Re: [GUSDEV] GeneticMarker view

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

i am not sure i like the idea of stuffing multiple aliases into one row.

steve

Deborah Pinney wrote:

> Aaron J. Mackey wrote:
>
>> A few notes/thoughts on the proposal:
>>
>> Why would a genetic marker be considered a sequence?   I guess you  
>> instead meant a view of dots.NaFeatureImp?
>
>
>
> Yes I mistyped in the note, the view definition was  "FROM 
> DoTS.NAFeatureImp WHERE subclass_view='GeneticMarker' ".
>
>>
>> The relationships between a given set of markers are defined  
>> genetically (i.e. as linked loci with genetic distances measured in  
>> centiMorgans) with respect to a single genetic map (which 
>> corresponds  to a specific set of experimental crosses or an observed 
>> pedigree).   The same two markers may have different distances (or 
>> even be  unlinked) in a different map.
>
>
> Not all genetic marker sets are defined strictly genetically. When 
> location is a physical location on a sequence, this information can be 
> captured in the dots.nalocation table and a marker can have multiple 
> locations. When location is defined genetically in the stricter sense, 
> capturing the information is not as straight forward but can be done 
> using the same view and nalocation (note that there is a linkage_group 
> attribute in the proposed view as well as an 
> external_database_release_id) and a  marker can be represented by more 
> than one row in the nafeature view.
>
>>
>> A markers phenotype is often only its physical definition: SNP, 
>> SSLP,  SSCP, RFLP, etc.  Is this what the SO term is supposed to 
>> capture?   If so, what is the "type" field meant to capture?
>
>
>
> No, type was intended to capture the kind of marker represented in the 
> row as the ones you mention as well as markers not necessarily in SO 
> as blood groups or allozymes. The sequence_ontology_id is there 
> because all nafeature views have this attribute and of course it can 
> be used in the case where there is an approrpriate 
> sequenceontology.term_name.
>
>>
>> As mentioned elsewhere, organism/strain should probably be a single  
>> foreign key into the taxonomy table.
>
>
> Yes, I agreed with Chris and this was dropped.
>
>>
>> Measures of heterogeneity and penetrance are also specific to a 
>> given  population study, and are not universally true.  I could 
>> imagine  these and other attributes of a given study being captured  
>> independently.  This will be an important area of growth in the next  
>> 10 years as widescale familial genotyping becomes more prevalent.
>
>
>
> These are nullable so not required from every study. Perhaps we don't 
> want these attributes and they can be eliminated. The data I intended 
> to load don't have these values but this is only one example and these 
> are values often associated with markers.
>
>>
>>
>> Markers may have multiple aliases.
>
>
>
> Yes, this is true. We can decide not to enter a value into this 
> attribute as it is nullable or we can have a list as the attribute is 
> a varchar2(1000).
>
>>
>>
>> Thanks,
>>
>> -Aaron
>>
>> 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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>>
>> -- 
>> Aaron J. Mackey, Ph.D.
>> Project Manager, ApiDB Bioinformatics Resource Center
>> Penn Genomics Institute, University of Pennsylvania
>> email:  am...@pc...
>> office: 215-898-1205 (Goddard) / 215-746-7018 (PCBI)
>> fax:    215-746-6697
>> postal: Penn Genomics Institute
>>         Goddard Labs 212
>>         415 S. University Avenue
>>         Philadelphia, PA  19104-6017
>>
>
>
>
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