Back in 2006 in a short post entitled "Building the encyclopedia of life" I wrote that GenBank is a potentially rich source of information on host-parasite relationships.

Déjà vu is a scary thing. Four years ago I released a mapping between names in TreeBASE and other databases called TBMap (described here: doi:10.1186/1471-2105-8-158). Today I find myself releasing yet another mapping, as part of my NCBI to Wikipedia project. By embedding the mapping in a wiki, it can be edited, so the kinds of problems I encountered with TbMap, recounted here, here, and here.

Given that the Twitter stream tagged #vizbi will fade away soon, I've grabbed most of the links I tweeted during VIZBI 2011 and have put them here.

I've spent the last three days at VIZBI, a Workshop on Visualizing Biological Data, held at the Broad Institute in Boston (note that "Broad" rhymes with "Code"). A great conference in a special venue that includes the DNAtrium. Videos of the talks will be online "real soon now", look for the keynotes, which were full of great ideas and visualisations.

More zoom viewer experiments (see previous post), this time with a linked map that updates as you browse the tree (SVG-capable browser required). As you browse the frog classification the map updates to show the location of georeferenced sequences in GenBank from the taxa in the part of the tree you are looking at. The map is limited to not more than 200 localities, and many frog sequences aren't georeferenced, but it's a fun way to combine

Now we'll bring the awesome. Mendeley have announced The Mendeley API Binary Battle, with a first prize of $US 10,0001, and some very high-profile judges (Juan Enriquez, Tim O'Reilly, James Powell, Werner Vogels, and John Wilbanks). Deadline for submission is August 31st 2011, with the results announced in October. The criterion for judging are:How active is your application? We’ll look at your API key usage.How viral is the app?

Following on from my previous post on microcitations I've blasted all the citations in Nomenclator Zoologicus through my microcitation service and created a simple web site where these results can be browsed.The web site is here: http://iphylo.org/~rpage/nz/.To create it I've taken a file dump of Nomenclator Zoologicus provided by Dave Remsen and run all the citations through the microcitation service, storing the results in a simple database.

One of the challenges of linking databases of taxonomic names to the primary literature is the minimal citation style used by nomenclators (see my earlier post Nomenclators + digitised literature = fail).For example, consider Nomenclator Zoologicus.

BioStor has had a Twitter account @biostor_org for a while, but it's not been active.

Continuing experiments with a zoom viewer for large trees (see previous post), I've now made a demo where the labels are clickable. If the NCBI taxon has an equivalent page in Wikipedia the demo displays and link to that page (and, if present, a thumbnail image). Give it a try athttp://iphylo.org/~rpage/deeptree/3.htmlor watch the short video clip below: Zoomable viewer with Wikipedia thumbnails from Roderic Page on Vimeo.

Mendeley has added a feature which makes it easier to use Mendeley with repositories such as BioStor and BHL.