[Go] Spliceform column in GAF

[Rama Balakrishnan]

Chris,

I am trying to understand this proposal. So please bear with me.

Column 17 is optional and column 12 is mandatory. If you don't know  
the spliceform of the product in col 2 and hence leave col 17 as  
blank, then what would you put in column 12?
Because as I understand the proposal, what is in Col12 should reflect  
the type of the spliceform in col 17?

Thanks,

Rama

On Sep 10, 2008, at 10:51 AM, Chris Mungall wrote:

>
> If a group submitted annotations for two records corresponding to  
> the same gene this would be in violation. The most likely way for  
> this to happen would be when a MOD submits annotations to both  
> UniProtKB IDs and MOD IDs.
>
> On Sep 10, 2008, at 10:34 AM, Stoddard, Alexander wrote:
>
>> I do not clearly understand the following part of the spec regarding
>> non-redundant canonical entities:
>>
>> "In addition the GAF must be non-redundant with respect to canonical
>> entities in a genome"
>>
>> Chris, would you please give an example of how a GAF file could be
>> redundant with respect to canonical entities and how to correct the
>> example?
>>
>> Thank you,
>> Alex Stoddard
>>
>>
>> -----Original Message-----
>> From: go-bounces at genome.stanford.edu
>> [mailto:go-bounces at genome.stanford.edu] On Behalf Of Chris Mungall
>> Sent: Tuesday, September 09, 2008 5:30 PM
>> To: go list; Paul D Thomas
>> Subject: [Go] Spliceform column in GAF [was Re: [Gofriends]  
>> Redundancy
>> ingo_XXXXXX-assocdb-tables/dbxref.txt]
>>
>> [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_Splicefor
>> ms
>>
>> 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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