[BioSQL-l] left_value and right_value in taxon table

[Hilmar Lapp]

On Apr 11, 2008, at 8:50 PM, Martin MOKREJŠ wrote:
>>> On Apr 8, 2008, at 11:58 AM, aaron.j.mackey at gsk.com wrote:
>>> > I believe that the first thing the load_ncbi_taxonomy.pl script  
>>> > does is to
>>> > wipe out everything already in the table.
>>> That may have been in true in its beginnings but hasn't been for  
>>> a long time :-) It only updates changed nodes, adds new ones, and  
>>> deletes retired ones (unless you say --nodelete). The script does  
>>> recompute *all* nested set values, though.
>> Ahh right, I remember all that now.  It was the wiping out of the  
>> left/right values that I was thinking of.
>> Thanks,
>> -Aaron
>
> Hi,
>
> Maybe you have meant the other taxonomy loading script? ;-)
>
> http://code.open-bio.org/svnweb/index.cgi/biosql/view/biosql-schema/ 
> trunk/scripts/load_itis_taxonomy.pl

This loads a taxonomy too, but into the PhyloDB tables (because the  
ITIS taxonomy consists of multiple hierarchies, not a single one like  
NCBI).

>
> <quote>
> You can use this script to load the taxonomy data into a fresh  
> instance of
> biosql. Otherwise an already existing ITIS tree will be deleted first.
> </quote>
>
> I just don't understand why the very first sentence of the  
> documentation
> within the scripts says something about 'update':
>
> <quote>
> This script loads or updates a biosql schema with phylodb extension
> with the ITIS taxonomy as a phylogenetic trees, one tree for each
> kingdom.
> </quote>

The 'update' here is forward looking :) At this point there won't  
really be an update as any existing trees within the ITIS namespace  
are deleted first.

	-hilmar

>
>
> Regards,
> Martin
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-- 
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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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