As part of the TreeBASE name mapping exercise, I've come across some interesting names, such as "Diplura". This is a homonym, meaning that more than one taxon has this name. This can complicate life somewhat.

As noted on the Society of Systematic Biology (SSB) web site, the journal Phyloinformatics has disappeared. It only published eight papers, but this still represents lost effort, and some of the papers are highly relevant to issues I'm interested in. Luckily, with the help of the Internet Archive's "wayback machine", and a PDF sent by Paul Sereno, I've put all the PDFs on the SSB web site. You can get them here.

Molecular Phylogenetics and Evolution carries two articles debating the application of names to trees, which reflects tensions between two codes of nomenclatures (ICZN and Phylocode). Alain Dubois (doi:10.1016/j.ympev.2006.06.007 and David Hillis (doi:10.1016/j.ympev.2006.08.001) present rather different views.

Just wanted to write this example down before I loose it. Browsing Bill Piel's trees in Google Earth, and was looking at Lee et al.'s paper (doi:10.1111/j.1365-294X.2005.02707.x) on Physalaemus pustulosus . Searching in iSpecies.org lead to records in GenBank, whereupon I stumble on the fact that in GenBank it is Engystomops pustulosus (Taxonomy ID: 76066). Following up the reference on the NCBI taxonomy page, I find a PDF of

Stumbled across New Infrastructures for Knowledge Production: Understanding E-science while writing about TAXACOM on the iSpecies blog. The book is edited by Christine Hine, who has an article entitled The politics and practice of accessibility in systematics, which I think will be part of Past, Present & Future of Research in the Information Society.

I've now put a simple demo of the PygmyBrowse tree browser up here. It's a simple toy just to demo the idea.

I've previously bemoaned the lack of a decent way to display and navigate through phylogenies. Ryen White, a graduate of Glasgow's Computer Science department and now at Microsoft Research is coauthor of of cool paper on viewing large trees in small spaces.

EditGrid is an online collaborative spreadsheet tool that I stumbled across via Ogle Earth. It strikes me thjat this could be a way to create phylogenetic data sets collaboratively. As a quick test I grabbed the Vertebrates example file that comes with MacClade, exported the NEXUS file as a table, opened it in Excel, then uploaded the Excel file to EditGrid. You can see the results here.

One of my (forever) ongoing projects is to map taxon names in TreeBASE to names in external databases (such as uBio) as a way of checking that the names are correct, adding the ability to handle synonyms, and hierarchical queries (see my earlier post for more details). Now, many names in TreeBASE aren't in any of the major name databases (fossils seem particularly poorly supported), which means hunting on Google for the name.

Just finished reading Small Pieces Loosely Joined. It's a fabulous essay on the nature of the Web. The more I read it the more it confirms my fear that most people talking about biological taxonomy and biodiversity on the Web simply don't "get" the Web. Adopting the Web successfully will require a willingness to accept error, ambiguity, and downplaying "expertise" and "authority". It will be interesting to see what happens.

I gave a talk today ("Dude, where's my tree?") at the Evolution 2006 meeting at Stony Brook. It was intended as a somewhat tongue-in-check overview of some issues concerning TreeBASE, and broader areas of biodiversity informatics, making use of ants as an example (see my SemAnt project). Michael Donoghue took me aside after the talk and made some interesting points.