[Bioperl-l] loading data to biosql tables

[Angshu Kar]

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
> -------------------------------------------------------------
>
>
>