[Bioperl-l] loading data to biosql tables

Hilmar Lapp hlapp at gmx.net
Thu Dec 8 11:55:21 EST 2005

Any reason you didn't instantiate the rest of the schema? Any scripts  
and software that have been written against BioSQL will certainly  
expect the rest of the schema be present ...

Bioperl-db is the BioSQL language binding for Bioperl, so that's what  
you will want to use. It comes with a script load_seqdatabase.pl to  
load any format supported by Bioperl.

However, bioperl-db does expect all of Biosql to be present ...


On Dec 7, 2005, at 6:12 PM, Angshu Kar wrote:

> Hi,
> I've created 5 tables (taxon, taxon name, bioentry, biosequence,
> biodatabase) in my postgresql database (linux box) using the biosql  
> schema
> ddl from
> http://cvs.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/biosql-schema/sql/ 
> biosqldb-pg.sql?rev=1.29&cvsroot=biosql&content-type=text/vnd.viewcvs- 
> markup
>  .
> Now I want to load the tables with arabidopsis data. Could you please  
> let me
> know where can I find such scripts for pgsql? And also I find at
> http://bio.perl.org/Core/Latest/index.shtml that the DB module has not  
> been
> updated since 2001. Do I need to install that? Or are there some new
> releases?
> I'll be obliged if you can guide.
> Thanks,
> Angshu
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757

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