[BiO BB] Obtaining lineage information from an NCBI taxId

James Wagner jrwagner at sfu.ca
Thu Sep 27 16:44:18 EDT 2007

Hello, I was just trying to obtain the full phylogenetic lineage from a
given NCBI taxonomy ID using BioPerl. What i am discovering is that some of
these ids are missing names at certain levels. For example, for ID 1166 at

the lineage

from the tooltips one can see that this is information for the Kingdom,
Phylum, Order, and Genus respectively, but Family and Class are missing.
While I can get this lineage from BioPerl, I cannot figure out how to find
out specifically that Family and Class are missing, and I was wondering if
there was some way to script NCBI (or anywhere else) to retrieve this
without resorting to screen scraping, as these tool-tips are the only place
that I can seem to find this information. Or is there some sort of rule in
bacterial taxonomy that I can apply to make this easier?


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