My latest tweak to BioNames is to add colour to the phylogenies. Terminal nodes with the same name are labelled with the same background colour. For example, here is a tree for fiddler and ghost crabs: The colours make it easier to see that this tree has a mixture of a few sequences from divergent taxa, and a lot of sequences from the same taxa. Note that you can now also download the SVG drawing of the tree.

In 2011 I wrote a short post about DeepDyve, a service where you could rent access to an article. DeepDyve has launched a "5-Minute Freemium" service where you can view an article online for 5 minutes, for free. You have to log in, either with DeepDyve or using Facebook, but no actual money changes hands. If you want to read for longer, or download an article then you have to get out your credit card.

One reason I built BioNames (and the related digital archive BioStor) was to create tools to help make sense of taxonomic names. In exploring databases such as GBIF and the NCBI taxonomy every so often you come across cases where things have gone horribly wrong, and to make sense of them you have to drill down into the taxonomic literature.

I've created a short screencast showing some of the phylogenies in BioNames. If you want to see these for yourself here are the links: Ocypodinae (ghost and fiddler crabs) Osedax (bone worms) Agaonidae (fig wasps) BioNames and phylogenies from Roderic Page on Vimeo.

One of the things that didn't make last week's deadline for launching BioNames was the inclusion of phylogenies.

I've added a simple "dashboard" to BioNames to display some basic data about what is in the database. Apart from a table of the number of bibliographic identifiers in the database (currently there are 54,422 publications with DOIs, for example), there are some graphic summaries. These are a bit slow to load as they are created on the fly.

One consequence of having a database of literature with external identifiers such as DOIs is that we can plug into a bunch of external services to get additional information about a reference. For example, altmetric can take a DOI and display some article level metrics. As an experiment I've added code for altmetric badges to the web page in BioNames that displays publications.

BioNames (http://bionames.org) is live. Getting to this point was supported by funding from EOL as part of their Computable Data Challenge. The award from EOL is paying for Ryan Schenk to work on the interface and overall design of the web site, and over the last few weeks we've been working increasingly frantically to get things ready. "Ready" is a relative concept.

I've stumbled on a case where two different publishers have issued different DOIs for the same articles. In this case, Springer and J-State both publish the Japanese Journal of Ichthyology (ISSN 0021-5090). The following article: is published by Springer with the DOI http://dx.doi.org/10.1007/BF02914322, and this DOI is registered with CrossRef. J-Stage publish the same article, with the DOI (http://dx.doi.org/10.11369/jji1950.36.196).

This week promises to be *cough* interesting. The deadline for the BioNames project is the end of the week (May 31st), and all I have right now is a blank web page (gulp). Behind the scenes data is being cleaned, mushed, and reconciled, and CSS, Javascript, and HTML are being wrangled. It's going to be tight, but hey, what could possibly go wrong...?

I've been banging on about having citable, persistent identifiers for specimens, so was suitably impressed when Derek Sikes posted a comment on iPhylo that Arctos already does this. For example, here is a DOI for a specimen: http://dx.doi.org/10.7299/X7VQ32SJ. So, we're all done, right? Not quite.