[annotation] RNA trimethylguanosine cap binding query

[Harold Drabkin]

To use binding for the creation of a covalent bond is just absolutely 
incorrect.  This is just basic undergraduate chemistry. 

Modifying the definition is fine; I would add both statements.  
However,  if anyone has used this in this way it is wrong. Those 
annotations should stricken when found.  I cannot see any "but".  
Although we do not obviously have the time to revisit each one, in the 
cases Val found,  they should be removed; they were incorrect use of the 
term binding.


hjd

Alexander Diehl wrote:
> While I agree that common annotation practice has been to exclude 
> covalent bonds between gene products and other entities (including 
> other proteins), the fact that this has not be specifically excluded 
> by the definition of 1135 MF binding terms suggests to me the there 
> could be in fact be many annotations using these binding terms that 
> include covalent bonds.  Per standard GO practice, we should obsolete 
> all 1135 binding terms, provide equivalent, but redefined new binding 
> terms, to force people to reexamine their annotations.
>
> Clearly, we are not going to do this.  So in fact, I recommend that we 
> do not change the definitions at all, although perhaps we could add a 
> comment like, "Note that binding terms are not intended for annotation 
> of covalent bonds."
>
> -- Alex
>
>
> Midori Harris wrote:
>> Has this gone into SF? (hint, hint)
>>
>> should be easy to fix ...
>>
>> On Wed, 16 Jan 2008, Harold Drabkin wrote:
>>
>>> Hopefully a script can be designed to add this as a sentence to the 
>>> end of each definition!
>>>
>>> hjd
>>>
>>> Karen Christie wrote:
>>>> while you're right that terms inherit from their parents, it's 
>>>> still probably better to fix it everywhere, so that people who only 
>>>> look at a specific term and not all its parents get the 
>>>> non-covalent idea clearly.
>>>>
>>>> -Karen
>>>>
>>>>
>>>> On Wed, 16 Jan 2008, Harold Drabkin wrote:
>>>>
>>>>> I actually noticed that the core term, binding, with def of :    
>>>>> The selective, often stoichiometric, interaction of a molecule 
>>>>> with one or more specific sites on another molecule.
>>>>> is missing the non-covalent idea; fixing it in this term should 
>>>>> suffice for it's children
>>>>>
>>>>>
>>>>> The Oxford bible: binding: the act or process by which one 
>>>>> molecule attaches to another by noncovalent forces.
>>>>>
>>>>>
>>>>> Valerie Wood wrote:
>>>>>> yes thanks it seems obvious now, although I think I have some 
>>>>>> rogue annotations to fix for GPI binding to fix.! This might be 
>>>>>> obvious to everyone, but it might be worth adding 'non covalent' 
>>>>>> to all of the binding term defs just to emphasise. Its quite 
>>>>>> clear when you read the 'RNA trimethylguanosine cap binding def, 
>>>>>> but I'm not sure that it is for some of the others. thanks
>>>>>>
>>>>>> val
>>>>>>
>
>