[Bioperl-l] taxonomic information handler

[Jason Stajich]

I think we would like someone to do the Taxonomy namespace for sure.

I have written a connector to NCBI to retrieve ncbi_taxaid for an organism
name, its in scripts/taxa.  Would love to be able to populate a whole data
object as well if we can design one.

Would be great if someone (other than me) would flesh out the
Bio::Taxonomy objects.  There was a proposed relational structure from
Matthew that may have made its way a module of the biosql schema.

Dan would you be brave enough to propose a set of objects which relate a
taxanomic hierarchy?  This might utilize objects such as Bio::Graph but I
wouldn't worry about that right now.  I would drive this based on use
cases that you have for taxonomic data.

-jason

On Mon, 30 Sep 2002, Dan Kortschak wrote:

> Hi All, I've recently just moved a script from doing a taxonomic query
> through the NCBI/Entrez interface with GenPept to performing the same kind
> of thing locally on my box. It works, but is horrendously inefficient
> space wise (I didn't feel like messing around with the SQL side of things
> so the taxdump is all kept in perl arrays to do the lookups - looks coyly
> down at his feet :/). Is there work going into a Bio::Taxonomy type class?
>
> Just curious.
> Dan
>
>

-- 
Jason Stajich
Duke University
jason at cgt.mc.duke.edu