Progress on a phylogeny wiki

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. At a glance we see that the study area is central America.

This study published the following tree:

The tree is displayed using my 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 project (doi: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 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.

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 (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 can use this command to enable users to toggle between different labels, so that you can have either a tree like this:

or a tree like this:

Phylogenies in a wiki

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. For example, one OTU is labelled "Diomedea nigripes". This links to the page for 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). The table on the page showing the tree displays this information as well.



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), 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.