Re: [Gusdev-gusdev] Inconsistency among Sequence tables

[Chris S. <sto...@pc...>]

Yes, this is something we can easily fix and certainly should.
Chris
ps. I think this may reflect the history and bias of CBIL's view of 
GUS. The history is that when we started varchars were limited to 255 
but being NA-centric we fixed NASequence but not AASequence.

On Jan 26, 2005, at 4:07 PM, ju...@cs... wrote:

>
> 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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>
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