[Go] Fwd: GAF changes, addition of new columns

[Doug howe]

If I recall correctly, the minimal required change would be to include a 
blank column 16 and a column 17 with the gene ID for the gene that was 
annotated (same as column 2 for many of us), right?  Then when we gain 
the ability to populate column 16 or curate to splice variants, column 
16 would contain the proper data, column 2 would contain the ID of the 
splice variant ID which was annotated, and column 17 the ID of the gene 
from which splice variant was derived...  Should be easy to add the two 
new columns to the GAF.  Database and curation interface changes would 
take some time.
-Doug


Michael Ashburner wrote:
> I agree, Michael
>
> On 20 May 2008, at 19:31, Judith Blake wrote:
>
>> I feel that we should include this in the newsletter.  MGI might not 
>> get into our db, but we can manipulate the GAF file if required and I 
>> don't see a problem with that.
>>
>> judy
>>
>>
>> Mike Cherry wrote:
>>> Decision needed.
>>>
>>> There has been no comments from the software group.  I feel we could 
>>> include the date(s) for GAF format change in the newsletter that is 
>>> in final edits now.
>>>
>>> I'll be traveling until Saturday so I hope someone else can make 
>>> sure this is decided and included in the newsletter.
>>>
>>> -Mike
>>>
>>>
>>> Begin forwarded message:
>>>
>>>> *From: *Mike Cherry <cherry at stanford.edu <mailto:cherry at stanford.edu>>
>>>> *Date: *May 19, 2008 8:52:38 AM PDT
>>>> *To: *software-group Group <software-group at genome.stanford.edu 
>>>> <mailto:software-group at genome.stanford.edu>>
>>>> *Subject: **GAF changes, addition of new columns*
>>>>
>>>> Hi,
>>>>
>>>> Everyone asks me when the new columns will become required.  What 
>>>> do you all think?
>>>>
>>>> I'd suggest September or October.  We need to define a date.  A GO 
>>>> newsletter will go to press, so to speak, this week.  The next 
>>>> newsletter will be in August.  That will give two newsletters 
>>>> announcing the change, and having the switch over date be a month 
>>>> or two after the August newsletter.
>>>>
>>>> Part of this is when can groups start submitting a GAF with the 
>>>> additional columns, and when would it become manditory?  There are 
>>>> two additional columns involved, the long reserved column for 
>>>> properties (column 16) and the newly agreed one for canonical gene 
>>>> name (column 17).
>>>>
>>>> Any counter proposals?  Concerns?  I've heard from Harold that this 
>>>> change will take a few months for the MGI software staff to put 
>>>> into production.
>>>>
>>>> -Mike
>>>
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>>>
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