[annotation] RNA trimethylguanosine cap binding query

[Midori Harris]

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
>> 
>