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.

Time to make some notes. I've been playing with using Sematic Mediawiki to create a database of taxonomic names, literature, specimens, sequences, and phylogenies. One challenge is to come up with simple ways to model these entities, in a way that makes both data entry simple and querying as simple as possible. Some things are straightforward. For example, a publication can be modelled like this: OK, I've ignored the attributes.

Last night BBC One aired David Attenborough's Charles Darwin and the Tree of Life, which featured a lovely "fly through" the tree of life: In conjunction with the TV show, the Wellcome Trust has launched the Interactive Tree of Life, a Flash-based view of the tree of life. There's also a blog about the project. Here's a demo of the tree: The tree looks very nice, and a lot of work has gone into it, but I am somewhat underwhelmed.

Well, not Darwin himself, exactly. The Evolution Directory (better known as "EvolDir") is a mailing list run by Brian Golding at McMaster University, Ontario. It's widely used by evolutionary biologists to post announcements about jobs, courses, conferences, software, and other topics of interest to the community.

One problem I've encountered in building a bibliographic database is the different ways author names are written. For example, for papers I've authored my name may be written as "Roderic D. M. Page" or "R. D. M. Page". Googling about this problem I came across Dror Feitelson's paper On identifying name equivalences in digital libraries.

Yes, I know this is ultimately a case of the "genius of and", but the more I play with the Semantic Mediawiki extension the more I think this is going to be the most productive way forward. I've had numerous conversations with Vince Smith about this. Vince and colleagues at the NHM have been doing a lot of work on "Scratchpads" -- Drupal based webs sites that tend to be taxon-focussed.

Test of google-code-prettify: class Voila { public: // Voila static const string VOILA = "Voila"; // will not interfere with embedded tags.

I learnt today that my Elsevier Challenge entry didn't make the final cut. This wasn't unexpected. In the interests of "open science" (blame Paulo Nuin) here is the feedback I received from the judges: I think this is a pretty fair evaluation of my entry. I was making a case for what could be done, rather than providing a specific bit of kit that could make this happen right now.

One advantage of flying to the US is the chance to do some reading. At Newark (EWR) I picked up Guy Kawasaki's "Reality Check", which is a fun read. You can get a flavour of the book from this presentation Guy gave in 2006. While at MIT for the Elsevier Challenge I was browsing in the MIT book shop and stumbled across "Google and the Myth of Universal Knowledge" by Frenchman Jean-Noël Jeanneney. It's, um, very French.

Stata Center. MIT Originally uploaded by Roderic Page Quick post about the Elsevier Challenge, which took place yesterday in the wonderful Stata Center at MIT. It was a great experience.