Re: [GUSDEV] GeneticMarker view

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

Chris Stoeckert wrote:

You're right about centimorgans, I originally had float and somehow 
dropped it. Also, there is an sres.phenotype table of which I was not 
aware.  Do you know if there is an accepted  phenotype ontology that is 
not mammal centric?  This leads to the question raised by Steve's 
comment that a  foreign key has to be included in the superclass view 
and imp table. Do we want to add phenotype as a foreign key? There 
probably should be a CV for genetic marker type but I haven't seen it 
and SO  terms don't cover them (blood groups for example) so I'm not 
sure that type can be a reference to another table. You're probably 
right about the organism and strain being covered by the taxon_id in the 
NASequence Imp view. Those are probably appropriate for the SeqVariation 
view but not for GeneticMarker and I'll drop them. On second thought, I 
think product should probably be dropped as phenotype is probably the 
correct association and already an attribute. I was trying to anticipate 
a variety of data sets (I'm only dealing with a single example) so I 
included linkage_group but I'm not sure whether this attribute is needed. 

Here is an altered view definition:
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,
INT1 as phenotype,
STRING3 as type,
STRING4 as linkage_group,
FLOAT1 as centimorgan,
STRING5 as measure_of_heterogeneity,
STRING6 as penetrance,
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'


> 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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