Re: [Gusdev-gusdev] Inconsistency among Sequence tables

[<ju...@cs...>]

As I continue to work with the ExternalAASequence view,
I find another discrepancy with other Sequence views/tables.

Compare the size the description field between NASequenceImp and
AASequenceImp.

 DoTS.NASequenceImp DESCRIPTION   VARCHAR2(2000)
 DoTS.AASequenceImp DESCRIPTION   VARCHAR2(255)

255 characters is often two small to include the entire name
of a sequence from a fasta file.  Enlarging the
DoTS.AASequenceImp description field to 2000 and
and passing this field to the several views on AASequenceImp
would be greatly appreciated as well.

Thanks, Josef


Chris Stoeckert <sto...@pc...> writes:
>
> Hi Josef,
> Your comments are very timely in light of our plans to release GUS 3.5
> shortly which is meant to address issues such as you raise. Mike sent
> mail earlier today on this but please see
> http://gusdb.org/wiki/index.php/Gus3.5RoadMap
>
> I think that you are right about the need for taxon_id. Note that it
> should probably go in AASequenceImp (the table) and be inherited by all
> views. Anyone have a problem with that for GUS 3.5?
>
> Note that both AASequence and ExternalAASequence are views with
> AASequence as the "superclass" view. external_database_release_id is a
> named attribute of the parent table and so is inherited by all views.
>
> Cheers,
> Chris
>
> On Jan 25, 2005, at 3:15 PM, ju...@cs... wrote:
> >
> > I recently began working with the DoTS.ExternalAASequence table for
> > the first time, and I noticed several discrepancies with this
> > table and the DoTS.ExternalNASequence and DoTS.NASequence tables,
> > one of which I feel is serious.
> >
> >                    name            taxon_id    description
> > external_database_release_id
> >                    varchar2(255)   number(12)  varchar2(2000)
> > number(10)
> >
> > ExternalNASequence  yes            yes         yes              yes
> > NASequence          no             yes         yes              no
> > ExternalAASequence  yes            no          yes              yes
> > AASequence          no             no          yes              yes
> >
> >
> > Looking at the above chart, we see that both AASequence
> > and ExternalAASequence lack the taxon_id.  This surely must
> > be an oversight, I cannot imagine why such a thing
> > could be intentional.
> >
> > A minor annoyance is that NASequence and AASequence lack a
> > "name varchar2(255)" column and therefore must have all text
> > regarding a sequence in the description column.  For query
> > and display purposes, it is very useful to be
> > able to refer to a sequence by a shorter handle.
> >
> >
[...]

Daphne Preuss Laboratory
Molecular Genetics and Cell Biology
The University of Chicago
ju...@cs...

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