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 see A thing so awesome as the Tree That links us all in paths of genes Down into depths of time unseen; Whose many branches spreading wide House wondrous creatures of the tide, Ocean deep and mountain tall, Darkened cave and waterfall.
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. It's also gathered a lot of cruff as I've worked on ways to map article citations to the rather messy metadata in BHL.
Benoît Fontaine et al. recently published a study concluding that average lag time between a species being discovered and subsequently described is 21 years. The paper concludes: This is a conclusion that merits more investigation, especially as the title of the paper suggests there is an appalling lack of efficiency (or resources) in the way we decsribe biodiversity.
CrossRef have released CrossRef Metadata Search a nice tool that can take a free-form citation and return possible matches from CrossRef's database. If you get a match CrossRef can take the DOI and format for you it in a variety of styles using DOI content negotiation. If, like me, you spend a lot of time trying to find DOIs (and other identifiers) for articles by first parsing citations into their component parts, then this is good news.
It is well known that phylogeny databases such as TreeBASE capture a small fraction of the published phylogenies. This raises the question of how to increase the number of trees that get archived.