Having made a first stab at mapping NCBI taxa to Wikipedia, I thought it might be fun to see what could be done with it. I've always wanted to get quantum treemaps working (quantum treemaps ensure that the cells in the treemap are all the same size, see my 2006[!] blog post for further description and links). After some fussing I have some code that seems to do the trick.
The 52,956 links from NCBI to Wikipedia that I've been busy creating are now "live." If you go to a NCBI taxon such as Sphaerius you'll see something like this:Clicking the "Wikipedia" link takes you to the Wikipedia page for this taxon.
PLoS recently announced a dedicated iPad app, that covers all the PLoS Journals, and which is available from the App Store. Given the statement that "PLoS is committed to continue pushing the boundaries of scientific communication" I was expecting something special.
In an earlier post I discussed linking NCBI taxonomy to Wikipedia. One way to tackle this is to add NCBI Taxonomy ID to Wikipedia pages. I reopened the case for adding the Taxonomy IDs to the Taxobox on each taxon page, but this met with substantial resistance.
In an earlier post I expressed my amazement that my venerable Nexus Data Editor (NDE) still had users, meaning I had to rebuild the installer so users could install NDE on Windows Vista. Now, Thomas Hauser has gone one better and created an installer for Mac OS X. Given that NDE is a Windows-only program, this is quite a feat. Thomas uses Mike Kroenenberg's (@k3erg) WineBottler to create a version of NDE that can be run on a Mac.
One of the potentially powerful features of TreeBASE II is availability of a RDF version of a study. This means that, in principle, one could take the RDF for a TreeBASE study, combine it with RDF from other sources, and generate a richer view of a particular study.
I've been playing a little with TreeBASE II, and the more I do the more I want to pull my hair out. Broken URLs The old TreeBASE had a URL API, which databases such as NCBI made use of. For example, the NCBI page for Amphibolurus nobbi has a link to this taxon in TreeBASE.
Continuing the Friday folly theme, below is a screencast of a linked data browser that uses the same ideas as last week's screencast, but uses a custom browser I've written to display the results in a more user-friendly way. Linking the data together from Roderic Page on Vimeo.The demo is live, you can view it at http://iphylo.org/~rpage/browser/www/uri/http://bioguid.info/doi:10.1371/journal.pone.0001787.
I've written a note on the Wikipedia Taxobox page making the case for adding NCBI taxonomy IDs to the standard Taxobox used to summarise information about a taxon. Here is what I wrote:Some discussion has ensued on the Taxobox page, all positive. I'm blogging this here to encourage anyone who as any more thoughts on the matter to contribute to the discussion.
Cooliris is a web browser plugin that can display a large number of images as a moving "infinite" wall. It's Friday, so for fun I added a media RSS feed to BioStor to make the BHL page scans available to Cooliris.
Time for a Friday folly. I've made a clunky screencast showing an example of linking biodiversity data together, using bioGUID as the universal wrapper around various data sources.