[Bioperl-l] loading data to biosql tables

[Hilmar Lapp]

You should download the current biosql-schema from CVS. If my 
recollection is correct then you are on Postgres, so you will want to 
run the file biosqldb-pg.sql through psql. You do not need the other 
Postgres related files there. The rest of the repository, aside from 
support for other RDBMSs (mysql, Oracle, and HSQL), contains 
documentation, an ERD of the schema, and the script for loading the 
NCBI taxonomy database.

	-hilmar

On Dec 9, 2005, at 1:58 PM, Angshu Kar wrote:

> Hi Hilmar,
>
> I'm obliged that you showed me the light. I reanalyzed the schema and 
> found that its no use working with a truncated version of 
> biosql-schema and now I'm planning to install the entire schema. Could 
> you please let me know where can I find the script for that for a Pg 
> db?
>
> Thank you so much. Else I would have to face a lots of problem in the 
> later half of my project.
>
> Gratefully,
> Angshu
>
> On 12/9/05, Hilmar Lapp <hlapp at gmx.net> wrote:Angshu, 
> load_seqdatabase.pl is a script that utilizes the language
>> binding library bioperl-db to load sequences and annotation into
>> Biosql. The object-relational mapping code is all over bioperl-db.
>>
>> I'm sorry, but if you believe it is worth fiddling with that
>> object-relational code to 'save' instantiating a few more tables then
>> you're welcome to do so but you're essentially on your own.
>>
>> Also, if you'd like to work with a schema the language binding of 
>> which
>> allows to arbitrarily drop tables from the schema and still work then
>> Biosql/bioperl-db may not be for you.
>>
>>         -hilmar
>>
>> On Dec 9, 2005, at 7:10 AM, Angshu Kar wrote:
>>
>> > Hi Hilmar,
>> >
>> > In the load_seqdatabase.pl script could you please tell me where you
>> > are inserting the data into the db tables, so that I can try and
>> > modify that part to insert data only to the tables that I need ?
>> >
>> > Thanks,
>> > Angshu
>> >
>> >
>> > On 12/8/05, Hilmar Lapp <hlapp at gmx.net> wrote: 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 ...
>>  >>
>> >> -hilmar
>> >>
>> >> 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
>> >> >
>> >> > _______________________________________________
>> >> > Bioperl-l mailing list
>> >> > Bioperl-l at portal.open-bio.org
>> >> > http://portal.open-bio.org/mailman/listinfo/bioperl-l
>> >> >
>> >> >
>> >> --
>> >> -------------------------------------------------------------
>> >> Hilmar Lappemail: lapp at gnf.org
>> >> GNF, San Diego, Ca. 92121phone: +1-858-812-1757
>> >> -------------------------------------------------------------
>> >>
>> >>
>> >>
>> --
>> -------------------------------------------------------------
>> Hilmar Lapp                            email: lapp at gnf.org
>> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
>> -------------------------------------------------------------
>>
>>
>>
-- 
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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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