Re: [GUSDEV] [ApiDB] issue: ExternalNaSequence, VirtualSequence and NaSequence

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

Debbie,
Thanks for putting this out to the gusdev list. Has anyone added this  
to the GUS bug tracker for schema?

Chris

On Mar 2, 2007, at 3:46 PM, pi...@pc... wrote:

> I agree with this. In fact, the current database being used by our  
> mammalian
> DoTS build has incorporated a source_id into the assembly view of
> NASequence. I
> believe (could be wrong on this) that this is the only view without a
> source_id.   So this would clear the way to having source_id in the
> super class
> for the "official" GUS schema. Are all the nasequenceimp views  
> using the same
> field for source_id? Are there other views missing a source_id?
>
>
>
>
> Quoting Steve Fischer <sfi...@pc...>:
>
>> folks-
>>
>> we've been again reminded of the issue that toxo stores its  
>> chromosome
>> sequence in VirtualSequence while the other two use  
>> ExternalNaSequence.
>>
>> this means that we cannot re-use sql code, which is a headache.
>>
>> our proposed solution is to upgrade NaSequence view (the  
>> superclass) to
>> have a source_id column.   We feel that this is correct semantically,
>> and also solves our problem.
>>
>> the semantics are that:
>>  (1) NaSequence already has an external_database_release_id, which
>> makes no sense w/o source_id
>>  (2) the pair (external_database_release_id, source_id) has  
>> "universal"
>> semantics (ie, not just limited to "external" sequences).  that
>> semantics is "dataset and stable_id"
>>
>> steve
>> _______________________________________________
>> ApiDB mailing list
>> Ap...@pc...
>> https://mail.pcbi.upenn.edu/mailman/listinfo/apidb
>>
>
>
>
>
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