[BioSQL-l] Re: Biosql-ora

[Jansen E Lim]

Hilmar Lapp wrote:

> The Oracle version of the schema in biosql is out-dated. I need to
> update it. bioperl-db works well with the (current :) version of the
> Oracle schema, that's what we use here internally.

Yes. Please, please update the Oracle version. :)

>
>
> I promise to update this by tonight (PST :). Sorry about that. You're
> the first one asking for the Oracle version. Let me know if you are
> serious about using it, and I'll consider moving the native repository
> into biosql-schema (as opposed to an import, which it is now).

Yes. I'm quite serious about the Oracle version. We're really an Oracle shop
here
but I thought I'd do the PostgreSQL version first (under duress, of course)
at the
suggestion of a PostgreSQL user.

> Also, I
> have constrained the Oracle version pretty rigorously, which wasn't
> appropriate in all places. I.e., sometimes I have to relax column
> widths etc to accommodate input data, and you will want to be made
> aware of such changes if they happen and if you run it seriously. That
> is, I'd post that to the list then too.
>
> On another note, the Oracle version adds some considerable
> sophistication on the database server end. It comes with a complete
> PL/SQL API, materialized views for fast name lookup and genome mapping,
> and with context indexes. Even though it may all run on Oracle 8i, I
> can't guarantee. I develop on 9i. For utilizing the additional
> features, it will help if you're somewhat familiar with Oracle.

Great.  We have 8.1.7.4 and 9i release 2 to work with.  This will really be
helpful.
I prefer working with Oracle since that's the platform I've been using for
nine years.  I
also wanted to compare the loading speed vs Pg.

>
>
>         -hilmar
>
> On Tuesday, January 28, 2003, at 11:44  AM, Jansen E Lim wrote:
>
> > Hi Hilmar,
> >
> > [...]
> > I tried using the Oracle verion of biosql and I wasn't sure it I could
> > use it as is.  There seems to be
> > quite a difference in the schema (table names are prefixed with SG_,
> > new column names, etc) between the PostgreSQL version.  Would it be
> > possible to get a list of what needs changing to make it work?
> > [...]
> >
> > Again, thank you for taking time to explain.
> >
> > Regards,
> > -Jansen
> >
> >
> >
> >
> --
> -------------------------------------------------------------
> Hilmar Lapp                            email: lapp at gnf.org
> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
> -------------------------------------------------------------