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

[Bindu G. <bi...@pc...>]

string1 in VirtualSequence is 'confidence', which Toxo is not using.  
it should be pretty straightforward to flip this with string2  
(source_id).

Bindu

On Mar 2, 2007, at 4:19 PM, Steve Fischer wrote:

> 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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