

::: {style="float:right"}
:::

  
  
Continuing the saga of making sense of the mammal classification in
Wikipedia, I\'ve done a quick comparison with the Mammal Species of the
World (third edition) classification. MSW is the default taxonomic
reference used by [WikiProject
Mammals](http://en.wikipedia.org/wiki/Wikipedia:WikiProject_Mammals#Taxonomy).
I downloaded the MSW taxonomy [as a CSV
file](http://www.bucknell.edu/MSW3/) (warning, it\'s big), and wrote a
script to pull out the classification as a [GML
file](http://bioguid.info/demos/msw/msw.gml) (my preferred graph
format).  
  
Based on some earlier work with Gabriel Valiente, I wrote a simple
program that takes two trees and highlights the nodes in common to the
two trees. I then input into this program the MSW tree, and the largest
component of the [graph of Wikipedia
mammals](http://iphylo.blogspot.com/2009/08/mammal-tree-from-wikipedia.html).
The MSW tree has 13582 nodes, the Wikipedia tree has 6287. Note that
Wikipedia has more taxa than these 6287 nodes suggest, but they aren\'t
connected to the largest tree (often due to intermediate nodes in the
classification lacking a page in Wikipedia). The two trees have 4935
nodes in common (again, this number will be a little low, there are some
weird taxon names due to problems parsing Wikipedia).  
  
**MSW versus Wikipedia**  
Below is a the MSW classification with taxa in Wikipedia shown in red.  

::: {style="text-align:center;"}
![w-msw.jpg](http://lh4.ggpht.com/_Gct8lVAxKqQ/SpwEcr5t4bI/AAAAAAAAAhY/p3bXj9Xdh-k/w-msw.jpg?imgmax=800){border="0"
width="425" height="478"}
:::

  
  
\[Larger scale view
[here](http://bioguid.info/demos/msw/w/w-msw.html)\]  
  
The impression given is that most Wikipedia mammal pages are in MSW,
with some notable exceptions, including higher level taxa such as
[Afrotheria](http://en.wikipedia.org/wiki/Afrotheria), and extinct taxa
such as the
[Multituberculata](http://en.wikipedia.org/wiki/Multituberculata). Some
extant taxa are missing due to synonymy. For example, Wikipedia gives
the scientific name of [Anthony\'s
pipistrelle](http://en.wikipedia.org/wiki/Anthony%27s_pipistrelle) as
*Pipistrellus anthonyi*, whereas MSW has it as *Hypsugo anthonyi*.  

::: {style="font-size:12px"}
As an aside, Wikipedia pages often get muddled about parentheses around
taxonomic author names. The authority is in parentheses if the current
genus is not the original genus the species was placed. Hence,
*Pipistrellus anthonyi* (Tate, 1942) should actually be *Pipistrellus
anthonyi* Tate, 1942, as Tate originally described this taxon as a
species of *Pipistrellus* (see
[hdl:2246/1783](hdl.handle.net/2246/1783)). However, the name *Hypsugo
anthonyi* (Tate, 1942) does need parentheses.
:::

  
  
Some Wikipedia taxa also postdate the publication of MSW, such as
[Philander deltae](http://en.wikipedia.org/wiki/Philander_deltae) (see
[doi:10.1644/05-MAMM-A-065R2.1](http://dx.doi.org/doi:10.1644/05-MAMM-A-065R2.1)).  
  
  
**Wikipedia versus MSW**  
When we do the reverse comparison we see something rather different.  
  

::: {style="text-align:center;"}
![msw-w.jpg](http://lh3.ggpht.com/_Gct8lVAxKqQ/SpwFHQuJEZI/AAAAAAAAAhc/-0Pln00c3OQ/msw-w.jpg?imgmax=800){border="0"
width="425" height="438"}
:::

  
  
\[Larger scale view
[here](http://bioguid.info/demos/msw/m/msw-w.html)\]  
  
This is the MSW tree, coloured red where the MSW taxon has a page in
Wikipedia. There are big gaps, some of which are due to those pages
being in another component (in other words, many \"missing\" taxa do
have pages in Wikipedia, they are just not properly linked to the bigger
tree). MSW is also rich in subspecies, which tend to lack their own
pages in Wikipedia (possibly a good thing in the cases of taxa such as
pocket gophers).  
  
It would be nice to make these comparisons automatic, and develop tools
so that managing taxonomy in Wikipedia could be made easier.  


Continuing the saga of making sense of the mammal classification in Wikipedia, I've done a quick comparison with the Mammal Species of the World (third edition) classification. MSW is the default taxonomic reference used by WikiProject Mammals.

Messages de Rogue Scholar

Large graph viewer experiments

Comparing Wikipedia and Mammal Species of the World classifications