Re: [Gusdev-gusdev] unique sequence designator for DoTS.NASequence

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

terry-


in general external_database_release_id and source_id should be unique, 
if, of course, the source_id is a primary key for the external db.

steve

Terry Clark wrote:

>Hi Bindu and others,  
>You might have seen that I made a few minor
>changes to 
>   GUS::Common::Plugin::LoadGeneFeaturesFromXML::makeChromosome()
>to get the TIGR Arabidopsis genome uploaded into GUS working 
>because the sequence identification mapping is not yet worked out.
>I have some questions and comments about this.
>
>In the plugin at makeChromosome() there is a query performed 
>to determine whether the submitted sequence is in the db. 
>The approach that is in place uses a query selecting entries 
>based on attributes values for:
>   i) taxonomy, ii) external_release_id, and iii) source_id
>There is some code commented out here, since the plugin 
>is under construction.
>
>It's not clear to me that the intent of source_id is
>to uniquely identify the sequence. Is that so?
>Presently, source_id is constructed from with the hardwiring
>in the mapping         vvvv that we're working on.
>      source_id = ASMBL_ID_2_stringMap + ASMBL_ID
>The source_id above is a unique name by virtue of ASMBL_ID.
>
>On the other hand, NAME is an attractive self-documenting GUS 
>attribute that tempts me to use it for the query checking for novelty.
>In the plugin, NAME was/is set to CLONE_NAME, which seems fine,
>although with the caveat for TIGR, this is labeled as for their
>internal use.
>
>In the TIGR XML, the CLONE_NAME and ASMBL_ID are two alternative candidates 
>for uniquely naming a sequence. TIGR documents CLONE_NAME for internal
>use and ASMBL_ID for external use in uniquely identifying a sequence.
>
>I punted for now by adding the condition to the query
>   $ena_gus->setName($T->{ASSEMBLY}->{HEADER}->{CLONE_NAME})
>i.e., the attributes
>   i) taxonomy, ii) external_release_id, and iii) CLONE_NAME
>
>What do you think? 
>
>Terry
>
>
>
>
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