[Bioperl-l] Taxonomy hierarchy extraction

George Heller george.heller at yahoo.com
Mon Jun 18 13:07:59 EDT 2007


What exactly is the "node n" in the query below. When I issue this query, it says, 
   
  relation "node" does not exist.
   
  I tried to use the get_all_Descendents method but it looks like in order to do a recursive call it calls the method each_Descendent. This method is not implemented in Bio::DB::Taxonomy. It just has a single line,
   
  shift->throw_not_implemented();
   
  Thanks.
  George.

Hilmar Lapp <hlapp at gmx.net> wrote:
  I'm a bit confused - it sounds like you have set up a local BioSQL 
database and loaded the NCBI taxonomy into the database. You can now 
use simple SQL to retrieve all descendants of a node in the tree 
given its NCBI taxonID such as

SELECT tn.*, tnm.name FROM taxon tn, taxon_name tnm, node n
WHERE
n.ncbi_taxon_id = :taxonID
AND tn.left_value > n. left_value
AND tn.right_value < n.right_value
AND tn.taxon_id = tnm.taxon_id
AND tn.name_class = 'scientific_name'

BioPerl doesn't have a Taxonomy::biosql module yet (though this would 
seem like a worthwhile thing to add), so you can't use the 
Bio::DB::Taxonomy interface to do this against a BioSQL instance.

However, BioPerl does have support for the flat-file download of the 
NCBI taxonomy database and indexes it, so you can simply use 
Taxonomy::{get_taxon,get_all_Descendants} using the flatfile download 
to achieve what you wanted to do in a less than 5 lines of perl.

Although the recursive implementation of Taxonomy::get_all_Descendants 
() won't be lightning fast, it may still be perfectly fine for your 
application - are you sure it is not?

-hilmar

On Jun 18, 2007, at 12:21 AM, George Heller wrote:

> Thanks. And how can I assign the $node here in the below code, such 
> that I can reference it to a particular taxon id record? I want to 
> retrieve all the descendents from the taxonomy hierarchy, given a 
> particular taxon id.
>
> I have a local db setup, in which I have uploaded data using the 
> load_ncbi_taxonomy.pl script.
>
> Thanks.
> George
>
> Jason Stajich wrote:
> I assume you already figured out how to setup a local taxonomydb?
>
>
> You just want the extant species/leaves of the tree
>
>
> my @extant_children = grep { $_->is_Leaf } $node->get_all_Descedents;
>
>
>
> -jason
> On Jun 17, 2007, at 11:41 AM, George Heller wrote:
>
> Hi all,
>
>
> Can anyone point me to some example that uses the 
> get_all_Descendents method from Bio::DB::Taxonomy? I am a newbie at 
> this, and I am not quite sure how to implement it.
>
>
> Thanks.
> George
>
>
> Sendu Bala wrote:
> George Heller wrote:
> Hi all,
>
>
> I am looking at extracting the taxonomy hierarchy for some taxon 
> ids.
> What I plan to do is, for a given taxon id, say 33090, I want to
> extract all taxon ids that are children of this species. I do not
> just want the immediate children, but the children's children and so
> on.
>
>
> Any ideas on the way I can go about doing this?
>
>
> Well, you'll use Bio::DB::Taxonomy presumably, and 
> each_Descendent in
> some kind of looping structure. Most easily a recursing sub.
>
>
> If you happen to code up something neat and efficient, why not 
> share it
> with us and we could add it to the Taxonomy module(s).
>
>
>
>
>
>
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> Jason Stajich
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