[BioSQL-l] load_ncbi_taxonomy.pl

[Chris Fields]

The script is included with the biosql schema package:

http://cvs.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/biosql-schema/?cvsroot=b
iosql

The reason it's included here instead of with bioperl-db is that the script,
though perl, is not specifically used just for bioperl-db.  It was designed
to be independent of Bioperl, therefore can be used to load taxonomy for any
BioSQL database.  I think this is mentioned somewhere (in the INSTALL file
or README, maybe) but I'm not sure...

Christopher Fields
Postdoctoral Researcher - Switzer Lab
Dept. of Biochemistry
University of Illinois Urbana-Champaign 


> -----Original Message-----
> From: biosql-l-bounces at lists.open-bio.org [mailto:biosql-l-
> bounces at lists.open-bio.org] On Behalf Of Gerben Menschaert
> Sent: Monday, April 24, 2006 9:53 AM
> To: biosql-l at lists.open-bio.org
> Subject: [BioSQL-l] load_ncbi_taxonomy.pl
> 
> Hello,
> 
> In the bioperl-db INSTALL file I saw that it's necessary to preload the
> ncbi
> taxonomy:
> 
> ####################################################
> LOAD THE NCBI TAXONOMY
> You should pre-load the NCBI taxonomy database using the
> scripts/load_ncbi_taxonomy.pl script in the BioSQL package.
> Otherwise you will see errors from mis-parsed organisms when you
> attempt to load sequences.
> ####################################################
> 
> I cannot find this load_ncbi_taxonomy.pl script. Is this (parsing the
> organism info correctly) taken care of in the load_seqdatabase.pl script
> now?
> 
> Regs,
> Gerben Menschaert
> 
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