[annotation] RNA trimethylguanosine cap binding query

[Karen Christie]

I see your point. Perhaps the existing term "anchored to external 
side of plasma membrane" is as far as component should go. To go farther 
with what type of molecule is used for the anchor, would be the domain of 
some other ontology.

-Karen


On Thu, 17 Jan 2008, Midori Harris wrote:

> Well, there are myristoyl group anchors too, if I recall correctly. But I'm 
> not convinced that the type of anchor is really cellular component territory, 
> so I'm inclined to avoid the more specific term(s) on those grounds.
>
> m
>
> On Thu, 17 Jan 2008, Karen Christie wrote:
>
>> 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
>>> 
>> 
>