Well, the LSID discussion has just exploded in the last few weeks.

This October 22-24 there is a phyloinformatics workshop at the e-Science Institute in Edinburgh, Scotland, hosted in conjunction with the Isaac Newton Institute for Mathematical Sciences's Phylogenetics Programme. The invited speakers are: Prof.

Based on my recent experience developing an OpenURL service (described here, here, and here), linking this to a reference parser and AJAX tool (see David Shorthouse's description of how he did this), and thoughts on XMP, maybe it's time to try and articulate how this could be put together to make taxonomic literature more accessible.

The TDWG-GUID mailing list for this month has a discussion of whether TDWG should commit to LSIDs as the GUID of choice. Since the first GUID workshop TDWG has pretty much been going down this route, despite a growing chorus of voices (including mine) that LSIDs are not first class citizens of the Web, and don't play well with the Semantic Web.

Oops. One big problem with drawing trees in Google Earth is that the Earth, sadly, is not flat. This means that widely distributed clades cause problems if I draw straight lines between nodes in the tree. For geographically limited clades (such as the Hawaiian kaytidids shown earlier) this is not really a problem. But for something like plethodontid salamanders (data from TreeBASE study S1139, see doi:10.1073/pnas.0405785101), this is an issue.

Now, for something completely different. I've been playing with Google Earth as a phylogeny viewer, inspired by Bill Piel's efforts, the cool avian flu visualisation Janies et al. published in Systematic Biology (doi:10.1080/10635150701266848), and David Kidd's work. As an example, I've taken a phylogeny for Banza katydids from Shapiro et al. (doi:10.1016/j.ympev.2006.04.006), and created a KML file.

OK, we're on a roll. After adding Journal of Arachnology and Pysche to my OpenURL resolver, I've no added the American Museum of Natural History's Bulletins and Novitates . In an act of great generosity, the AMNH has placed its publications on a freely accessible DSpace server.

Time to bring some threads together. I've been working on a tool to parse references and find existing identifiers. The tool is at http://bioguid.info/references (for more on my bioGUID project see the blog). Basically, you paste in one or more references, and it tries to figure out what they are, using ParaTools and CrossRef's OpenURL resolver.

Added the Biodiversity Heritage Library blog to my links on my blog, then noticed that BHL have disabled comments. So, we can view their progress, but can't leave comments. Sigh, I wonder whether BHL has quite grasped that one of the best uses of a blog is to interact with the people who leave comments, in other words, have a conversation.

Continuing on this theme of embedded metadata, this is one reason why DNA barcodingis so appealing. A DNA barcode is rather like embedded metadata -- once we extract it we can look up the sequence and determine the organism's identity (or, at least whether we've seen it before). It's very like identifying a CD based on a hash computed from the track lengths.

Following on from the previous post, as Howison and Goodrum note, Adobe provides XMP as a way to store metadata in files, such as PDFs. XMP supports RDF and namespaces, which means widely used bibliographic standards such as Dublin Core and PRISM can be embedded in a PDF, so the article doesn't become separated from its metadata. Adobe provides a developers kit under a BSD license.