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.
Stumbled across a really nice paper (Why can't I manage academic papers like MP3s?) while reading commentary on Tim O'Reilley's post about FreeBase. In response to Danny Ayer's post, Tim O'Reilly wrote Howison and Goodrum make some interesting points, especially about how easy it is to get (or create) metadata for a CD, especially when compared to handling academic literature.
postgenomic is a great way to keep up with science blogs. For example, searching for encyclopedia of life pulls up all sorts of interesting posts. A sampling: Island of doubt SciGuy My Biotech Life Pharnagula These are not the only blogs, and as always the comments left by others on these blogs is also fascinating. My sense is there is a "wow" factor based on the the publicity, coupled with not inconsiderable skepticism about content.
My paper on mapping TreeBASE names to other databases is out as provisional PDF on the BMC Bioinformatics web site (doi:10.1186/1471-2105-8-158 -- not working yet). The abstract: The TBMap web site needs some work, it's really only intended to document the mapping. Once I've tweaked and updated the mapping, I hope to use it in my forthcoming all-sining, all-dancing, phylogeny database...
Lucy Odling-Smee has a short piece on EoL in Nature (doi:10.1038/news070508-7), quoting a certain Page chap as saying Not the most insightful thing I've ever said. One of the issues Lucy's piece highlights is the long term sustainability of electronic resources like EoL. The whole issue of digital curation is worrying, given the transient nature of many electronic resources.
Mitch Leslie has written an article on EoL (doi:10.1126/science.316.5826.818). It starts: Déjà vu because the defunct All-Species Foundation -- also covered in Science (doi:10.1126/science.294.5543.769) -- had much the same ambitions six years ago. It is easy to be sceptical, but I think it was Rudi Giuliani who said "under promise, over deliver." Wise words.
David Shorthouse has entered the blogsphere with his iSpiders blog.
Following on from my earlier grumble about how the catalogue of Life handles literature, I've spent an afternoon mapping publications in the "itis".publications table in a copy of ITIS to external GUIDs, such as DOIs, Handles, and SICIs in JSTOR. The mapping is not complete by any means, but gives an idea of how many publications have GUIDs.You can view the mapping here.
A bit more browsing of the Catalogue of Life annual checklist for 2007 reveals a rather annoying feature that, I think, cripples the Catalogue's utility. With each release the checklist grows in size. From their web site: However, with each release the identifiers for each taxon change.
The Encyclopedia of Life web site is up, together with some rather breathless publicity and this cool movie. Of course, it's all vapourware just now. I'm involved in some of the informatics in an advisory role. It will be interesting to see what happens. Let's hope that the fate of EoL will be different to that of the similarly ambitious All Species. Oh, and then there's SpeciesBase... For some reaction see Slashdot.