[annotation] RNA trimethylguanosine cap binding query

[Karen Christie]

Considering that we already have "anchored to external side of plasma 
membrane", it doesn't seem out of line to make a more specific child term. 
Are there other anchors other than GPI anchors?

-Karen


On Thu, 17 Jan 2008, Alexander Diehl wrote:

> Anyone for 'anchored to external side of plasma membrane via GPI anchor' as 
> an is-a child of 'anchored to external side of plasma membrane ; GO:0031362', 
> or even 'anchored to membrane via GPI anchor'?  I would be quite happy with 
> this solution, and we could remap the SwissProt keyword 'GPI-anchor'.
>
> Thanks,
>
> Alex
>
>
>
> Valerie Wood wrote:
>> Why don't we obsolete GPI binding  and create a new term (it only has 31 
>> manual annotations which appear to be mainly incorrect), plus the IEA 
>> mappings, which we have already established are wrong.
>> 
>> I can't think of any other binding term which may have been used 
>> inconsistently in this way. I don't really know why we did this, but as now 
>> see  I originally requested the term I will take the blame for establishing 
>> this bad practice. 
>> I have an alternative way to curate PTMs (and I guess most others do) so 
>> I'll just reannotate using this method. It would be useful to have a way to 
>> collect PTMs consistently with and between orgs, but as Karen C said, they 
>> don't belong in GO.
>> 
>> We could then add a comment to all of the other binding terms to say that 
>> they are ONLY intended  for non-covalent modifications.
>> 
>> Would everyone be happy with this?
>> 
>> Val
>> 
>> 
>> 
>> 
>> Harold Drabkin <hjd at informatics.jax.org> wrote: 
>>> 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
>>>>>>>>>
>>>>>>>>>
>>>> 
>>>
>>> 
>>
>> 
>
>
> -- 
> 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
>