17 August 2010

Radish: Pulling Up Taxonomic Hierarchies From Leaf to Root

I've just released a small open-source Java library called Radish. It contains tools for interfacing with uBio (and hopefully other services in the future), with the purpose of looking up a taxon's hierarchy. It does this by synthesizing multiple taxonomies into a single graph. Here, for example, is the graph produced by looking up Homo sapiens Linnaeus 1758 (click the image to enlarge):

This is a synthesis of several taxonomies. Some have more ranks than others, but they all converge on a single chain, with the exception of the taxa above the "phylum level", where at least two of them use different schemes. (Although it may be tempting to synonymize Biota and "Cellular life", or Animalia and Metazoa, these are not objective synonymies, and arguably the former is a bad idea anyway.) Ideally the library would be able to figure out that "Cellular life" includes Biota (if the latter is a crown clade), and that Animalia either includes or is a synonym of Metazoa, but it can only work with the data it's given.

Why the name "Radish"? From the project's wiki:
The English word "radish" is derived from Latin "radicem" (nominative: "radix"), meaning "root". (This is also where the word "radical" comes from.) The idea of the Radish library is that by "grabbing a leaf" (i.e., selecting a smaller taxon), you can "pull up the root" (i.e., extract that taxon's hierarchy of supertaxa, up to the root of all life).
Radish is part of a larger project I am working on ... I should have more to say about that in the near future....

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