[Go] Spliceform column in GAF

[Stoddard, Alexander]

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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> Gofriends at geneontology.org
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>

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