[Biopython] local taxonomy search

[Peter]

On Sun, Jun 21, 2009 at 1:45 AM, Xie, Boya<BX1030 at ecu.edu> wrote:
> Hi Peter,
>
> Thank you for your reply!
>
> What I want is giving an species name or gi number, find which
> kingdom, class, phylum, order, family it belongs to. And I want
> to do this locally.
>
> Thanks,
>
> Tina

I see. Well, the NCBI Entrez tool is online only so you can't use that.

You could download the NCBI taxonomy from the FTP site and parse
it yourself (the nodes.dmp file is just a simple text file):
ftp://ftp.ncbi.nih.gov/pub/taxonomy/

Another option would be to use BioSQL. It would be more work to setup,
and you'd need to know SQL to use it, but a BioSQL database includes
taxon tables and BioSQL provides a script to download and import the
NCBI taxonomy, see here for details:
http://biopython.org/wiki/BioSQL#NCBI_Taxonomy

Peter