gusdev-gusdev

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

[<pi...@pc...>]

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
>

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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>

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

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

As I mentioned in another gusdev mail thread, I would like (Frank) to  
generate a list of proposed changes to incorporate into a GUS 3.6  
release hopefully sometime this month. If those on the gusdev list  
agree then sometime next month we will start assigning changes for  
supported plug ins.

Chris

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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>> Join SourceForge.net's Techsay panel and you'll get the chance to  
>> share your
>> opinions on IT & business topics through brief surveys-and earn cash
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>>
>>
>
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[GUSDEV] Changes to be incorporated into GUS 3.6

[Frank I. <inn...@pc...>]

Over the next few weeks I will be reviewing the amendments that been 
submitted to our change management tracker, as well as the changes made 
less formally to instances of GUS 3.5 installs within our own lab.  We 
are also seeking input from other GUS users, to review what changes they 
have made to their base GUS 3.5 installations.  If you have any changes 
or additions that you would like to also be considered for the next 
release, please email me with your suggestions.  Thanks.

-Frank

Frank Innamorato
Database Administrator
Computational Biology and Informatics Laboratory
Penn Center for Bioinformatics
1410 Blockley Hall
423 Guardian Drive
University of Pennsylvania
Philadelphia, PA 19104


Chris Stoeckert wrote:
> As I mentioned in another gusdev mail thread, I would like (Frank) to  
> generate a list of proposed changes to incorporate into a GUS 3.6  
> release hopefully sometime this month. If those on the gusdev list  
> agree then sometime next month we will start assigning changes for  
> supported plug ins.
>
> Chris
>   

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
>>>
>>>
>>>
>>
>>
>>
>>
>> --------------------------------------------------------------------- 
>> ----
>> Take Surveys. Earn Cash. Influence the Future of IT
>> Join SourceForge.net's Techsay panel and you'll get the chance to  
>> share your
>> opinions on IT & business topics through brief surveys-and earn cash
>> http://www.techsay.com/default.php? 
>> page=join.php&p=sourceforge&CID=DEVDEV
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>> Gus...@li...
>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>
>>
> _______________________________________________
> ApiDB mailing list
> Ap...@pc...
> https://mail.pcbi.upenn.edu/mailman/listinfo/apidb

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
>>
>
>
>
>
> ---------------------------------------------------------------------- 
> ---
> Take Surveys. Earn Cash. Influence the Future of IT
> Join SourceForge.net's Techsay panel and you'll get the chance to  
> share your
> opinions on IT & business topics through brief surveys-and earn cash
> http://www.techsay.com/default.php? 
> page=join.php&p=sourceforge&CID=DEVDEV
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