[BioSQL-l] taxonomy stuff

[Hilmar Lapp]

The species adaptor works, but obviously it wouldn't let you do the 
kind of query you mention. The taxonomy objects are not hooked up yet I 
believe.

Would you be uncomfortable going directly to SQL? I.e., is this not a 
one-off project?

	-hilmar

On Wednesday, April 2, 2003, at 08:34  AM, Jason Stajich wrote:

> Aaron - how far along is the taxonomy stuff?  If I wanted to query for 
> a
> all the taxids that are within a specific division or even kingdom?
>
> Is there a taxonomy adaptor I can start working with and possibly
> extending.  I want to do the basic process of filtering my BLAST hits 
> to
> only those within certain clades.
>
> I'm mapping gi -> taxaid from the table available from NCBI and then
> wanting to restrict to only those gi #s in my list.
>
> I'm happy to write things, just curious where they stand.  I realize we
> don't quite have the richer taxonomic objects up to speed in bioperl to
> represent everything in the taxondb just yet.
>
> -jason
>
> --
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu
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>
-- 
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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