gene naming in CHADO - gene I.D concatenation on uniquename

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gene naming in CHADO - gene I.D concatenation on uniquename

claudia
Hi,
   I'm wondering if anyone has any information regarding how identical
gene or analysis names get renamed in chado by concatenating the feature
or gene I.D on to the end of the "uniquename", in an so.gene table for
example, and is there any way to control the concatenation?

Thanks,

Claudia


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Re: gene naming in CHADO - gene I.D concatenation on uniquename

Scott Cain
Hi Claudia,

Typically, the GFF ID gets used as a feature's uniquename, however, if
using that as the uniquename would violate the unique constraint on
the feature table of (uniquename, type_id, organism_id), then the
loader will attach the feature_id to the GFF ID with a hyphen to make
it unique.

This happens in the uniquename_validation method in
Bio::GMOD::DB::Adapter (which is in the Chado distribribution).  If
you want to modify the behavior, you can subclass
Bio::GMOD::DB::Adapter and then tell the bulk loader to use the
subclass instead (I think the subclass has to be named
Bio::GMOD::DB::Adapter::something--I created that functionality, but
honestly haven't tested it much).

Scott


On Wed, May 4, 2011 at 1:57 PM, claudia <[hidden email]> wrote:

> Hi,
>   I'm wondering if anyone has any information regarding how identical
> gene or analysis names get renamed in chado by concatenating the feature
> or gene I.D on to the end of the "uniquename", in an so.gene table for
> example, and is there any way to control the concatenation?
>
> Thanks,
>
> Claudia
>
>
> ------------------------------------------------------------------------------
> WhatsUp Gold - Download Free Network Management Software
> The most intuitive, comprehensive, and cost-effective network
> management toolset available today.  Delivers lowest initial
> acquisition cost and overall TCO of any competing solution.
> http://p.sf.net/sfu/whatsupgold-sd
> _______________________________________________
> Gmod-devel mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-devel
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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management toolset available today.  Delivers lowest initial
acquisition cost and overall TCO of any competing solution.
http://p.sf.net/sfu/whatsupgold-sd
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Re: gene naming in CHADO - gene I.D concatenation on uniquename

claudia
Hi Scott,
  Thank you for the quick reply. It seems that when I query MAKER
results in gbrowse from a database I created with a CHADO schema and I
know contains duplicate I.D's, Gbrowse returns the error stated below,
which does not occur in a db without duplicates. This brings me back to
an original question I had regarding how I can assign a reference I.D to
each unique project ( and be visible to the end user)  I load that will
potentially contain duplicate I.D's, and thus be able to query the
results in Gbrowse.

Thanks,
Claudia



On 04/05/2011 2:15 PM, Scott Cain wrote:

> Hi Claudia,
>
> Typically, the GFF ID gets used as a feature's uniquename, however, if
> using that as the uniquename would violate the unique constraint on
> the feature table of (uniquename, type_id, organism_id), then the
> loader will attach the feature_id to the GFF ID with a hyphen to make
> it unique.
>
> This happens in the uniquename_validation method in
> Bio::GMOD::DB::Adapter (which is in the Chado distribribution).  If
> you want to modify the behavior, you can subclass
> Bio::GMOD::DB::Adapter and then tell the bulk loader to use the
> subclass instead (I think the subclass has to be named
> Bio::GMOD::DB::Adapter::something--I created that functionality, but
> honestly haven't tested it much).
>
> Scott
>
>
> On Wed, May 4, 2011 at 1:57 PM, claudia<[hidden email]>  wrote:
>> Hi,
>>    I'm wondering if anyone has any information regarding how identical
>> gene or analysis names get renamed in chado by concatenating the feature
>> or gene I.D on to the end of the "uniquename", in an so.gene table for
>> example, and is there any way to control the concatenation?
>>
>> Thanks,
>>
>> Claudia
>>
>>
>> ------------------------------------------------------------------------------
>> WhatsUp Gold - Download Free Network Management Software
>> The most intuitive, comprehensive, and cost-effective network
>> management toolset available today.  Delivers lowest initial
>> acquisition cost and overall TCO of any competing solution.
>> http://p.sf.net/sfu/whatsupgold-sd
>> _______________________________________________
>> Gmod-devel mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-devel
>>
>
>

------------------------------------------------------------------------------
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management toolset available today.  Delivers lowest initial
acquisition cost and overall TCO of any competing solution.
http://p.sf.net/sfu/whatsupgold-sd
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Re: gene naming in CHADO - gene I.D concatenation on uniquename

Scott Cain
Hi Claudia,

Can you send some sample GFF that demonstrates the problem?  I don't
really understand the nature of the problem in the abstract.

Also, in the future, it would be better to send email of this type to
the schema mailing list, as more people will see it.

Thanks,
Scott


On Wed, May 4, 2011 at 2:43 PM, claudia <[hidden email]> wrote:

> Hi Scott,
>  Thank you for the quick reply. It seems that when I query MAKER results in
> gbrowse from a database I created with a CHADO schema and I know contains
> duplicate I.D's, Gbrowse returns the error stated below, which does not
> occur in a db without duplicates. This brings me back to an original
> question I had regarding how I can assign a reference I.D to each unique
> project ( and be visible to the end user)  I load that will potentially
> contain duplicate I.D's, and thus be able to query the results in Gbrowse.
>
> Thanks,
> Claudia
>
>
>
> On 04/05/2011 2:15 PM, Scott Cain wrote:
>>
>> Hi Claudia,
>>
>> Typically, the GFF ID gets used as a feature's uniquename, however, if
>> using that as the uniquename would violate the unique constraint on
>> the feature table of (uniquename, type_id, organism_id), then the
>> loader will attach the feature_id to the GFF ID with a hyphen to make
>> it unique.
>>
>> This happens in the uniquename_validation method in
>> Bio::GMOD::DB::Adapter (which is in the Chado distribribution).  If
>> you want to modify the behavior, you can subclass
>> Bio::GMOD::DB::Adapter and then tell the bulk loader to use the
>> subclass instead (I think the subclass has to be named
>> Bio::GMOD::DB::Adapter::something--I created that functionality, but
>> honestly haven't tested it much).
>>
>> Scott
>>
>>
>> On Wed, May 4, 2011 at 1:57 PM, claudia<[hidden email]>  wrote:
>>>
>>> Hi,
>>>   I'm wondering if anyone has any information regarding how identical
>>> gene or analysis names get renamed in chado by concatenating the feature
>>> or gene I.D on to the end of the "uniquename", in an so.gene table for
>>> example, and is there any way to control the concatenation?
>>>
>>> Thanks,
>>>
>>> Claudia
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> WhatsUp Gold - Download Free Network Management Software
>>> The most intuitive, comprehensive, and cost-effective network
>>> management toolset available today.  Delivers lowest initial
>>> acquisition cost and overall TCO of any competing solution.
>>> http://p.sf.net/sfu/whatsupgold-sd
>>> _______________________________________________
>>> Gmod-devel mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-devel
>>>
>>
>>
>
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
WhatsUp Gold - Download Free Network Management Software
The most intuitive, comprehensive, and cost-effective network
management toolset available today.  Delivers lowest initial
acquisition cost and overall TCO of any competing solution.
http://p.sf.net/sfu/whatsupgold-sd
_______________________________________________
Gmod-devel mailing list
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