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

[Michael Ashburner]

Modified protein is my vote

M
On 10 Sep 2008, at 21:45, 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.
>
> Should we add some examples illustrating this?
>
> On Sep 9, 2008, at 3:30 PM, Chris Mungall wrote:
>
>> [redirected to GO]
>>
>> The change Mike speaks of is for the new spliceform column in the  
>> GAF.
>>
>> I have specced this out here:
>>
>> 	http://wiki.geneontology.org/index.php/ 
>> GAF_Spliceform_Column_Proposal
>>
>> Note that most of you will have read the previous document  
>> describing current practices for annotating alternate spliceforms:
>>
>> 	http://wiki.geneontology.org/index.php/ 
>> Annotation_of_Alternate_Spliceforms
>>
>> But you won't have read the fully formulated proposal, as I only  
>> put it on the wiki today.
>>
>> Note that this proposal was ratified at the SLC GOC meeting, but  
>> the majority of the discussion was at the RefG portion of the  
>> meeting. It's particularly important that folks who weren't at  
>> this part read and understand the proposal. Ratification at the  
>> GOC meeting may have been premature as I only intended to sketch  
>> out a solution collaboratively at that meeting.
>>
>> Once the above wiki page is in shape, we should send an  
>> announcement to gofriends (promptly, as it is of relevance to the  
>> current discussion below), all data providers and consumers, and  
>> then after that in the newsletter and on the main GO docs.
>>
>> As Mike says we are aiming for a introduction some time in 2009.  
>> It's important that anyone involved with producing GAFs is aware  
>> of the changes and is OK with this timetable.
>>
>> Cheers
>> Chris
>>
>> On Sep 9, 2008, at 1:22 PM, Mike Cherry wrote:
>>
>>> There is a change coming to the format of the gene association  
>>> file which will solve this problem.  Annotations to proteins,  
>>> gene, transcripts, etc for a particular locus will be identified  
>>> as such.  The change should occur in 2009.
>>>
>>> -Mike
>>>
>>>
>>>> From: "Quaid Morris" <quaid.morris at gmail.com>
>>>> To: "Gabriel Berriz" <gberriz at hms.harvard.edu>
>>>> Subject: Re: [Gofriends] Redundancy in go_XXXXXX-assocdb-tables/ 
>>>> dbxref.txt
>>>> Cc: gofriends at genome.stanford.edu
>>>>
>>>> Hi Gabriel,
>>>>
>>>> It looks like in the example that you gave RGD ID 1302948 is a  
>>>> gene ID and
>>>> ENSRNOP00000034933 is a protein ID.  Are all your examples like  
>>>> this?  Maybe
>>>> there are circumstances when it's possible to annotate a  
>>>> specific isoform
>>>> and others when only the gene can be annotated.
>>>>
>>>> Q
>>>>
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>>>
>>
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>
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