[annotation] RNA trimethylguanosine cap binding query

[Harold Drabkin]

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
>>>
>>>
>>> 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.
>>>>>>
>>>>>>
>>>>>>
>>>>
>>>
>>>