Re: [Gusdev-gusdev] representing gene symbols

[Joan M. <ma...@pc...>]

Hi all,

I thought the point of this discussion was to figure out how to 
integrate into the tables which contain (or were created to contain) 
manual gene annotation assignments
the gene information which we get from MGI/Gene cards sequence mappings. 
(although we may want to make recreate these tables for this and/or if 
PSU has certain needs) .

BTW, although a gene symbol is approved it can also change (MGI versions 
for instance and also they have -pending), so this is another case where 
changes can occur.  

As it stands now,  in the gene table we have the attribute gene_symbol 
where the approved human or mouse gene symbol is written for each gene 
when added by the annotator.
Also, in the gene table there is name, where I envisioned using the new 
annotation tool, the approved gene name would be written. 

approved gene_symbol = Fzd4
approved gene name = frizzled homolog 4 (Drosophila)


https://www.cbil.upenn.edu/cgi-bin/dotsgenes-curator/schemaBrowser.pl?db=GUSdev&table=DoTS::Gene&path=DoTS::Gene

Now for the Current dots.GeneSynonym table, the annotator can add gene 
symbol synonyms for the gene and this is where they are written.

https://www.cbil.upenn.edu/cgi-bin/dotsgenes-curator/schemaBrowser.pl?db=GUSdev&table=DoTS::GeneSynonym&path=DoTS::GeneSynonym

I created GeneAlias for other (not approved) gene names for a gene to be 
used by the new annotation tool.

https://www.cbil.upenn.edu/cgi-bin/dotsgenes-curator/schemaBrowser.pl?db=GUSdev&table=DoTS::GeneAlias&path=DoTS::GeneAlias


For genes, they can have gene symbol synonyms and also gene name aliases.
It not necessarily the case where every gene symbol synonym has a gene 
name alias which corresponds to it, as in the approved case above
or vice versa.




Joan



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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