Saturday, December 31, 2005

Edit script for classifications

One of the first concrete things to emerge from this research is a paper with Gabriel Valiente entitled An edit script for taxonomic classifications.

Abstract The NCBI taxonomy provides one of the most powerful ways to navigate sequence data bases but currently users are forced to formulate queries according to a single taxonomic classification. Given that there is not universal agreement on the classification of organisms, providing a single classification places constraints on the questions biologists can ask. However, maintaining multiple classifications is burdensome in the face of a constantly growing NCBI classification. In this paper, we present a solution to the problem of generating modifications of the NCBI taxonomy, based on the computation of an edit script that summarises the differences between two classification trees. Our algorithms find the shortest possible edit script based on the identification of all shared subtrees, and only take time quasi linear in the size of the trees because classification trees have unique node labels.

The basic idea is to look for matching subtrees in two classifications (labelled rooted trees), then compute a script that transforms one tree into another. I think the idea is neat, and we have a basic implementation available (written C++ using Graph Template Library). Haven't yet made practical use of it though...

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