[BioSQL-l] left_value and right_value in taxon table

[Martin MOKREJŠ]

>> 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

<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>


Regards,
Martin