[Go] Spliceform column in GAF

Wed Sep 10 13:41:15 PDT 2008

But this would be the type for the locus/gene/whatever that encodes  
the gene product, not the gene product itself.

On Sep 10, 2008, at 12:01 PM, Mike Cherry wrote:

> I think column 12 should be mandatory.  I'd suggest locus when you  
> don't know.  However locus is not in SO.  The root node of SO is  
> region, it follows our usage with GO, use the root node.
>
> -Mike
>
> On Sep 10, 2008, at 11:29 AM, Chris Mungall wrote:
>
>>
>> On Sep 10, 2008, at 11:13 AM, Rama Balakrishnan wrote:
>>
>>> 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?
>>
>> protein, if it's a protein-coding gene. RNA if RNA-coding etc.
>>
>> I didn't document the case where the gene has not been molecularly  
>> characterized and we have IGI annotations. I'm open to suggestions  
>> here. Perhaps the best thing is to allow this column to be blank if  
>> we truly do not know if the gene is protein coding or not.
>>
>> However, if the gene is known to be protein coding yet the  
>> particular spliceform is not known then the type column should be  
>> protein
>>
>>> Because as I understand the proposal, what is in Col12 should  
>>> reflect the type of the spliceform in col 17?
>>
>> Yes, but we're making the open-world assumption here: absence of  
>> data does not mean an absence of the entity in reality.
>>
>> Thanks for the questions, looks like the document needs work to  
>> make it more readable.
>>
>> We only had a very cursory discussion of the type column in SLC,  
>> and we certainly didn't give people time to absorb the ramifications.
>>
>>>
>>> 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
>>>>>>>
>>>>>> _______________________________________________
>>>>>> Gofriends mailing list
>>>>>> Gofriends at geneontology.org
>>>>>> http://fafner.stanford.edu/mailman/listinfo/gofriends
>>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Go mailing list
>>>>> Go at geneontology.org
>>>>> http://fafner.stanford.edu/mailman/listinfo/go
>>>>>
>>>>
>>>> _______________________________________________
>>>> Go mailing list
>>>> Go at geneontology.org
>>>> http://fafner.stanford.edu/mailman/listinfo/go
>>>
>>>
>>
>> _______________________________________________
>> Go mailing list
>> Go at geneontology.org
>> http://fafner.stanford.edu/mailman/listinfo/go
>
>