load_ncbi_taxonomy.pl

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load_ncbi_taxonomy.pl

Sue Huse
I would like to update our local gmod database from the NCBI Taxon Database.
I have a rather old copy of load_ncbi_taxonomy.pl.  Is that still the
appopriate way to create a local database copy, and if so, where can I
find the latest version of the script?

-Sue Huse
--------------------------------------------------------------------
Bay Paul Center for Comparative Molecular Biology and Evolution
Marine Biological Laboratory, Woods Hole, MA
[hidden email]



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Re: load_ncbi_taxonomy.pl

Scott Cain-2
Hi Sue,

I think you are asking about a BioSQL database, which I don't know much
about.  You should ask on the bioperl mailing list,
[hidden email] .

Scott


On Wed, 2005-12-07 at 09:14 -0500, Sue Huse wrote:

> I would like to update our local gmod database from the NCBI Taxon Database.
> I have a rather old copy of load_ncbi_taxonomy.pl.  Is that still the
> appopriate way to create a local database copy, and if so, where can I
> find the latest version of the script?
>
> -Sue Huse
> --------------------------------------------------------------------
> Bay Paul Center for Comparative Molecular Biology and Evolution
> Marine Biological Laboratory, Woods Hole, MA
> [hidden email]
>
>
>
> -------------------------------------------------------
> This SF.net email is sponsored by: Splunk Inc. Do you grep through log files
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> searching your log files as easy as surfing the  web.  DOWNLOAD SPLUNK!
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> _______________________________________________
> Gmod-devel mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-devel
--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                         [hidden email]
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory



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Re: load_ncbi_taxonomy.pl

Hilmar Lapp-2
Actually the script doesn't use Bioperl and hence comes directly with  
Biosql. You can download the latest version from Biosql CVS. If you  
have any question about it, send email to [hidden email].

Scott is right though - the script expects a Biosql schema.

        -hilmar

On Dec 7, 2005, at 7:14 AM, Scott Cain wrote:

> Hi Sue,
>
> I think you are asking about a BioSQL database, which I don't know much
> about.  You should ask on the bioperl mailing list,
> [hidden email] .
>
> Scott
>
>
> On Wed, 2005-12-07 at 09:14 -0500, Sue Huse wrote:
>> I would like to update our local gmod database from the NCBI Taxon  
>> Database.
>> I have a rather old copy of load_ncbi_taxonomy.pl.  Is that still the
>> appopriate way to create a local database copy, and if so, where can I
>> find the latest version of the script?
>>
>> -Sue Huse
>> --------------------------------------------------------------------
>> Bay Paul Center for Comparative Molecular Biology and Evolution
>> Marine Biological Laboratory, Woods Hole, MA
>> [hidden email]
>>
>>
>>
>> -------------------------------------------------------
>> This SF.net email is sponsored by: Splunk Inc. Do you grep through  
>> log files
>> for problems?  Stop!  Download the new AJAX search engine that makes
>> searching your log files as easy as surfing the  web.  DOWNLOAD  
>> SPLUNK!
>> http://ads.osdn.com/?ad_id=7637&alloc_id=16865&op=click
>> _______________________________________________
>> Gmod-devel mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-devel
> --  
> -----------------------------------------------------------------------
> -
> Scott Cain, Ph. D.                                          
> [hidden email]
> GMOD Coordinator (http://www.gmod.org/)                      
> 216-392-3087
> Cold Spring Harbor Laboratory
>
>
>
> -------------------------------------------------------
> This SF.net email is sponsored by: Splunk Inc. Do you grep through log  
> files
> for problems?  Stop!  Download the new AJAX search engine that makes
> searching your log files as easy as surfing the  web.  DOWNLOAD SPLUNK!
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> _______________________________________________
> Gmod-devel mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-devel
>
--
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------



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