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.

It's Friday, so time for some random, half-baked ideas. Imagine that we have a database of evolutionary trees, and these overlap for a set of taxa that we are interested in. How do we summarise these trees? One approach is to make a supertree. It would be useful to display the subtrees that went into making this supertree, if only to give an idea of how much they agree with the supertree. How to do this?

Rutger Vos asked on Twitter "What would people want/expect from taxon searching on TreeBASE?". This is a good question, and one which motivated the work I did on TBMap (see doi:10.1186/1471-2105-8-158), which developed a mapping between TreeBASE taxa and other databases. In that paper I published a table showing the effectiveness of string and hierarchical queries of TreeBASE.

In the wiki examples I've been developing I've been trying to model names using the TDWG LSID vocabularies, particularly TaxonName. Roger Hyam has obviously put a huge amount of work into developing these, and they handle just about everything I need. However, I think that there's one thing missing, namely a way to express the logical relationship between the parts of a multinomial taxonomic name.

As part of my Quixotic attempt to construct a wiki of taxonomic names, I'm building a database of names and links. My current plan is to seed this with the NCBI taxonomy. What I want to do is flesh out the NCBI taxonomy with authorities and links to the original literature. At the moment the NCBI taxonomy is almost "nude", lacking links to the literature behind the names.

Vince Smith has produced a nice flyer for my forthcoming talk at The Natural History Museum on March 17th (11-12). It will be a busy day as I'm also talking at the British Library in the evening (6pm - 8:30pm), for which Sarah Kemmitt has produced a flyer, and set up a discussion forum on Nature Network. With all this effort going into the artwork, I'd better actually come up with something useful to say.

Reading a recent TAXACOM thread (Species Pages - purpose) my sense is that some people are arguing that "species pages" would be time consuming to create, aren't much good for taxonomists (to quote Mike Dallwitz "In brief, to make simplified and attractive information about taxa easily available to casual users?"), and nobody gets credit for making them.

Another issue I'm trying to get my head around is how to deal with labels in phylogenies. These can be any number of things, such as GenBank sequences, specimen codes, taxon names, abbreviations of taxon names, laboratory codes, etc. Here's my quick attempt to model these: This sketches various levels of indirection to go from a label in a tree to a taxon name.

I rather skirted around the notion of "taxonomic concepts" in the previous post, partly because it's easy to end up with trying to have a concept for each utterance every made by a taxonomist, and that doesn't seem, er, scalable. So, I have a more limited view of a taxonomic concept, namely a name attached to some data.

Modelling taxa is a bit trickier. I've sketched my ideas for distinguishing name strings and taxonomic names earlier. That's the easy stuff. What about "taxonomic concepts" and "OTUs"? As a first pass, I'm looking at linking taxon names to classifications via GUIDs.