Monday, November 24, 2008
What is a study about? Treemaps of taxa
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.
I've settled (for now, at least) on using a treemap of images of the taxa in the study. I've played with treemaps before, and have never been totally convinced of their utility. However, in this context I think they work well. For each paper I extract the taxonomic names (via the Genbank sequences linked to the paper), group them into genera, and then construct a treemap where the size of each cell is proportional to the number of species in each genus. Then I harvest images from Flickr and/or Yahoo's image search APIs and display a thumbnail with a link to the image source.
I'm hoping that these treemaps will give the user an almost instant sense of what the study is about, even if it's only "it's about plants". The treemap above is for Frost et al.'s The amphibian tree of life (doi:10.1206/0003-0090(2006)297[0001:TATOL]2.0.CO;2), the one to the right is for Johnson and Weese's "Geographic distribution, morphological and molecular characterization, and relationships of Lathrocasis tenerrima (Polemoniaceae)".
Note that the more taxa a study includes the smaller and more numerous the cells (see below). This may obscure some images, but gives the user the sense that the study includes a lot of taxa. The image search isn't perfect, but I think it works well enough for my purposes.