University of Glasgow

Roderic Page

Last week I was at the NSF \"Assembling, Visualising and Analysing the
Tree of Life\" Ideas Lab, run by
[KnowInnovation.com/](http://www.knowinnovation.com/). It was an
interesting experience, essentially a structured week of brainstorming
ideas.  
  
One thing I came away with is the feeling that our notions of the \"tree
of life\" are fuzzy, contradictory, and often probably unobtainable.
It\'s tempting to imagine all sorts of wonderful visualisations, and
loose sight of building something that is useful. Perhaps it\'s time
instead to think of \"Tree of Life version 0.1\".  
  
Imagine taking the NCBI taxonomy as a starting point. Yes it\'s
incomplete, and has almost no fossils, but it\'s freely available and
linked to a lot of data. Let\'s use a Google Maps-like viewer along the
lines I [explored earlier this
year](http://iphylo.blogspot.com/2011/03/zooming-large-tree-now-with-thumbnails.html).  
  
Then add annotation \"tracks\" to the tips. As a first pass these could
be taken from the [NCBI
LinkOut](http://www.ncbi.nlm.nih.gov/projects/linkout/) service, such as
the NCBI-Wikipedia mapping <http://iphylo.org/linkout>.  
  
![Ncbi
1](http://lh3.ggpht.com/-me96WuCex7s/Tll7STe0lrI/AAAAAAAAA-Y/T1Nqw-JZlYk/ncbi-1.png?imgmax=800 "ncbi-1.png"){style="display:block; margin-left:auto; margin-right:auto;"
border="0" width="400" height="410"}  
  
The NCBI tree is a classification rather than a phylogeny, so we could
add greater phylogenetic content by linking to phylogenetic databases,
such as [TreeBASE](http://www.treebase.org) and
[PhyLoTA](http://phylota.net). Imagine clicking on a node in the NCBI
taxonomy and seeing a display of all the phylogenies centred on that
node:  
  
![Ncbi
02](http://lh5.ggpht.com/-lAqpz4FgoEA/Tll7TUcuhpI/AAAAAAAAA-c/Hg3jDIdlSGw/ncbi-02.png?imgmax=800 "ncbi-02.png"){style="display:block; margin-left:auto; margin-right:auto;"
border="0" width="400"}  
  
Now we have a way to navigate a large tree, view annotations, and
display phylogenetic trees. All of this could be done fairly easily. The
key is to have services keyed by the NCBI tax_id used to identify nodes
on the tree.  
  
Among the next steps would be to add additional \"tracks\", perhaps
based on curated links analogous to the wiki-based NCBI-Wikipedia
mapping. For example, very basic habitat data (marine or terrestrial)
could be added, or geography, or host relationships (could be based in
part on the data already in GenBank).  
  
Given that the NCBI tree continues to grow, subsequent versions could be
released as the tree changes. Or we could \"fork\" the NCBI tree and
start to refine it based on phylogenetic information, and add taxa that
aren\'t in the genome databases (these taxa will need consistent
identifiers so we can map annotations on to them as well). Perhaps we
could use something like
[Git](http://en.wikipedia.org/wiki/Git_(software)) to manage this tree,
and to handle the necessary merging of updated versions of the NCBI
tree. People could edit the tree, or indeed fork it and come up with
their own.  
  
![Logo tmp reasonably
small](http://lh6.ggpht.com/-Lj8I4ebWeao/Tll7UA88ybI/AAAAAAAAA-g/cDWvJYHkz0c/logo_tmp_reasonably_small.png?imgmax=800 "logo_tmp_reasonably_small.png"){border="0"
width="128" height="128" style="float:right;"}There are lots of ways to
visualise trees (see [TreeVis.net](http://treevis.net) for some great
examples), but what I\'m after is a tool that is useful, that gives us a
sense of what we know and what we don\'t. I suspect that one of the
reasons we\'ve struggled with visualising the tree of life is that there
are lots of different notions about what it\'s for. In this case, I want
a tool to navigate data about organisms, one that we can easily add
annotations too.  
  
  


Last week I was at the NSF "Assembling, Visualising and Analysing the Tree of Life" Ideas Lab, run by KnowInnovation.com/. It was an interesting experience, essentially a structured week of brainstorming ideas.One thing I came away with is the feeling that our notions of the "tree of life" are fuzzy, contradictory, and often probably unobtainable.

Publicaciones de Rogue Scholar

Tree of Life 0.1 - annotating the NCBI taxonomy