[go] AmiGO and annotation qualifiers

[Ben Hitz]

I am of the opinion that to a naive user, the qualifiers are useless,  
at best.   They are such a small fraction of the annotations that  
dropping them completely would not significantly effect coverage or  
information content of the go association database as a whole.

That being said, they are not going away.   I would recommend the  
following:
By default, amigo just does not display any "qualified" associations.
There could be a "show advanced" or "show qualifiers" option which  
would have to be explicitly checked to display them.   Then we can  
chose a display option best suited to the "advanced user" (which is  
pretty much GOC people only), and not worry about fooling or  
confusing a newbie.

I also think they should be moved to distinct GA files, but that is a  
separate issue.

Ben
On Jan 29, 2008, at 6:00 AM, 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
>
>
>
>

--
Ben Hitz
Senior Scientific Programmer ** Saccharomyces Genome Database ** GO  
Consortium
Stanford University ** hitz at genome.stanford.edu