Continuing the theme of visualising phylogenies, one thing which strikes me is the parallel between genome browsers that display annotation "tracks" (such as the UCSC Genome Browser) and illustrations of "chronograms" with geological periods and accompanying data, such as sea levels, isotope levels, etc. In my haste I couldn't find an example with a sea-level track, but I know they exist. The chronogram at right comes from Steppan et al.

VLDB2005 has some interesting papers. One which caught my eye is Efficiently Processing Queries on Interval-and-Value Tuples in Relational Databases [PDF] by Enderle et al. Why?

Amber Frid-Jimenez: has a really nice page showing document icons that reflect the words contained in the document. Neat idea, and has a lot of potential. One obvious extension to phylogenetics would be to represent the taxonomic coverage in a similar style, so people could very quickly find studies on related sets of organisms simply by browsing.

I've updated my extension to resolve LSIDs in Firefox so that it works with version 1.5.0.1 (the most recent version of Firefox). The extension is available from Mozdev. It may take a little while for the mirrors to update with the new version, so if you get a "404" when trying to download, you may need to come back later. IBM's LSID project have their own Firefox extension LSID Launchpad for Firefox, which is a lot slicker than mine.

Having read Rob McCool's articles on Rethinking the Semantic Web (brought to my attention by Bob McMorris' comment on my earlier post on globally unique identifiers), I think he makes very interesting points, but they are not all relevant to whether biodiversity informatics adopts RDF.

I attended the TDWG-GUID workshop on Global Unique Indenitifers (GUIDs) held at NESCent, which has issued a report. Essentially, the aim of this work is to deploy globally unique identifiers for digital objects in biodiversity informatics, such as taxon names, specimen records, images, etc. The workshop settled on LSIDs (Life Science Identifiers), which is a sensible choice.

Yet more cool stuff from information aesthetics, this time a comparison of search results from Google and Yahoo. Given my own talk on Google versus Yahoo and the death of taxonomy?, this page certainly caught my eye.

I came across this version of treemaps a little while ago, but this post on information aesthetics reminds me to add this to the list of cool things that are worth thinking about when considering how to visualise the Tree of Life. Isn't it gorgeous?

On Saturday I gave a short invited talk at the CIPRES all hands meeting in Austin. Not sure if I'll be invited back after this, but I think it was worth saying a few things that somebody, somewhere should be saying. You can grab the PowerPoint slides here.

How does a person who is not expert in a group of organisms find a good phylogeny to use for their work? Think of somebody interested in animal behaviour who needs a tree for their birds of fish. Ignoring the answers "ask a systematist" or (even worse) "become a systematist and build the tree themselves", how do we answer this query?

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.