[Bioperl-l] loading data to biosql tables

[Angshu Kar]

Hi Hilmar,

I've run the biosqldb-pg.sql through psql successfully. It has created 28
tables. :(
Are there any other possibilities?

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