[Bioperl-l] loading data to biosql tables

[Hilmar Lapp]

On Dec 10, 2005, at 6:38 PM, Angshu Kar wrote:

> Hi Hilmar,
>
> I've run the biosqldb-pg.sql through psql successfully. It has created 
> 28 tables. :(

That sounds good. Why are you unhappy about it?

> Are there any other possibilities?

To achieve what?

	-hilmar

>
> Thanks,
> Angshu
>
>
> On 12/10/05, Hilmar Lapp <hlapp at gmx.net> wrote: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 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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