Re: [Gusdev-gusdev] representing gene symbols

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

the full gene name is something like (i'm making this up) "Breast Cancer 
1"  and the symbol is "BRCA1"

steve

Arnaud Kerhornou wrote:

> Steve
>
> What do you call a full gene name and what is the gene symbol ?
>
> cheers
> Arnaud
>
> Steve Fischer wrote:
>
>> folks-
>>
>> right now in GUS, we have a bunch of tables and attribute that relate 
>> to gene symbols, names and aliases:
>>
>> Dots::Gene.name
>> Dots::Gene.gene_symbol
>> Dots::GeneAlias
>> Sres::DbRef.gene_symbol   (this is pretty clearly a hack.  DbRef is 
>> intended to store references to external database entries.  it is 
>> hackish to encode in the schema that we assume that such entries are 
>> gene records.  they could easily be proteins or journals, whatever)
>>
>> This schema is being used by the DoTS project to hold both automated 
>> assignments of gene_symbol (Sres::DbRef) and manual assignments.  The 
>> problem for the DoTS project is that these disparate ways of making 
>> assignments are not managed as a coherent whole. The manual and 
>> automated assignments are not queried together. I am thinking that we 
>> should consider a different approach, one modeled on how we store GO 
>> assignments.  It seems that Gene symbols and GO terms are very 
>> similar.  they are both amenable to contolled vocabs, and are both 
>> assigned by automated and manual operations.  This pattern may apply 
>> to other types of annotation as well.
>>
>>
>> 1. introduce a GeneName table:
>>   GeneName.gene_name_id
>>   GeneName.name    --- the full name
>>   GeneName.symbol  -- the symbol
>>
>> 2. introduce a GeneSynonym table:
>>    GeneSynonym.gene_name_id     -- the GeneName it is a synonym for
>>    GeneSynonym.name                  -- the full name of the synonym
>>    GeneSynonym.symbol               -- the symbol
>>
>> these tables are treated as controlled vocabularies, downloaded from 
>> sites such as HUGO and MGI.
>>
>>
>> 3. introduce a GeneNameAssociation table -- a mapping between Gene 
>> and GeneName (better name for this??)
>>   GeneNameAssociation.gene_id
>>   GeneNameAssociation.gene_name_id
>>   GeneNameAssociaction.review_status_id
>>   GeneNameAssociaction.is_not
>>   probably adopt here an instance and evidence mechanism similar to 
>> go assocation.
>>
>> note that this implies a m-m relationship between gene and gene name. 
>> while this might not be true in the ideal sense, it may well be true 
>> for tentative data, which is what we often have.  so, this model 
>> accepts that unfortunate fact, and does the best to preserve as much 
>> info as we can.
>>
>
>
>
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