The latest issue of Wired has an article on DNA barcoding, entitled "A Simple Plan to ID Every Creature on Earth". The article doesn't say much that will be new to biologists, but it's a nice intro to the topic, and some of the personalities involved.
The rather frail nature of biodiversity services (some of the major players have had service breaks in the last few weeks) has prompted me to revisit Dave Vieglais's BigDig and extend it to other services, such as uBio, EOL, and TreeBASE, as well as DSpace repositories and tools such as Connotea.The result is at http://bioguid.info/status/. The idea is to poll each service once an hour to see if it is online.
D. Ross Robertson has published a paper entitled "Global biogeographical data bases on marine fishes: caveat emptor" (doi:10.1111/j.1472-4642.2008.00519.x - DOI is broken, you can get the article here). The paper concludes:As I've noted elsewhere on this blog, and as demonstrated by Yesson et al.'s paper on legume records in GBIF (doi:10.1371/journal.pone.0001124) (not cited by Robertson), there are major problems with geographical information
Among the many ways to display trees, degree of interest (DOI) trees strike me as one potentially useful way to display trees such as the NCBI taxonomy. For background see, e.g. doi:10.1145/1133265.1133358 (or Google "degree of interest trees").The thing that would make this really useful is if an application was written that, like Google Earth, supported a simple annotation file format.
Next few weeks will be busy with term starting, kids visiting, and other commitments, so time to jot down some ideas. The first is to have a Wiki for taxonomic names. Bit like Wikispecies, but actually useful, by which I mean useful for working biologists. This would mean links to digital literature (DOIs, Handles, etc.), use of identifiers for names and taxa (such as NCBI taxids, LSIDs, etc.), and having it pre-populated with data.
My delicious tags as a Wordle. In my defense I've not had nearly enough coffee today.
Just to provide a sense of how much data I want to analyse for the Challenge, I have the XML, PDF, and images for 1687 articles from Molecular Phylogenetics and Evolution to play with.
Last week I was at NESCent's 2008 Community Summit. As part of that meeting a few of us had a breakout group on "Biodiversity and phylogenetics". Brian O'Meara took some spectacularly thorough notes, including the pithy:S[wofford]: What? Julia Clarke and I were advocating data mining, not entirely successfully.
I've been using ISSN's (International Standard Serial Number) to uniquely identify journals, both to generate article identifiers, and as a parameter to send to CrossRef's OpenURL resolver. Recently I've come across journals that change their ISSN, which has fairly catastrophic effects on my lookup tools.
Starting to get serious about the Grand Challenge. First step is to parse the XML data Elsevier made available. Sadly this is only for Molecular Phylogenetics and Evolution for 2007, I would have liked the whole journal in XML to avoid hassles with parsing PDF. However, XML is not without it's own problems.