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.
My paper "Taxonomic names, metadata, and the Semantic Web" has appeared in Biodiversity Informatics .
Well, turns out Bill's not the only one putting trees on Google Earth. Declan Butler pointed me to Ogle Earth, where there is a teaser of some work on guiology.
The penny just dropped (duh!). Having mentioned Bill Piel's very cool visualisation of phylogenies on Google Earth what about the other cool use of Google Earth in biology, namely Declan Butler's displays of the march of avian flu? Instead of standard diagrams like this one from the Ruben Donis' paper in Emerging Infections Diseases : why not take phylogenies for avian flu virus and add them to the data Declan is displaying?
Bill Piel has created a cool tool for creating KMZ files of phylogenies for Google Earth. From the web site: Google Earth (available for Windows and Mac OS X) is opening up all sorts of possibilities for biodiversity informatics (ants being one of the first examples). What is cool about Bill's work is that it departs from simple locality records.
Pyramica boltoni Originally uploaded by Roderic Page. Fussing around with ants, I stumbled across this paper (doi:10.1653/0015-4040(2006)89[1:PBANSO]2.0.CO;2) (if the DOI doesn't work, try this link), which describes a new species, Pyramica boltoni . This paper is Open Access, so the question arises, how do I get it into a triple store?
So, when I started this blog I promised to write something about phyloinformatics, and the goal of a phylogenetic database. I've been playing around with various ideas, some of which have made it online, but most remain buried on various hard drives until they get written up to the state they are useable.
My Taxonomic Search Engine is back online (mostly). This tool to search multiple databases for scientific names was another casualty of hacking. Having been developed under PHP 4, it needed some work to play nice with PHP 5. The changes were minor, and mainly concerned changes in code involving XPath and XSLT. I've commited these changes to SourceForge.