Bryan Drew and colleagues have published a piece in PLoS Biology bemoaning the lack of databased phylogenies: This is an old problem (see for example "Towards a Taxonomically Intelligent Phylogenetic Database" doi:10.1038/npre.2007.1028.1), but alas the solution proposed by Drew et al. is also old: In my opinion, as soon as you start demanding people do something you've lost the argument, and you're relying on power ("you don't get to publish

Notes on fonts in trying decipher some bat names (and sort out some synonyms). It can be difficult to tell "œ" (o + e) from "æ" (a + e) in some texts.

One feature I've always wanted to have in BioNames is a timeline of taxonomic names. ION has one (see here), but I wanted a way to go from the timeline to the actual publications.

Continuing the theme of the failings of the GBIF classification I've been playing further with cluster maps to visualise the problem (see this earlier post for an introduction).Browsing through bats in GBIF I keep finding the same species appearing more than once, albeit in different genera.

GBIF is asking for views on how it should license of data in the GBIF network. The full consultation document is available from Google Drive and DropBox.

Readers of this blog will know that I'm sceptical about the current value of linked data and RDF in biodiversity informatics. But I came across an interesting paper on RDF and biocuration that suggests a good "use case" for RDF in constructing and curating taxonomic databases.The paper is "Catching inconsistencies with the semantic web: a biocuration case study" (PDF here) by Jerven Bolleman and Sebastien Gehant.

In a previous post (Learning from eLife: GitHub as an article repository) I discussed the advantages of an Open Access journal putting its article XML in a version-controlled repository like GitHub. In response to that post Pensoft (the publisher of ZooKeys ) did exactly that, and the XML is available at https://github.com/pensoft/ZooKeys-xml.OK, "now what?" I hear you ask.

Since 2009 I've been running a service that takes posts to the EvolDir mailing list and sends them to a Twitter stream at @EvolDir. This service was running on a local machine which has died. Rather than wait until I rebuild that server (again), I looked around for other ways to recreate this service.

Playing with my eLife Lens-inspired article viewer and some recent articles from ZooKeys I regularly come across articles that are incorrectly marked up. As a quick reminder, my viewer takes the DOI for a ZooKeys article (just append it to http://bionames.org/labs/zookeys-viewer/?doi=, e.g. http://bionames.org/labs/zookeys-viewer/?doi=10.3897/zookeys.316.5132), fetches the corresponding XML and displays the article.Taking the article

Quick note to highlight the following publication: This paper outlines the methods used by the BOLD project to cluster sequences into "BINS", and touches on the issue of dark taxa (taxa that are in GenBank but which lack formal scientific names). Might be time to revisit the dark taxa idea, especially now that I've got a better handle on the taxonomic literature (see BioNames) where the names of at least some dark taxa may lurk.

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.