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.

I've submitted my entry for the Elsevier Grand Challenge. The paper describing the entry is available from Nature Precedings (doi:10.1038/npre.2008.2579.1). The web site demo is at http://iphylo.org/~rpage/challenge/www/. I'm now officially knackered.

One byproduct of playing with the Challenge Demo is that I come across some rather surprising results.

I've put the my Elsevier Challenge demo online. I'm still loading data into it, so it will grow over the next day or so. There's also the small matter of writing a paper on what's under the hood of the demo. Feel free to leave comments on the demo home page. For some example of what the project does, take a look at Mitochondrial paraphyly in a polymorphic poison frog species (Dendrobatidae;

One of the things I've struggled with most in putting together a web site for the challenge is how to summarise that taxonomic content of a study. Initially I was playing with showing a subtree of the NCBI taxonomy, highlighting the taxa in the study. But this assumes the user is familiar with the scientific names of most of life. I really wanted something that tells you "at a glance" what the study is about.

Elsevier have released this video about the challenge, featuring a few of the contestants. I couldn't get my act together in time to send anything useful, and having seen the 16 gigabytes song (full version here), I'm glad I didn't -- there's just no way I could compete with Michael Greenacre and Trevor Hastie.

Bibliographic coupling is a term coined by Kessler (doi:10.1002/asi.5090140103) in 1963 as a measure of similarity between documents. If two documents, A and B, cite a third, C, then A and B are coupled. I'm interested in extending this to data, such as DNA sequences and specimens. In part this is because within the challenge dataset I'm finding cases where authors cite data, but not the paper publishing the data.

As part of the slow rebuild of bioguid.info, and as part of the Challenge, I've started making an OpenURL resolver for specimens. Partly this is just a wrapper around DiGIR providers, but it's also a response to the lack of GUIDs for specimens.

Just to provide a sense of how much data I want to analyse for the Challenge, I have the XML, PDF, and images for 1687 articles from Molecular Phylogenetics and Evolution to play with.