Re: [Gusdev-gusdev] Inconsistency among Sequence tables

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

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

Great;

Here is another inconsistency, which I have brought up
on the list before. Both GeneFeature and NAFeature
have a "name varchar2(30)" field though it
is useful to store the entire text that a GenBank file
may have for a feature.  GeneFeature has "gene varchar2(2000)"
but NAFeature lacks a varchar2(2000) field.  Perhaps
something such as "description varchar2(2000)" could be
added to NAFeature?  The NAFeature view is really hurting
for a field to store a long string of text.

> 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?

I agree that that is the right way to do it.  Sometimes
I mistakenly use the word table, when I mean view.

Thanks, Josef

>
> 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
> >
> >
> [...]