The LSID discussion has flared up (again) on the TDWG mailing lists. This discussion keeps coming around (I've touched on it here and here), this time it was sparked by the LSID SourceForge site being broken (the part where you get the code is OK). Some of the issues being raised include: Nobody uses LSIDs except the biodiversity informatics crowd, have we missed something?

The e-Biosphere online forum has a topic entitled Why open source code?

The e-Biosphere meeting in London June 1-3 has announced a The e-Biosphere 09 Informatics Challenge: The "real time" aspect of the challenge seems a bit forced.

My British Library Talk Science presentation is now available online as a podcast.

Here's the video of my talk at the NHM (courtesy of Vince Smith). Going Digital - by Rod Page from Vince Smith on Vimeo.

Busy day yesterday, giving two talks, one at The Natural History Museum, one at the British Library. Slides for the NHM talk are below.

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.