The TreeBASE team have announced that TreeBASE II has been released. I've put part of the announcement on the SSB web site. Given that TreeBASE and I have history, I think it best to keep quiet and see what others think before blogging about it in detail. Plus, there's a lot of new features to explore. Take it for a spin and see what you think.

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.

I'm revisiting the idea of building a wiki of phylogenies using Semantic Mediawiki. One problem with a project like this is that it can rapidly explode.

At the start of this week I took part in a biodiversity informatics workshop at the Naturhistoriska riksmuseets, organised by Kevin Holston. It was a fun experience, and Kevin was a great host, going out of his way to make sure myself and other contributors were looked after. I gave my usual pitch along the lines of "if you're not online you don't exist", and talked about iSpecies, identifiers, and wikis.

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.

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.

Hasan Jamil has released PhyQL, a visual system for querying phylogenetic information. To quote from the web site: There is also a YouTube screencast: I haven't had a chance to play with it yet. PhyQL was originally described by Jamil et al. "Querying phylogenies visually", BIBE 2001 (doi:10.1109/BIBE.2001.974405).

In an earlier post I described the TBMap database (doi:10.1186/1471-2105-8-158), which contains a mapping of TreeBASE taxon names onto names in other databases. While this is one step towards making it easier to query TreeBASE, what I'd really like is to link the data in TreeBASE to sources such as GenBank and specimen databases.

My paper on mapping TreeBASE names to other databases is out as provisional PDF on the BMC Bioinformatics web site (doi:10.1186/1471-2105-8-158 -- not working yet). The abstract: The TBMap web site needs some work, it's really only intended to document the mapping. Once I've tweaked and updated the mapping, I hope to use it in my forthcoming all-sining, all-dancing, phylogeny database...