[Go] 'binding issues' item listed on the GO Consortium meeting agenda

[Jim Hu]

On Mar 23, 2009, at 5:25 PM, Benjamin Hitz wrote:

>>>
>>
>> If P binds specifically to X, and X is_a Y, then P binds  
>> specifically to Y. this is built in to the is_a relation, there is  
>> absolutely no getting around this.
>>
>> Fortunately CHEBI does not make an is_a relation directly between  
>> any of these terms. Instead they are all is_a children of  
>> "adenosine 5' phosphate"
>>
>> http://obofoundry.org/obo/CHEBI:15422+CHEBI:16761+CHEBI:16027.png
>>
>> (CHEBI calls this by the plural "adenosine 5' phosphate*s*", which  
>> is wrong and will need to be changed in CHEBI. They are open to this)
>>
>> This means that if P binds to an ATP molecule, it is also the case  
>> that P binds to an adenosine 5' phosphate molecule. Does this seem  
>> reasonable?
>
> That should work fine... except for those gene products which bind  
> only AMP and ATP (should such a beastie exist)   I guess they can be  
> annotated separately.  Or "NOT ADP binding"

What?!!!  This sounds screwy to me.  Are you saying one can infer  
meaningful AMP binding from ATP binding?  I hope I'm misreading you.

>
>>
>>
>>> And I suppose there are many cases where a protein can bind  
>>> related chemicals with different non-zero affinities, so that if  
>>> one annotated binding to one there may be a good chance it would  
>>> bind another. Should there be a rule in how one interprets the  
>>> annotation line so as to not read any relationships among things  
>>> in the target ontology to the actual single term designated as the  
>>> target for the GO annotation? (hope this is clear).fcc
>
> This a good point and highlights another reason (perhaps not yet  
> broached) that "binding" terms should be used only with extreme care  
> - if at all.

Perhaps, but using precomposed terms, as we do now, doesn't make it  
any better.


>
> What is "binding"?  Km <= 10^6?  Km < Physiological concentration  
> under some condition?  The definition of GO:0005488 is hopelessly  
> vague on this: "The selective, often stoichiometric, interaction of  
> a molecule with one or more specific sites on another molecule."
>
> selectivity:  undefined
> "often stoichometric": often qualifier makes this irrelevent
> interaction: undefined
> "specific sites": undefined

I suspect that if one scrapes almost any part of GO hard enough, you  
get into similar conundra.

Jim


>
>
> Apologies in advance to GOC:ceb and GOC:mah, not meaning to critique  
> your work or you personally.
>
>
> Ben
>
>
> --
> Ben Hitz
> Senior Scientific Programmer
> Saccharomyces Genome Project
> Stanford University
> hitz at genome.stanford.edu
>
>
>
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=====================================
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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