[annotation] RNA trimethylguanosine cap binding query

[Alexander Diehl]

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
>>>>>


-- 
Alexander Diehl, Ph.D.
Senior Scientific Curator
Mouse Genome Informatics
The Jackson Laboratory
600 Main Street
Bar Harbor, ME  04609

email:  adiehl at informatics.jax.org
work:  +1 (207) 288-6427
fax:  +1 (207) 288-6131