[go] partitioning gene association files

[Mike Cherry]

On Jan 30, 2008, at 10:14 AM, Chris Mungall wrote:

> We need a smarter way of downloading association files
>
> I have marked this high priority on the web presence tools (ie  
> amigo) tracker:
>
> http://sourceforge.net/tracker/index.php?func=detail&aid=1882857&group_id=36855&atid=494390
>

With that I think this current thread has concluded.

SGD has decided not to push for a separate file for IEA annotations.   
We will do what everyone else already does and provide the IEA  
annotations from GOA in our regular file with everything it already  
contains.  Providing the GOA annotations is a GOC requirement and thus  
with the addition of the GOA IEAs we will be in compliance with that  
requirement.  We will work on more text for the header of our gene  
association file to describe the change.  We will also have emails  
announcements and notices in the GO and SGD newsletters.

I believe all the discussion on this thread really points to the great  
need of an interface that provides access the GOC annotations.  That  
way users can select the evidence types, qualifiers, taxon IDs, ...  
that they want to retrieve.  Plus they can specify the output format:  
classic gene association format, OBO, ... they like.  The file(s) that  
each project uploads to the GO CVS is still what it is but for the  
users it should become secondary to the data download interface.

Lets move discussion of the new interface to the web presence working  
group.

-Mike