Here's a sketch of my vision of how to make something like the original PLoS Hubs vision (see The demise of the @PLoS Biodiversity Hub: what lessons can we learn? for background). In the blog post explaining the vision behind PLoS Hubs (Aggregating, tagging and connecting biodiversity studies), David Mindell wrote:So, first up, some basic principles. The goal (only slightly tongue in cheek) is for the user to never want to leave the site.

I'm a big fan of the work Nature publishing group is doing in experimenting with new methods of publishing, such as their iOS apps (which inspired me to "clone" their iPhone app) and the Encode app with the concept of "threads". But there's an aspect of the iPad app that puzzles me: Nature's app doesn't know that a linked article elsewhere in Nature is also available using the app.

Jonathan Eisen recently wrote that the PLOS Hub for Biodiversity is soon to be retired, and sure enough it's vanished from the web (the original URL hubs.plos.org/web/biodiversity/ now bounces you straight to http://www.plosone.org/, you can still see what it looked like in the Wayback Machine).Like Jonathan, I was involved in the hub, which was described in the following paper:In retrospect PLoS's decision to pull the hub is not surprising.

One of goals of BioNames is to be more than simply another taxonomic database. In particular, I'm interested in the idea of having a platform for viewing taxonomic publications. One way to think about this is to consider the experience of viewing Wikipedia. For any given page in Wikipedia there will be links to other, related content in Wikipedia.

In browsing the GBIF classification in BioNames I keep coming across cases of wholesale duplication of taxa.

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.I've added support for DeepDyve to BioNames.

One reason I built BioNames (and the related digital archive BioStor) was to create tools to help make sense of taxonomic names.

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.