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Quantifying Specificity of GO Terms

Waclaw Kusnierczyk Waclaw.Marcin.Kusnierczyk at idi.ntnu.no
Wed Apr 18 01:12:34 PDT 2007


This is exactly the problem.  Coding is the least painful part.
Both the length of the path from a node to the root and the count of 
annotations say more about how well explored and interesting the 
particular part of the GO is than about any sort of specificity of the 
GO term.

One possibility that I've been advocating for a while is to measure 
specificity in terms of a GO term's correspondence with the taxon/taxa 
in the taxonomy of species, for which organisms the term may be sensibly 
  used to talk about.  This would not, of course, solve those of your 
problems that are not related to the classification of organisms, but 
might help solve others.

vQ


Sorin Draghici wrote:
> Tobias,
> 
> How exactly would you define the specificity of a GO term? If we had an 
> exact definition, we could possibly write a piece of software that could 
> do it.
> 
> Sorin
> 
> Tobias Sayre wrote:
>> Dear GO Friends,
>>
>> I am working on a project that involves curation of protein data that 
>> includes GO terms, and it would be very helpful if I had some 
>> numerical quantification of the specificity of each term.  It is 
>> possible to manually examine each term to determine this specificity, 
>> but because there is a large amount of data, I would like to automate 
>> the process.  I understand that there is no reliable way to do this 
>> simply using the level in the DAG hierarchy, but I am wondering if any 
>> of you might have a work-around.
>>
>> Thanks,
>>
>> Tobias Sayre
> 

-- 
Wacek Kusnierczyk

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