Re: [Gusdev-gusdev] representing gene symbols

[Angel P. <an...@pc...>]

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