Re: [Gmod-schema] Re: rad schema

[Jonathan C. <cra...@sn...>]

n Tue, 25 Feb 2003, Allen Day wrote:
> Just had a chance to download this.  Lots of SQL files in the
> distribution, trying to sort out what's relevant to me.  Are all the
> RAD-specific tables in the gus30-rad3* files?

Hi Allen-

I work with Angel on the GUS database project, of which RAD is now a
component, and so I'm going to chime in.  (We also share an office,
which has to count for something.)  All the RAD-specific tables *are*
defined in the gus30-rad3* files, although RAD also uses some tables
that are defined elsewhere.  For example, information on bibliographic
references and contacts (e.g., people and institutions) can be found
in the SRes ("Shared Resources") schema, along with a number of
controlled vocabularies and ontologies.  Tracking and access control
information is kept in the Core schema and almost all sequence
data (e.g., oligo and cDNA sequences) are stored in the DoTS schema.

So, yes, the rad3* files contain all the RAD-specific tables, but not
all of the RAD tables (i.e., precisely the ones *not* specific to RAD.)
Angel has mentioned the possibility of putting together a RAD-only
distribution that includes all of the tables used by RAD (and nothing
else), but that's probably not something we'll have in the immediate
future.  Our main concern at the moment is making the system (as a
whole) more portable, and once that's done it should in theory be
relatively easy to package up a distribution that excludes the non-RAD
tables.

I should also mention that the latest versions of all the schema files
are in a public CVS repository, kindly hosted by the Sanger Institute,
and they can be accessed over the web:

<http://cvsweb.sanger.ac.uk/cgi-bin/cvsweb.cgi/GUS/Model/schema/oracle/?cvsroot=GUS&f=h>

In addition to the schema there's an Ant-based build system that
partly automates the process of creating a new database instance from
the schema files (and generating the Perl modules that make up the
Perl object layer and a bunch of other things too.)  The documentation
is sketchy thus far but will be posted at <http://www.gusdb.org> when
finished.

Regards,

Jonathan