Re: [Gusdev-gusdev] representing gene symbols

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

i separated the synonyms from the names because i understood that HUGO 
and MGI have standardized that information, ie, that there is an 
approved name.

about the ExternalDatabaseRelease FK, yes, that sounds good.  i was only 
providing a sketch here.

the is_not is there for the same reason it is there for GO assocations: 
the association was made automatically, but a curator says it "is not" true.

steve

Angel Pizarro wrote:

> Steve Fischer wrote:
>
>> folks-
>> 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.
>
>
> Why do you want to separate the synonyms? It is implying that the 
> GeneName table has an "approved" name and only one approved name, but 
> approved by whom and what about alternate sources of information?  
> Also there should be a ExternalDatabaseRelease FK reference here. I 
> would store all names in a single table and handle the 'approved' 
> names either by a query to the ExternalDBRel (if you always prefer one 
> authority to others) or in the GeneNameAssociation table with a bit 
> column.
>
>>
>>
>> 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 
>
>
> Why "is_not" ? Is this a hold-over from GO terms? I don't see how it 
> applies to GeneName.
>
>
> Angel
>
>
>
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