My short note on "Wikipedia as an Encyclopaedia of Life" has appeared in Organisms Diversity &

Being in an unusually constructive mood, I've spent the last couple of days playing with the TreeBASE II API, in an effort to find out how hard it would be to replace TreeBASE's frankly ghastly interface.After some hair pulling and bad language I've got something to work. It's very crude, but gives a glimpse at what can be done.

The open access taxonomic journal ZooKeys has published a special issue with four papers, each available in HTML, PDF, and XML, the later being extensively marked up. Penev et al. ("Semantic tagging of and semantic enhancements to systematics papers: ZooKeys working examples", doi:10.3897/zookeys.50.538) describes the process involved in creating these XML files.

Now that I'm back in Glasgow, albeit rather jet-lagged, time for a quick summary of the first iEvoBio meeting, held at the Evolution meetings. I thought the meeting went very well, but perhaps I should leave that judgement to others.

In a moment of madness brought on by trying to make sense of 10 Mb of conference schedule for Evolution 2010, I extracted the text from the schedule and created a series of crude iCal files that I can add to my iCal calendar on my Mac (and hence sync to my iPhone). This way I can set reminders of specific talks I want to see.I'm making these ical files available here, on the understanding that you can use them entirely at your own risk (some

Having made a first stab at mapping NCBI taxa to Wikipedia, I thought it might be fun to see what could be done with it. I've always wanted to get quantum treemaps working (quantum treemaps ensure that the cells in the treemap are all the same size, see my 2006[!] blog post for further description and links). After some fussing I have some code that seems to do the trick.

The 52,956 links from NCBI to Wikipedia that I've been busy creating are now "live." If you go to a NCBI taxon such as Sphaerius you'll see something like this:Clicking the "Wikipedia" link takes you to the Wikipedia page for this taxon.

PLoS recently announced a dedicated iPad app, that covers all the PLoS Journals, and which is available from the App Store. Given the statement that "PLoS is committed to continue pushing the boundaries of scientific communication" I was expecting something special.

In an earlier post I discussed linking NCBI taxonomy to Wikipedia. One way to tackle this is to add NCBI Taxonomy ID to Wikipedia pages. I reopened the case for adding the Taxonomy IDs to the Taxobox on each taxon page, but this met with substantial resistance.

In an earlier post I expressed my amazement that my venerable Nexus Data Editor (NDE) still had users, meaning I had to rebuild the installer so users could install NDE on Windows Vista. Now, Thomas Hauser has gone one better and created an installer for Mac OS X. Given that NDE is a Windows-only program, this is quite a feat. Thomas uses Mike Kroenenberg's (@k3erg) WineBottler to create a version of NDE that can be run on a Mac.

One of the potentially powerful features of TreeBASE II is availability of a RDF version of a study. This means that, in principle, one could take the RDF for a TreeBASE study, combine it with RDF from other sources, and generate a richer view of a particular study.