BioOne sucks. Really, really, sucks. I have lost count of the number of times they break DOIs. These are supposed to be the gold standard globally unique identifier, and BioOne continually buggers them. For example, take this URL: http://www.bioone.org/perlserv/?request=get-abstract&doi=10.1600/02-14.1. Note the doi=10.1600/02-14.1 bit at the end.

Partly inspired by Pedro Beltra's post Open Science project on domain family expansion about using Google Code as a project management system, I've started to populate the iPhylo project. At this stage I'm uploading some scripts for parsing and extracting bibliographic records, and adding wiki pages describing how this is done, discussing different bibliographic identifiers, etc.

MarkMail is a great tool for searching mail archives. Although focussing on software development projects, they are open to requests, so last week I asked if they could index TAXACOM. My pitch was that TAXACOM is a long running list full of interesting conversations, has been the subject of scholarly study (Christine Hine's book I mentioned earlier), and is topical given interest in biodiversity and the Encyclopedia of Life.

I've just discovered Nicolas Garcia Belmonte's JavaScript Information Visualization Toolkit (JIT). Wow! This is very cool stuff (and no Flash). To quote from the web site: Nicolas also links to a talk by Tamara Munzner, which I've embedded below to remind myself to watch it.

Trivial as this may seem, I'm trying to find out who designed this "Open Access" logo, and whether there are some original files for it. I've seen this logo (or variations on it) on the PLoS web site, the open access publisher Hindawi Publishing, and the Mac OS X program Papers uses it. It's driving me nuts that I can't find the original.

The more I play with GBIF the more I come across some spectacular errors. Here's one small example of what can go wrong, and how easy it would be to fix at least some of the errors in GBIF. This is topical given that the recent review of EOL highlighted the importance of vetting and cleaning data.

I started this blog with the goal of documenting my own efforts to make a database of evolutionary trees, based on ideas sketched in hdl:10.1038/npre.2007.1028.1. I've felt that the major task is link phylogenies to other information, such as taxon names, specimens, localities, images, publications, etc. That is, to embed trees in a broader context.

The dissection of the colossal squid ( Mesonychoteuthis hamiltoni ) specimen from Antarctica has been getting a lot of coverage. Pangs of homesickness, especially seeing Steve O'Shea enthusing about the beast. Steve was a contemporary at Auckland Uni when I was a student.

Last month I was at the MBL in Woods Hole, taking part in the review of the Biodiversity Informatics Group. BIG is responsible for the EOL web site. I chair the Informatics Advisory Group, which provides advice to BIG, and it was our task to produce an evaluation of where things stood. I've written a post on the Encyclopaedia of Life blog about some of the big challenges facing EOL as it moves into its second year.

Bit of a rarity these days.

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