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[software-group] Re: [web-presence] WPWG transcript and notes

Chris Mungall cjm at fruitfly.org
Thu Jan 24 12:11:46 PST 2008


On Jan 24, 2008, at 11:08 AM, Seth Carbon wrote:

> WPWGers,
>
> Sorry that it took so long--here are the notes and transcript for the
> Monday WG:
>
> http://gocwiki.geneontology.org/index.php/WPWG-20080122
> http://gocwiki.geneontology.org/index.php/WPWG-20080122-transcript
>
> In summary, the new action items are:
>
> *) compare the different displays of the term qualifier and come up  
> with
> better ways of displaying the qualifiers (everyone)
>
> *) contact the GO list and ask for clarification about which  
> display to
> use (amelia)
>
> *) ask chris about splitting the gp count by qualifier (seth)

you mean by contributes_to, the NOT operator etc?

should be a wiki item...

unfortunately it is expensive to pre-compute the gp counts in any way  
that a single gp can end up in two partitions.

we currently partition by gp db name - no gp can be in > 1. this has  
the advantage that we can get the correct total by summing the  
numbers at query time.

however, if we have a partition that does not split gps in this way  
we can't sum across the partitions, which means we have to pre- 
compute for all combinations.

This may not be so bad for the qualifiers however, since the  
qualifiers are relatively rare.

would you really want this for the NOT operator though? remember the  
semantics are easy to get confused here. Would you want:

all gps that are NOT GPCRs (ie include those that are asserted not-TM  
receptor in the count) - negation propagates up the graph

all gps that have a NOT annotation to some kind of GPCR - negation  
propagates as normal


> Please send any major changes to this thread for the people who don't
> have a watch on the wiki pages.
>
> Cheers,
>
> -Seth
>
>
>




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