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

Tue May 27 06:54:38 PDT 2008

Hi Suzi

We had already gone ahead and taken this back out again. Given the
holiday weekend we are now really struggling to make further changes and
get this out by the end of the week. I am about to send the latest
version to the GO list for comments.

While we could change it again and put this back in, I'm not sure I'm
very keen on having a link to a page that doesn't exist when the
newletter goes out - will people really check back a few weeks after
they receive the newletter? Only other suggestion is to write the online
proposal now and make this one the June newsletter with a shorter gap
before the next one.

Could we have a definitive GO top answer on this once you have looked at
the current version please?

Thanks,

Susan

On Fri, 2008-05-23 at 13:44 -0700, Suzanna Lewis wrote:
> 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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> >>
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> >
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> >
> 
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