University of Glasgow

Roderic Page

I\'ve made some progress on a [wiki of
phylogenies](http://iphylo.blogspot.com/2009/09/towards-wiki-of-phylogenies.html).
Still much to do, but here are some samples of what I\'m trying to do.  
  
First up, here\'s an example of a publication
<http://iphylo.org/treebase/Doi:10.1016/j.ympev.2008.02.021>:  

::: {style="text-align:center;"}
![wiki1.png](http://lh5.ggpht.com/_Gct8lVAxKqQ/S6AI2eevujI/AAAAAAAAAng/QlMt0a0NxII/wiki1.png?imgmax=800){border="0"
width="400" height="332"}
:::

  
In addition to basic bibiographic details we have links to GenBank
sequences and a phylogeny. The sequences are georeferenced, which
enables us to generate a map. At a glance we see that the study area is
central America.  
  
This study published the following
[tree](http://iphylo.org/treebase/Tree5692):  

::: {style="text-align:center;"}
![wiki2.png](http://lh6.ggpht.com/_Gct8lVAxKqQ/S6AKCLgVuPI/AAAAAAAAAno/9FbFnoJmQXU/wiki2.png?imgmax=800){border="0"
width="400" height="298"}
:::

  
The tree is displayed using my
[tvwidget](http://code.google.com/p/tvwidget/). A key task in
constructing the wiki is mapping labels used in TreeBASE to other
taxonomic names, for example, those in the NCBI taxonomy database. This
is something I first started working on in the
[TbMap](http://linnaeus.zoology.gla.ac.uk/~rpage/tbmap/) project
([doi:10.1186/1471-2105-8-158](http://dx.doi.org/10.1186/1471-2105-8-158)).
In the context of this wiki I\'m explicitly mapping TreeBASE taxa to
NCBI taxa. Taxa are modelled as \"namestrings\" (simple text strings),
OTUs (TreeBASE taxa), and taxonomic concepts (sets of observations or
taxa). For example, the [tree](http://iphylo.org/treebase/Tree5692)
shown above has numerous samples of the frog *Pristimantis ridens*, each
with a unique label (namestring) that includes, in this case, voucher
specimen information (e.g., \"Pristimantis ridens La Selva AJC0522
CR\"). Each of these labels is mapped to the NCBI taxon [*Pristimantis
ridens*](http://iphylo.org/treebase/Ncbi:228422).  
  
One thing I\'m interested in doing is annotating the tree. Eventually I
hope to generate (or make it easy to generate) things such as [Google
Earth
phylogenies](http://iphylo.blogspot.com/2007/06/google-earth-phylogenies.html)
(via georeferenced sequences and specimens). For now I\'m playing with
generating nicer labels for the terminal taxa. As it stands if you
download the original tree from TreeBASE you have the original
study-specific labels (e.g., \"Pristimantis ridens La Selva AJC0522
CR\"), whereas it would be nice to also have taxonomic names (for
example, if you wanted to combine the tree or data with another study).
Below the tree you\'ll see a NEXUS NOTES block with the \"ALTTAXNAMES\"
command. The program [Mesquite](http://mesquiteproject.org/) can use
this command to enable users to toggle between different labels, so that
you can have either a tree like this:  

::: {style="text-align:center;"}
![wiki3.png](http://lh4.ggpht.com/_Gct8lVAxKqQ/S6AQ4ZWGGhI/AAAAAAAAAnw/RzJSeJF1BAk/wiki3.png?imgmax=800){border="0"
width="400" height="295"}
:::

  
or a tree like this:  

::: {style="text-align:center;"}
![wiki4.png](http://lh5.ggpht.com/_Gct8lVAxKqQ/S6AQ9V6XhlI/AAAAAAAAAn0/lCcIp2h93aU/wiki4.png?imgmax=800){border="0"
width="380" height="337"}
:::


I've made some progress on a wiki of phylogenies. Still much to do, but here are some samples of what I'm trying to do.  First up, here's an example of a publication http://iphylo.org/treebase/Doi:10.1016/j.ympev.2008.02.021:    In addition to basic bibiographic details we have links to GenBank sequences and a phylogeny. The sequences are georeferenced, which enables us to generate a map.

Progress on a phylogeny wiki

I\'m slowing trying to get phylogenies into the [wiki that I\'m playing
with](http://iphylo.blogspot.com/search?q=wiki). Here\'s an early
example, the TreeBASE tree
[T6002](http://itaxon.org/wikidev/TreeBASE:T6002), from the study [A
Phylogenomic Study of Birds Reveals Their Evolutionary
History](http://itaxon.org/wikidev/Doi:10.1126/science.1157704). The
tree is displayed using my
[tvwidget](http://code.google.com/p/tvwidget/). Below are listed the
OTUs in the tree in a crude table. The idea is that this table will
contain a mapping between OTU labels and taxa. For example, one OTU is
labelled \"Diomedea nigripes\". This links to the page for [Diomedea
nigripes](http://itaxon.org/wikidev/Diomedea_nigripes), which provides
some basic information on this name, including the statement that ITIS
regards the correct name for this bird to be [Phoebastria nigripes
(Audubon,
1839)](http://itaxon.org/wikidev/Phoebastria_nigripes_%28Audubon%2C_1839%29).
The table on the [page showing the
tree](http://itaxon.org/wikidev/TreeBASE:T6002) displays this
information as well.  
  
[![](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg5RJYudW6EXf80aTgJD9pwj5-rald4bEUIHHHU-K101-bJnQ7-M_S884FSUSgTz36AmclNFC3L53n8euZCKKMvkW7oEuK3ZYKzXqpsOoYbUNildW38B4TYslLuLLZ1WRTjF_0h/s400/T6002.png){#BLOGGER_PHOTO_ID_5310038155670822898
style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;width: 400px; height: 283px;"
border="0"}](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg5RJYudW6EXf80aTgJD9pwj5-rald4bEUIHHHU-K101-bJnQ7-M_S884FSUSgTz36AmclNFC3L53n8euZCKKMvkW7oEuK3ZYKzXqpsOoYbUNildW38B4TYslLuLLZ1WRTjF_0h/s1600-h/T6002.png){onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}"}  
  
This is all terribly incomplete and crude, but it gives a sense of where
this is going. The plan is to import in bulk the trees and the mappings
(from, say, [TBMap](http://darwin.zoology.gla.ac.uk/~rpage/tbmap)), as
well as the names themselves, and associated literature (including the
TreeBASE studies) and then the trees will be embedded in richer data
about the taxa.


I'm slowing trying to get phylogenies into the wiki that I'm playing with. Here's an early example, the TreeBASE tree T6002, from the study A Phylogenomic Study of Birds Reveals Their Evolutionary History. The tree is displayed using my tvwidget. Below are listed the OTUs in the tree in a crude table. The idea is that this table will contain a mapping between OTU labels and taxa.

Messaggi di Rogue Scholar

Progress on a phylogeny wiki

Phylogenies in a wiki