[Go] addition of localization specific process terms ?

[Chris Mungall]

On Mar 4, 2009, at 10:33 AM, Jim Hu wrote:

> On Mar 4, 2009, at 11:49 AM, Chris Mungall wrote:
>
>> On Mar 4, 2009, at 7:59 AM, Jim Hu wrote:
>>
>>> On Mar 4, 2009, at 2:38 AM, Valerie Wood wrote:
>>>
>>>> Because of all of the arguments in favour  mentioned by Karen and  
>>>> Chris I  thought it was always necessary and required for  
>>>> curators to make the more granular annotation in these cases. We  
>>>> decided long ago that proliferation of the ontology was not an  
>>>> issue when pitched against accurate capture of biology, and  I  
>>>> wasn't aware that it was ever GO philosophy not to capture  
>>>> compartment specific processes in this way.
>>>
>>> I wasn't involved in GO when this was decided, but as someone who  
>>> does stuff on the software side as well as the annotation side, I  
>>> think proliferation of the ontology should be an issue that is not  
>>> dismissed so lightly.
>>
>> What are your concerns in particular?
>>>
>
> My two concerns are the obvious ones, nothing particularly  
> sophisticated:
>
> 1) performance, especially of web-based tools that have to display  
> GO with short processing times.  IIRC, AmiGO has had this problem -  
> traversing the ontology to find all the children and annotations to  
> children is slow enough that Mike had to write a cron job to kill  
> excess db queries that came from users getting impatient and  
> reloading the page while the traversal was in progress.  As the  
> ontology gets big, these traversals take longer.  Maybe there are  
> more efficient algorithms to deal with this, maybe AJAX partially  
> makes this tolerable, and maybe the problem is the same with post- 
> composition.  But it seems to me that at some point sheer size has a  
> performance hit.

This is more of a problem for when the user requests genes for a high- 
level term. Getting rid of more specific terms wouldn't help at all.

>
> 2) User interface.  When I browse the ontology to look for the  
> appropriate terms to do an annotation, there are nodes that would be  
> unreadable if precomposition was being done consistently.   
> Fortunately it isn't being done consistently at present.  For  
> example, look at the children of the positive and negative  
> regulation terms in the process ontology.  There are terms in there  
> for mRNAs for specific genes (oskar and bicoid)!  That strikes me as  
> being completely insane... if implemented for all regulated genes in  
> all organisms, that node would have hundreds of thousands of  
> children - it would be a large subset of UniProt/Genbank all at one  
> level.  Or worse, because many genes would be present at multiple  
> overpopulated nodes in GO.

I agree the UI problem is already hopeless (regardless of the  
specifics of oskar and bicoid).

The solution here are:

1. massive rethink of how we show the ontology to users
or
2. massive obsoletion of existing composed terms

I am discounting 2 out of hand, which leaves us with 1

> I shudder to think what the graph representations would look like.

Do the users always need to see a graph?

>
> <snip>
>>> I find the argument that one can't do an AND with some tools to be  
>>> more of an argument to improve the tools than an argument to do  
>>> extensive precomposition.  If we have to build GO practice around  
>>> the weakest tools, then we should also do explicit annotation all  
>>> the way up to root for every term, to handle tools that don't use  
>>> the true path rule.  I'm NOT advocating that!!
>>
>> I agree that we shouldn't avoid doing the right thing because of  
>> the weakest tools. I think we should have a plan for how we can  
>> support tools, but I think we first need to agree roughly on what  
>> the right thing is..
>
> I think everyone agrees with this!
>
> Jim
>
>
>>
>>>
>>> Jim
>>>
>>> =====================================
>>> Jim Hu
>>> Associate Professor
>>> Dept. of Biochemistry and Biophysics
>>> 2128 TAMU
>>> Texas A&M Univ.
>>> College Station, TX 77843-2128
>>> 979-862-4054
>>>
>>>
>>>
>>
>
> =====================================
> Jim Hu
> Associate Professor
> Dept. of Biochemistry and Biophysics
> 2128 TAMU
> Texas A&M Univ.
> College Station, TX 77843-2128
> 979-862-4054
>
>
>