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

Suzanna Lewis suzi at berkeleybop.org
Fri May 23 13:44:06 PDT 2008 

I'd like to see it in the next newsletter. We can indicate that people  
can expect the specifications for the change on June 20th. Perhaps  
even provide a URL that will be populated by June 20th.

The suggested dates seem reasonable to target, including October 1  
(Mike don't you think June 20th to Oct 1st is sufficient time?)

I fully concur on the SO IDs in the type column

-S

On May 22, 2008, at 3:37 PM, Mike Cherry wrote:

> I'm okay with most this however if the changes are not announced to  
> gofriends and in the newsletter until the first of August then  
> October 1 is too soon for the switch.  We know the GAF files are  
> used by many and two months is a bit short to be good to our users  
> and allow them a reasonable time to make needed changes.  Not  
> everyone will be able to jump on changing their scripts  
> immediately.  End of October or first of November would be better.
>
> That would also mean that all files would change at that time.  The  
> filtering script could add the extra columns if not in a GAF.  This  
> of course would not cover changes in the type column.
>
> One other thing that was discussed was the switch to using SO IDs in  
> the type column.  I like that idea.
>
> -Mike
>
>
> On May 22, 2008, at 2:23 PM, Chris Mungall wrote:
>
>>
>> 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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