Just a quick not to make a link between David Shorthouse's post about taxonomic consensus and distributed version control (Taxonomic Consensus as Software Creation), and Galen Charlton's article in The Code4Lib Journal (Distributed Version Control and Library Metadata). Some interesting food for thought here. Both mention Git.

Stumbled across the cool AgeNames service, described on the stratigraphy.net blog. Agenames takes some text and extracts stratigraphic terms from text. For example, it will extract geological time periods from text. It's a geological equivalent of uBio's taxonomic name extraction services. It would be fun to play with this as part of the iPhylo project.

Nice paper by Robert Huber and Jens Klump has appeared in Computers & Geosciences entitled "Charting taxonomic knowledge through ontologies and ranking algorithms" (doi:10.1016/j.cageo.2008.02.016). The paper is not open access, but you can get some background from the post How TaxonRank works. Here's the abstract.

Lab Times has an interesting article by Ralf Neumann that analyses Europe's publications in evolutionary biology for the period 1996-2006. On page 36 there is a table of the 30 most cited authors in Europe, and the top five most cited papers.

Mauro Cavalcanti has released e-Species, "a taxonomically intelligent biodiversity search engine" written in Python that mimics much of the functionality of iSpecies. The project is open source, with a SourceForge page, although no files seem to be available yet.

Mauro Cavalcanti brought Chris Anderson's The End of Theory article in Wired to my attention, part of the July issue on "The End of Science".Of course, the end of science is hyperbole of the highest order (as, indeed, is the "end of theory"). It is also ironic that in the same issue Wired confess to having gotten 5 predictions of the death of something hopelessly wrong (including web browsers and online music swapping, no less). However, I

Hasan Jamil has released PhyQL, a visual system for querying phylogenetic information. To quote from the web site:There is also a YouTube screencast:I haven't had a chance to play with it yet. PhyQL was originally described by Jamil et al. "Querying phylogenies visually", BIBE 2001 (doi:10.1109/BIBE.2001.974405).

I've put the first version of "tvwidget" into Google Code. This is a HTML-only widget to display large evolutionary trees (you can see how my thoughts on how to do this unfolded by following my earlier posts starting with Visualising very big trees, Part V). tvwidget itself is a C++ program that takes a tree and generates the image tiles and Javascript for the viewer.

I've added a service to bioGUID that takes a PDF and attempts to extract latitude and longitude data from the PDF, returning those co-ordinates in either a Google Earth KML file, or in JSON format.

Resurrecting iSpecies after moving it to a new folder on one of my servers, and browsing popular searches, I keep coming across clearly erroneous distributions. FishBase seems a major culprit. For example, the common pandora Pagellus erythrinus is a marine fish, yet GBIF displays numerous occurrences in mainland Africa (dots with black centre on map below).What gives?