[annotation] RNA trimethylguanosine cap binding query

[Midori Harris]

I can implement either; when the annotation list has reaced consensus, 
please put it in SourceForge. I'll do whatever I find there.

m

On Thu, 17 Jan 2008, 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
>>>>>> 
>
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