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

[Rama Balakrishnan]

I agree spliceform is too narrow, but just 'form' is too vague. I  
agree we should avoid "protein" for that column.
Also it is the spliceform identifier that goes in Col17 not the name  
of the spliceform. So we should append ID to the column name i feel.

Will gene_product_form_ID work?

rama

(ps: I posted this message once before but I don't think it came  
through. apologies if you receive it multiple times)


On Sep 11, 2008, at 9:16 AM, Karen Christie wrote:

> might be best to avoid use of the word 'protein' in the column title  
> since the GOC annotates RNA gene products as well
>
> -Karen
>
>
> On Thu, 11 Sep 2008, Michael Ashburner wrote:
>
>> 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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