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.
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 wroteHowison 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 doubtSciGuyMy Biotech LifePharnagulaThese 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 sayingNot 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.