Following on from my previous post about visualising the mammalian classification in Wikipedia, I've extracted the largest component from the graph for all mammal taxa in Wikipedia, and it is a tree. This wasn't apparent in the previous diagram, where the component appeared as a big ball due to the layout algorithm used.
The problem of displaying large taxonomic classifications on a web page continues to be an on again-off again obsession. My latest experiment makes use of Nicolas Garcia Belmonte's wonderful JavaScript Infovis Toolkit (JIT), which provides implementations of classic visualisations such as treemaps, hyperbolic trees, and SpaceTrees. SpaceTrees were developed at Maryland's HCIL lab, and that lab has applied them to biodiversity informatics.
Over on the EOL blog is a summary of a meeting Visualizing the Evolutionary Tree of Life. This sounds like it was a fun meeting, but part of me is suffering from déjà vu. Our community has tossed this subject around for a while now.
It's Friday, so time for some random, half-baked ideas. Imagine that we have a database of evolutionary trees, and these overlap for a set of taxa that we are interested in. How do we summarise these trees? One approach is to make a supertree. It would be useful to display the subtrees that went into making this supertree, if only to give an idea of how much they agree with the supertree.
Last night BBC One aired David Attenborough's Charles Darwin and the Tree of Life, which featured a lovely "fly through" the tree of life:In conjunction with the TV show, the Wellcome Trust has launched the Interactive Tree of Life, a Flash-based view of the tree of life. There's also a blog about the project. Here's a demo of the tree:The tree looks very nice, and a lot of work has gone into it, but I am somewhat underwhelmed.
Among the many weaknesses of my challenge demo is the way it simply dumps out a list of sequences (see comments on the demo.
One of the things I've struggled with most in putting together a web site for the challenge is how to summarise that taxonomic content of a study. Initially I was playing with showing a subtree of the NCBI taxonomy, highlighting the taxa in the study. But this assumes the user is familiar with the scientific names of most of life. I really wanted something that tells you "at a glance" what the study is about.
Mike Sanderson's wall of monitors is getting some attention. Cool as it looks (and I'm positively green with envy), this strikes me as the LCD equivalent of Science's suggestion that the reader print out a tree on several bits of paper doi:10.1126/science.300.5626.169. If we can fit the planet on a monitor, can't we fit the tree of life?
Found this while Googling. Demo by Perceptive Pixel of browsing the ITIS classification using their multi-touch technology. I want one...
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.