[go] AmiGO and annotation qualifiers

[Jim Hu]

On Jan 31, 2008, at 1:30 PM, Chris Mungall wrote:

>
> Unambiguous is good.
>
> A related question:
>
> Let's assume there is a NOT annotation for GO:0008047 enzyme  
> activator activity (is_a parent of proteasome activator activity)
>
> If you are on the page for GO:0008538 proteasome activator activity,  
> would you expect to see this annotation?

I'd expect to see this iff there is an unqualified annotation to the  
same product. In other words, this is only useful as a conflict flag  
IMO.

>
>
> I think most people's answer would be no, this would be too confusing.
>
> However, it is the case that anything that is not an enzyme  
> activator is by definition not a proteasome activator activity.
>
>
>
> On Jan 31, 2008, at 11:21 AM, Michael Ashburner wrote:
>
>> I prefer demo3 - it is clear and unambiguous.
>>
>> Michael
>>
>> Michael
>>
>> On 29 Jan 2008, at 14:00, 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
>>>
>>>
>>>
>>>
>>>
>>
>>
>

=====================================
Jim Hu
Associate Professor
Dept. of Biochemistry and Biophysics
2128 TAMU
Texas A&M Univ.
College Station, TX 77843-2128
979-862-4054


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