From the "wouldn't it be cool if" department, one thing I've often thought would be very handy would be a web site that listed sequences in GenBank that were known (or suspected) to be problematic (especially sequences thought to have been misidentified). What I'd like to see is a site called something like "GenBank Watch" (a ripe off of Search Engine Watch) where this information is recorded.

Bone Rooms, Bird Bodies, and Biodiversity Informatics is an old article now, but it's a nice summary of what biodiversity informatics is about.

One of the first concrete things to emerge from this research is a paper with Gabriel Valiente entitled An edit script for taxonomic classifications. The basic idea is to look for matching subtrees in two classifications (labelled rooted trees), then compute a script that transforms one tree into another.

Minor technical matter, but I've discovered that the news aggregator for Drupal doesn't read Atom feeds, such as those provided by Blogger, and hence the Atom feed for iPhylo (this blog) did show up in the Systematic Biology web site (which uses Drupal). A quick Google revealed this solution, and so FeedBurner to the rescue. The iPhylo feed on the Systematic Biology site is provided by FeedBurner, not directly from IPhylo.

The IEEE SMC Society's eNewsletter has short article on work in Jason Wang's group on struture-base queries.

Wednesday December 7th I gave a talk at the Systematics Association's AGM in London, with the slightly tongue in cheek title Google, Yahoo, and the end of taxonomy?. It summarises some of the ideas that lead me to create iSpecies.org. For fun I've made a Quicktime movie of the presentation. Sadly there is no sound. Be warned that if you are offended by even mild nudity, this talk is not for you.

iSpecies.org is a little toy I created to investigate how easy it would be to create a web page for each species of organism "on the fly" by using web services. That is, querying remote services, such as NCBI, Yahoo Image Search, and Google Scholar, and assembling the results into a single page.

When Europe was seriously considering a Tree of Life effort to match the NSF ATOL effort (for some background and a hint of politics involved, read the letter to Science by Vincent Savolainen and Mark W. Chase of Kew Gardens doi:10.1126/science.302.5652.1894a), I assembled a web page of various links that I felt were of interest. The EU's TOL effort collapsed, but the page lives on.

This is an area which has received a lot of attention. For some examples see Rebecca Shapley's Tree of Life Gallery, and the information aesthetics post. I've used hyperbolic trees in my (now rather old) Glasgow Taxonomy Name Server. To be honest, I've never felt that we've hit on a truly compelling way to visualise large trees.

For a short, but reasonably technical sumary of what I think the issues are, please read this "Technical Report", which I presented at the Workshop on Database Issues in Biological Databases (DBiBD) in Edinburgh in January 2005. This document is itself based on a BBSCR grant proposal which was funded. Here is the abstract.

iPhylo is where I hope to write (or perhaps more correctly, "brain dump") ideas on phyloinformatics, with special reference to my current hobby-horse -- the lack of a decent database of evolutionary trees. As well as thoughts, ideas, suggestions, and the occasional rant, I hope to be able to report on some progress along the way. Stay tuned...