[Go] Spliceform column in GAF [was Re: [Gofriends] Redundancyin go_XXXXXX-assocdb-tables/dbxref.txt]

[Chris Mungall]

Hi Peter - yes, this was my point "spliceform" is too narrow a term.

I'd rather avoid the already overloaded "species"

"modified protein" or "modified X" implies that we are awarding  
certain forms canonical status (I know I use the term "canonical" to  
indicate the allowed values for col 2, but I don't think this is the  
best term)

Rama's "Gene_Product_Form_ID" works for me



On Sep 11, 2008, at 6:14 AM, D'Eustachio, Peter wrote:

>
> There's a biological distinction getting lost here (though I'm not  
> sure of its relevance / importance in this specific context).  
> Spliceform is a feature of the mRNA "intermediate" between a genomic  
> DNA sequence and a protein product. Phosphorylation, ubiquitination,  
> lipidation, glycosylation, leader peptide sequence cleavage etc. are  
> all things that happen to the protein once it has been translated  
> from the particular mRNA variant that emerged from the spliceform  
> process.
>
> Peter
>
> -----Original Message-----
> From: go-bounces at genome.stanford.edu on behalf of Benjamin Hitz
> Sent: Wed 9/10/2008 4:58 PM
> To: Chris Mungall
> Cc: go list; Paul D Thomas
> Subject: Re: [Go] Spliceform column in GAF [was Re: [Gofriends]  
> Redundancyin go_XXXXXX-assocdb-tables/dbxref.txt]
>
>
> On Sep 10, 2008, at 1:45 PM, Chris Mungall wrote:
>
>>
>> One thing I neglected to mention in the proposal - although it is
>> not specifically excluded - is the ability to annotate beyond the
>> level of individual spliceforms down to phosphorylated and otherwise
>> modified versions of proteins. I recall people being generally in
>> favour of this.
>>
>> In this scenario, col2 would continue to be the gene or abstract
>> protein, but col 17 would have an identifier for the modified form
>> of a specific protein isoform.
>>
>> Given this, perhaps the column heading "spliceform" is too narrow.
>> Do we have any suggestions for something more general. "form" is
>> perhaps too abstract.
>
> Molecular Species?
>
> Ben
>
>
> --
> Ben Hitz
> Senior Scientific Programmer ** Saccharomyces Genome Database ** GO
> Consortium
> Stanford University ** hitz at genome.stanford.edu
>
>
>
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