[go] AmiGO and annotation qualifiers

Fri Feb 1 06:20:19 PST 2008

It is important to note that NOT is a very useful and potentially 
important piece of information. I just finished annotations of the gene 
products of two unrelated genes. Both of them made two isoforms by 
alternate splicing, resulting in a long form and a short form. The long 
form has an activity; the short form does not; both assemble with 
another protein equally as well; by adjusting the amount of the two 
isoforms, the activity of the resulting complex is regulated. Because we 
annotate to gene object, these each get two annotations, one for the 
long, one for the short. The short has the NOT qualifier. At the moment, 
the isoform ID is not displayed (but stored in special notes in our EI), 
nor is it in the GAF. However, since both annotations map to the same 
reference, a user should check it out.  
One often sees "NOT" when one isoform is nuclear, and one is not; or if 
a protein modification,such as phosphorylation, alters the activity of 
the protein. Again, we currently have no means of putting that in the 
GAF; however, I expect a user to be able to read the references 
associated with the annotation.  Additionally,  literature in question 
can often have apparently conflicting data because of differences in 
cell type, etc. The GAF is a summary of the totality of  information colle
In a separate discussion thread, to be taken up at SLC, we will start to 
address how we can make the extra data readily available. MODS that 
annotate protein ids directly do not have this dilema. cted.

In any event, it is fairly easy to parse a GAF and remove the qualifiers 
if one wants.

hjd

Jim Hu wrote:
>
> 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/%7Eaji/demo.html>
>>>> http://www.ebi.ac.uk/~aji/demo2.html 
>>>> <http://www.ebi.ac.uk/%7Eaji/demo2.html>
>>>> http://www.ebi.ac.uk/~aji/demo3.html 
>>>> <http://www.ebi.ac.uk/%7Eaji/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
>
>
>