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

[Karen Christie]

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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>>> 
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>> 
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