[go] AmiGO and annotation qualifiers

Chris Mungall cjm at fruitfly.org
Fri Feb 1 16:22:46 PST 2008 

On Feb 1, 2008, at 6:20 AM, Harold Drabkin wrote:

> 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 advance of this meeting I have started a page here:
http://gocwiki.geneontology.org/index.php/ 
Annotation_of_Alternate_Spliceforms

there were some useful comments at the managers meeting which I have  
not yet fully incorporated

I also made a few notes on the following page:
http://gocwiki.geneontology.org/index.php/Variant_annotation

I added signed comments to some of the MOD policies - I probably  
should have used the wiki discussion option. Tanya, can you check my  
comments re TAIR annotations?

> 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
>>
>>
>>
>
>

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