[annotation] RNA trimethylguanosine cap binding query

[Karen Christie]

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
>> 
>> 
>> Karen Christie <kchris at genome.stanford.edu> wrote: 
>>> Hi Val,
>>> 
>>> Yea, I agree with Harold that the term 'RNA trimethylguanosine cap 
>>> binding' should only be used for things that bind to the cap, once it's 
>>> been created.
>>> 
>>> What you're talking about, annotating the modification that occurs on the 
>>> RNA, is completely different, and I think perhaps, completely outside the 
>>> scope of GO.
>>> 
>>> -Karen
>>> 
>>> 
>>> On Wed, 16 Jan 2008, Harold Drabkin wrote:
>>>
>>> 
>>>> Valerie Wood wrote:
>>>> 
>>>>> I recently used the term RNA trimethylguanosine cap binding  to annotate 
>>>>> pombe telomerase RNA and represent the fact that this is 
>>>>> trimethylguanosine capped, but on re-reading the definition  I'm not 
>>>>> sure if this is correct?
>>>>> Can I use this for the modification itself?  or is it for gene products 
>>>>> which interact with a capped product?
>>>>> 
>>>> It represents some gene product that binds to the triMeG cap present on 
>>>> an mRNA. Not the gene product that makes the cap. A binding term should 
>>>> never be used for a covalent bond. Binding implies a reversible reaction 
>>>> at STP, with a Ka and Kd.
>>>> 
>>>> GPI anchor binding it meant to be used for something that binds the the 
>>>> GPI anchor and not covalently linked to it.
>>>>
>>>> 
>>>>> There do not appear to be any other annotations to this term despite 
>>>>> the fact that many RNAs are capped which is another reason which made me 
>>>>> suspect my usage may be wrong.
>>>>> 
>>>>> Should  the binding terms should only be used for non-covalent 
>>>>> modifications (although this is only in some of the binding defs?), and 
>>>>> does not represent the use of some terms. For instance GPI anchor 
>>>>> binding is used for a number of proteins which are GPI anchored, in 
>>>>> addition to proteins which bins the GPI moiety during GPI anchor 
>>>>> biosynthesis.
>>>>> 
>>>>> Cheers
>>>>> 
>>>>> Val
>>>>> 
>>>>> Def:
>>>>> Interacting selectively with the trimethylguanosine (m(3)(2,2,7)-GTP) 
>>>>> moiety located at the 5' end of some RNA molecules. Such trimethylated 
>>>>> cap structures, generally produced by posttranscriptional modification 
>>>>> of a 7-methylguanosine cap, are often found on snRNAs and snoRNAs 
>>>>> transcribed by RNA polymerase II, but have also be found on snRNAs 
>>>>> transcribed by RNA polymerase III. They have also been found on a subset 
>>>>> of the mRNA population in some species, e.g. C. elegans.
>>>>> 
>>>>>
>>>>>
>>> 
>>
>>