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

[Judith Blake]

Should some of this be discussed within the context of the PRO project?

Judy

Chris Mungall wrote:
> 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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