Re: [Gmod-schema] Re: rad schema

[Allen D. <all...@uc...>]

Jonathan,

Thanks for elaborating on this.  It's very useful, b/c as you may be
aware, I'm looking into porting the RAD portion of GUS into Chado.  
Knowing where the hooks into the rest of the schema are will help me write
the appropriate adapters to the rest of the Chado schema.

Should I be using cvs rather than the tarball snapshot?  Are there major 
changes coming to the RAD section?

-Allen

On Tue, 25 Feb 2003, Jonathan Crabtree wrote:

> 
> 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
> 
> 
> 
>