Re: [GUSDEV] GeneticMarker view

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

just a reminder that foreign keys have to go into the Imp table, and 
therefore into the superclass...
steve

Chris Stoeckert wrote:

> Hi Debbie,
> Some of the strings look like they might be numbers (e.g.,  
> centimorgan) or foreign keys to a controlled vocabulary (e.g.,  
> phenotype, type, organism, strain). Since NAFeatures have NASequence  
> which have taxon_id is "organism" really needed? Is product a protein  
> and therefore should be linked to an AA table? In other words, which  
> are the key attributes that should be intregrated with other data in  
> GUS and what can just go into a free text description field?
> Thanks.
> Chris
>
> On Aug 23, 2005, at 12:49 PM, Deborah Pinney wrote:
>
>> I suggest a new view of dots.NaSequenceImp that would be used to  
>> store genetic marker data. Genetic markers are a staple genetic  tool 
>> but include a large variety of data types, some of which may  be 
>> covered by other feature views. I am proposing this view for the  
>> variety of genetic marker data that are not specifically stored  
>> elsewhere. Below is a proposed view definition that requires review  
>> and probably modification.
>>
>> SELECT NA_Feature_ID as na_feature_id,
>> NA_SEQUENCE_ID as na_sequence_id,
>> SUBCLASS_VIEW as subclass_view,
>> NAME as name,
>> SEQUENCE_ONTOLOGY_ID as sequence_ontology_id,
>> PARENT_ID as parent_id,
>> EXTERNAL_DATABASE_RELEASE_ID as external_database_release_id,
>> SOURCE_ID as source_id,
>> PREDICTION_ALGORITHM_ID as prediction_algorithm_id,
>> IS_PREDICTED as is_predicted,
>> REVIEW_STATUS_ID as review_status_id,
>> STRING1 as alias,
>> STRING2 as phenotype,
>> STRING3 as type,
>> STRING4 as linkage_group,
>> STRING5 as centimorgan,
>> STRING6 as measure_of_heterogeneity,
>> STRING7 as penetrance,
>> STRING8 as organism,
>> STRING9 as strain,
>> STRING12 as product,
>> MODIFICATION_DATE as modification_date,
>> USER_READ as user_read,
>> USER_WRITE as user_write,
>> GROUP_READ as group_read,
>> GROUP_WRITE as group_write,
>> OTHER_READ as other_read,
>> OTHER_WRITE as other_write,
>> ROW_USER_ID as row_user_id,
>> ROW_GROUP_ID as row_group_id,
>> ROW_PROJECT_ID as row_project_id,
>> ROW_ALG_INVOCATION_ID as row_alg_invocation_id,
>> FROM DoTS.NAFeatureImp WHERE subclass_view='GeneticMarker'
>>
>>
>>
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>
>
>
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