[go] AmiGO and annotation qualifiers

[Judith Blake]

I like the first one and I like including the qualifiers in AmiGO.
http://www.ebi.ac.uk/~aji/demo.html 
The first one is the clearest.  I actually had to look around the others 
to find the qualifiers.
I think the default /should/ include the NOTs.  If a newbie is 
concerned, they can ask go-help or look around for documentation.  NOTs 
are important.

by nngene products do you mean the '3 associations' thing?  I have no 
idea what that means.

judy

Amelia Ireland wrote:
> Hi GO Consortium,
>
> There has been some discussion in the web presence working group about 
> the display of NOT annotations and annotations with qualifiers. There 
> are two issues; how to display the annotations with qualifiers, and 
> how gene product counts for terms with qualifiers should be displayed. 
> We'd like to get some feedback from the consortium on these issues 
> before releasing the new AmiGO.
>
> Annotations With Qualifiers
> ===========================
>
> I've made some mock ups of different possible arrangements here:
>
> http://www.ebi.ac.uk/~aji/demo.html
> http://www.ebi.ac.uk/~aji/demo2.html
> http://www.ebi.ac.uk/~aji/demo3.html
>
> These pages are viewing the GPs annotated to a term (and its 
> children), but a similar arrangement will be used to view the terms 
> with which a GP is associated.
>
> Which arrangement is the clearest? Things to consider:
>
> - how easy is it to see inconsistent annotations, e.g. the same GP has 
> a normal and a NOT annotation?
>
> - is it clear what the qualifier applies to?
>
> - some views (e.g. having the associations with operators/qualifiers 
> separated out) require extra calculations to generate and will hence 
> be slower
>
> - should the default view contain NOT annotations? Is a GO newbie 
> going to understand them?
>
> - is the 'nn gene products' link unambiguous in meaning? Is it helpful 
> to know how many GPs there are annotated to a term?
>
>
> Gene Product Counts
> ===================
>
> The WPWG discussed generating separate totals for numbers of GPs 
> annotated to a term without any qualifier and the no. of GPs annotated 
> to a term with each of the other qualifiers (currently the GP count 
> for a term *includes* any GPs annotated with 'contributes_to' and 
> 'colocalizes_with', but *excludes* NOT annotations). How useful would 
> this be, and is it intuitive to split the counts up thus, or is it 
> confusing (especially for GO newbies)? There is also this to bear in 
> mind:
>
> On 24 Jan 2008, at 20:11, Chris Mungall wrote:
>> On Jan 24, 2008, at 11:08 AM, Seth Carbon wrote:
>>> *) ask chris about splitting the gp count by qualifier (seth)
>>
>> you mean by contributes_to, the NOT operator etc?
>>
>> 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
>
>
>
> Any feedback would be gratefully received. Thanks!
>
> Amelia / the Web Presence Working Group.
>
> -- 
> Amelia Ireland
> GO Editorial Office,
> European Bioinformatics Institute, UK.
> Carbon neutral driving: http://www.targetneutral.com/TONIC/index.jsp
>
>
>
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