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

[Chris Mungall]

On Mar 23, 2009, at 3:55 PM, Harold Drabkin wrote:

>>> Chebi may have relationships between, for example, for  ATP, ADP,  
>>> and AMP, but a protein may bind very specifically to  one of them.
>>
>> 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?
> >> perhaps as long as it means "binds to some sort of adenosine 5'  
> phosphate molecule", not any or all....

"not all", of course. But this is no different from any other GO term.  
If P is involved in organ development, then every P is involved in the  
development of some organ, not all of them. "amino acid metabolism"  
means those processes in which some amino acid is metabolized, not all  
of them.