The rumour that Elsevier is buying Mendeley has been greeted with a mixture of horror, anger, peppered with a few congratulations, I told you so's, and touting for new customers:Here's some probably worthless speculation to add to the mix. Disclosure: I use Mendeley to manage 100,000's of references, and use the API for various projects.

Following on from my previous post bemoaning the lack of links between biodiversity data sets, it's worth looking at different ways we can build these links. Specifically, data can be tightly or loosely coupled. Tight coupling Tight coupling uses identifiers. A good example is bibliographic citation, where we state that one reference cites another by linking DOIs.

The journal Mycokeys has published the following paper:This paper contains a diagram that seems innocuous enough but which I find worrying:The nodes in the graph are "biodiversity megascience platforms", the edges are "cross-linkages and data exchange". What bothers me is that if you view biodiversity informatics through this lens then the relationships among these projects becomes the focus.

The Integrated Digitized Biocollections (iDigBio) project aims to advance digitising US biodiversity collections. They recently published a GUID Guide for Data Providers. In the PDF document I read this:My heart sank.

Say what you will about Elsevier, they are certainly exploring ways to re-imagine the scientific article. In a comment on an earlier post Fabian Schreiber pointed out that Elsevier have released an app to display phylogenies in articles they publish. The app is based on jsPhyloSVGand is described here.

Following on from the SVG experiments I've started to put some of the Javascript code for displaying phylogenies on Github. Not a repository yet, but as gists, little snippets of code. Mike Bostock has created http://bl.ocks.org/ which makes it possible to host gists as working examples, so you can play with the code "live".The first gist takes a Newick tree, parses it and displays a tree.

The following poem by David Maddison was published in Systematic Biology (doi:10.1093/sysbio/sys057) under a CC-BY-NC license.I think that I shall never seeA thing so awesome as the TreeThat links us all in paths of genesDown into depths of time unseen;Whose many branches spreading wideHouse wondrous creatures of the tide,Ocean deep and mountain tall,Darkened cave and waterfall.Among the branches we may findCreatures there of every

Quick test of an idea I'm playing with.

I'm trying to get my head around the data model used by ZooBank to store taxonomic names. To do this, I've built a graph for the species Belonoperca pylei described by Baldwin &

Quick note to self about possible way to using fuzzy matching when searching for taxonomic names. Now that I'm using Cloudant to host CouchDB databases (e.g., see BioStor in the the cloud) I'd like to have a way to support fuzzy matching so that if I type in a name and misspelt it, there's a reasonable chance I will still find that name. This is the "did you mean?" feature beloved by Google users.

Quick note on an experimental version of BioStor that is (mostly) hosted in the cloud. BioStor currently runs on a Mac Mini and uses MySQL as the database. For a number of reasons (it's running on a Mac Mini and my knowledge of optimising MySQL is limited) BioStor is struggling a bit.