Re: [Gusdev-gusdev] representing gene symbols

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

Joan-

can you explain what a gene alias is as opposed to a gene synonym?

thanks,
steve

Joan Mazzarelli wrote:

> 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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>
>
>
>
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