Re: [GUSDEV] GeneticMarker view

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

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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