Nothing like a little hubris first thing Monday morning...After various experiments, such as a triple store for ants (documented on the Semant blog) and bioGUID (documented on the bioGUID blog), I'm starting from scratch and working on a "database of everything". Put another way, I'm working on a database that aggregates metadata about specimens, sequences, literature, images, taxonomic names, etc.
Time for a rant. I spend a lot of time fussing with records from sources such as GenBank and DiGIR providers, trying to extract strings that might be identifiers, with a view to linking sequences to specimens (and thus to localities), sequences to publications, publications to GUIDs, etc.
Spent the week in Portugal at the EDIT Future Trends of Taxonomy meeting, held at the View from cave, at the beach in front of the Hotel Tivoli Almansor, Carvoeiro.
Quick note to self, having stumbled on the Wikipedia page on transitive reduction. Given a graph like this:the transitive reduction is:Note that the original graph has an edge a -> d, but this is absent after the reduction because we can get from a to d via b (or c). What's the point?
Paulo Nuin recently interviewed me for his Blind.Scientist blog. The interview is part of his SciView series.
One side effect of the trend towards digitising everything is that stuff one forgot about (or, perhaps, would like to forget about) comes back to haunt you. My alma mater , the University of Auckland is digitising theses, and my PhD thesis "Panbiogeography: a cladistic approach" is now online (hdl:2292/1999). Here's the abstract:1990. Ah, happy days...
Slides from the recent Phyloinformatics workshop in Edinburgh are now online at the e-Science Institute. In case the e-Science Institute site disappears I've posted the slides on slideshare. | View | Upload your ownHeiko Schmidt has also posted some photos of the proceedings, demonstrating how distraught the particpants were that I couldn't make it.
Interesting paper in PLoS ONE (doi:10.1371/journal.pone.0001124) on the quality of data housed in GBIF. The study looked at 630,871 georeferenced legume records in GBIF, and concluded that 84% of these records are valid.
Really just a shameless attempt to get one over David Shorthouse, but there has been some buzz about Very High Resolution X-Ray Computed Tomography (VHR-CT) of a fossil of Cenotextricella simon .The paper describing the work is in Zootaxa (link here). Zootaxa is doing great things for taxonomic publishing, but they really need to get some sort of stable identifier set up. Linking to ZooTaxa articles is not