Re: [Gusdev-gusdev] representing gene symbols

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

The model I was going for is a controlled vocab, ie, that gene names, 
symbols and synonyms are knowable without reference to a Gene object. 
 The act of associating a Name with a Gene is "annotating" the Gene, and 
may be tentative.  And, there may be more than one Gene that tentatively 
lays claim to that name (eg across species?).  IF that is the model we 
are going for, then i don't think i agree that synonyms should reference 
a gene directly.

We have seen a similar problem with "reference" sequence, ie, chosing 
one of a set to be representative.

Here is how i think it can work (my original w/ modfications as per this 
discussion and pending Joan's explanation of aliases).  The GeneName has 
a boolean 'approved' attribute.  If it is set, then that is the approved 
name.  Otherwise, the GeneName is equal to its synonyms, but has been 
(arbitrarily) chosen as the representative.   (The other way to do this 
is to lose GeneName.is_approved and allow GeneName.name and 
GeneName.symbol be nullable, indicating that there is no approved name yet).

 1. GeneName table:
      gene_name_id
      name                 -- the full name
      symbol              -- the symbol
      is_approved      -- boolean      

2.GeneSynonym table:
   gene_synonym_id
   gene_name_id       -- the GeneName it is a synonym for
   name                     -- the full name of the synonym
   symbol                  -- the symbol

3. GeneNameAssociation table -- a mapping between Gene and GeneName 
(better name for this??)
  gene_id
  gene_name_id
  review_status_id
  is_not
  gene_name_type_id          -- points to a controlled vocab of gene 
name types such as mentioned by Arnaud.

  probably adopt here an instance and evidence mechanism similar to go 
assocation.

Jonathan Crabtree wrote:

>
> Steve Fischer wrote:
>
>> 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)
>
>
> Yes, this is definitely a hack; I added some columns to the DbRef table
> because I wanted to store 2-3 specific pieces of information for MGI and
> GeneCards entries, without creating another table.  However, I disagree
> that I "encoded" in the schema the assumption that these DbRef entries
> are gene records; I think if you look more closely you will see that all
> of the newly-added columns (gene_symbol, chromosome, centimorgans) are
> NULLable.  Therefore the only assumption I am making is that one or more
> of these columns *may* be applicable to certain DbRefs.
>
>> 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
>
>
> Arnaud's point that a gene may have names, but no approved name is a good
> one.  It suggests that GeneSynonym should reference Gene, not GeneName.
> We might also consider renaming "GeneName" to "ApprovedGeneName" and
> "GeneSynonym" to "GeneName".  Arnaud's second point, that there are
> potentially several different categories of names, suggests that we
> follow the example of the TaxonName table, and add a 'name_class' column
> to GeneSynonym.  (This could also be a controlled vocabulary.)  Then I
> think the only remaining question is whether we are sure that the only
> kinds of approved names we will ever have are "gene name" and "gene 
> symbol".
>
> Jonathan
>
>
>
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