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

[Ben Hitz]

On Mar 23, 2009, at 4:12 PM, Jim Hu wrote:

> 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.

You are misreading me - and this question was already answered.

Although I can _chemically_ almost guarantee AMP binding to any  
substance that binds the adenosine bits of ATP.  Might have a Km of  
0.1M though.
>
> I suspect that if one scrapes almost any part of GO hard enough, you  
> get into similar conundra.
>
Well, the crux of the issue, of course, is that GO confines itself to  
"physiological relevant" molecular functions.  But that's the part  
that's hard to pin down.

Ben
--
Ben Hitz
Senior Scientific Programmer ** Saccharomyces Genome Database ** GO  
Consortium
Stanford University ** hitz at genome.stanford.edu