My views on TreeBASE are pretty well known. Lately I've been thinking a lot about how to "fix" TreeBASE, or indeed, move beyond it. I've made a couple of baby steps in this direction. The first step is that I've created a group for TreeBASE papers on Mendeley.
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. As an example, here is a quantum treemap for Laurasiatheria.
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.
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.
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.
Following on from the last post, I've now set up a trivial NCBI RDF service at bioguid.info/taxonomy/ (based on the ISSN resolver I released yesterday and announced on the Bibliographic Ontology Specification Group). If you visit it in a web browser it's nothing special. However, if you choose to display XML you'll see some simple RDF.
As part of my Quixotic attempt to construct a wiki of taxonomic names, I'm building a database of names and links. My current plan is to seed this with the NCBI taxonomy. What I want to do is flesh out the NCBI taxonomy with authorities and links to the original literature. At the moment the NCBI taxonomy is almost "nude", lacking links to the literature behind the names.
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.
Time for some fun. In between some tedious text mining I've been meaning to explore some visualisations of NCBI. Here's the first, inspired by Jörn Clausen's wonderful Live Earthquake Mashup (thanks to Donat Agosti for telling me about this). What I've done is take all the frog sequences in Genbank that are georeferenced, add the date those Genbank records were created, generate a KML file, and use Nick Rabinowitz's timemap to plot the KML.