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.

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.

James Rosindell's OneZoom tree viewer is out and the paper describing the viewer has been published in PLoS One (disclosure, I was a reviewer):Below is a video where James describes OneZoom.OneZoom is fun, and is deservedly attracting a a lot of attention. But as visually striking as it is, I confess I have reservations about fractal-based viewers. For a start they make it hard to get a sense of the relative size of taxonomic groups.

Robert M. Griffin (@GriffinEvo) has launched ProjectEvoMap. Rob explains:Below is a screen shot of part of the map.

tl;dr Readmill might be a great platform for shared annotation and correction of Biodiversity Heritage Library content.Thinking about accessing the taxonomic literature I started revisiting previous ideas.

We all have a "past" that we might not advertise widely, and my past includes flirting with panbiogeography.

Prompted by a conversation with Vince Smith at the recent Online Taxonomy meeting at the Linnean Society in London I've been revisiting touch-based displays of large trees. There are a couple of really impressive examples of what can be done. Perceptive Pixel I've blogged about this before, but came across another video that better captures the excitement of touch-based navigation of a taxonomy.

The release of the ENCODE (ENCyclopedia Of DNA Element) project has generated much discussion (see Fighting about ENCODE and junk). Perhaps perversely, I'm more interested in the way Nature has packaged the information than the debate about how much of our DNA is "junk." Nature has a website (http://www.nature.com/encode/) that demonstrates the use of "threads" to navigate through a set of papers.

Quick note that as much as I like that the Biodiversity Heritage Library is using DOIs, they are generating them for publications that already have them (or are acquiring them from other sources). For example, here are the two DOIs for the same article (formatted using the DOI Citation Formatter), one from BHL and one from the Smithsonian:The BHL DOI resolves to a page in BHL, the other DOI resolves to the a page in the Smithsonian Digital