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

[Steve F. <sfi...@pc...>]

ok, great.

no, source_id is string1 in one view and string2.  we'd have to adjust that.

in Api we plan on correcting this with a schema/data patch.

steve

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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