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

[Benjamin Hitz]

>>
>
> 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"

>
>
>> 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.

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


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