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

[Chris Mungall]

Sorry for the late response.

My feeling is this should be dropped from the current newsletter; it  
should wait until we can provide a URL that goes to a detailed  
specification.

Currently all we have is the wiki page I made prior to the meeting:

http://gocwiki.geneontology.org/index.php/ 
Annotation_of_Alternate_Spliceforms

This page is intended to give background so that the group could make  
an informed decision, it's not intended as the final spec

Also: although the proposal was accepted at the RefG meeting (see  
[1]), there were a number of issues that cropped up that have not yet  
been reflected in the above wiki page.

In particular, there was the issue of the meaning of the  
DB_Object_Type column. In my original proposal this would continue to  
retain the current meaning, i.e. the type of the entity referenced in  
col2 (i.e. the generic entity: a gene or generic protein). However,  
the majority of the participants at the meeting felt that this was  
not a good idea and that the type column should instead be the type  
of the entity referenced in the new col17 (ie the specific entity:  
e.g. a spliceform).

My original proposal was a standardization of best practice plus  
additional optional information with no change in meaning in existing  
columns; the revised form we decided at the meeting (not yet  
documented) involved a change in meaning. As such, it requires an  
especially long lead time.

The action items stated:

    1. update documentation
    2. write notice of changes to users
    3. individual data providers make sure that their input matches
    4. software changes as necessary

But didn't give any dates

I suggest:

June 6: The software group will create updated documentation on the wiki
	includes: a detailed specification GAF providers and consumers can  
follow
June 13: GOC provides feedback & refinement, signoff
June 20: email goes out to gofriends
August ?: announcement in newsletter
October 1: GAF files conforming to new spec go live

Note that the people who need to know most in advance probably read  
gofriends more than the newsletter (a hunch, I have no evidence for  
this)

I'm sympathetic to the view we should be as open as possible, but I  
worry about announcing too early and causing consternation and confusion

[1] http://wiki.geneontology.org/index.php/ 
Reference_Genome_Meeting_Minutes_April_2008#Annotation_Pipeline. 
2C_Part_1:_Generation_of_protein_sets_.28Suzi_Lewis.29

     *
           o ACTION ITEMS

    1. update documentation
    2. write notice of changes to users
    3. individual data providers make sure that their input matches
    4. software changes as necessary
    5. add header to gene association file
    6. syntex of gp2protein file will be provided by Mike and Chris

On May 20, 2008, at 11:01 AM, 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>
>> Date: May 19, 2008 8:52:38 AM PDT
>> To: software-group Group <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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