Following on from the discussion of BHL and DOIs, I stumbled across some remarkable work by Robert Cameron at SFU. Cameron has developed Universal Serial Item Names (USIN). The approach is spelled out in detail in Towards Universal Serial Item Names (also on Scribd). This lengthy document deals with how to develop user-friendly identifiers for journal articles, books, and other documents.
No, not taxonomy the discipline (although I've given a talk asking this question), but taxonomy.zoology.gla.ac.uk, my long-running web server hosting such venerable software projects as TreeView, NDE, and GeneTree, along with my home page.A series of power cuts in my building while I was away finally did for my ancient Sun Sparcstation5, running the CERN web server (yes, it's that old). I can remember the thrill (mixed with mild terror)
In a series of emails Chris Freeland, David Shorthouse, and I have been discussing DOIs in the context of the Biodiversity Heritage Library (BHL). I thought it worthwhile to capture some thoughts here.In an email Chris wrote:I think the perception that there are two "camps" is unfortunate.
Argh!!! The phyloinformatics workshop at Edinburgh's eScience Centre is underway (program of talks available here as an iCalendar file), and I'm stranded in Germany for personal reasons I won't bore readers with. The best and brightest gather less than an hour from my home town to talk about one of my favourite subjects, and I can't be there. Talk about frustration!
The kind people at Nature have taken pity on my rapidly fading research career, and have highlighted my note "Towards a Taxonomically Intelligent Phylogenetic Database" in Nature Precedings (doi:10.1038/npre.2007.1028.1) on the Nature web site. Frankly this is probably the only way I'll be getting into Nature ...
Here is a live demo of Pygmybrowse using the Catalogue of Life classification of animals provided by GBIF.
As yet another example of avoiding what I should really be doing, a quick note about a reworked version of PygmyBrowse (see earlier posts here and here). Last September I put together a working demo written in PHP. I've now rewritten it entirely in Javascript, apart from PHP script that returns information about a node in a classification. For example, this link returns details about the Animalia in ITIS.You can view the new version live.
While using iSpecies to explore some names (e.g., Sooglossus sechellensis in the Frost et al. amphibian tree mentioned in the last post, I stumbled across two papers that both described a new genus of frog for the same two taxa in the Seychelles.
I've tidied up the big phylogeny viewer mentioned earlier, and added a simple web form for anybody interested to upload a NEXUS or Newick tree and have a play. Examples:Ants from TreeBASEtrichodectid lice from TreeBASEBats from TreeBASEFrost et al amphibian treeTo create your own tree viewer, simply go to http://linnaeus.zoology.gla.ac.uk/~rpage/bigtrees/tv2/ and upload a tree.
The first pPod workshop happened last month at NESCent, and some of the presentations are online on the pPod Wiki. Although I'm a "consultant" I couldn't be there, which is a pity because it looks to have been an interesting meeting. When pPod was first announced I blogged some of my own thoughts on phylogenetics databases.