[Ontology-editors] muscle relaxation

[Midori Harris]

Hi Jen,

Thanks for fowarding this. Can you paste it into the SF item too (or I 
can, but that would add another layer of indirectnes ...)?

thanks,
m

On Mon, 8 Jun 2009, Jennifer Deegan (nee Clark) wrote:

> Hi,
>
> I have just received the response below from Paolo Lavader who is a muscle 
> expert at CRIBI in Padua. He is cc'd here.
>
> Thanks,
>
> Jennifer
>
> ====================
>
> Hi Jennifer,
>
> Thank you for writing me. I do not have very much to say about muscle
> relaxation:
>
> At the MOLECULAR LEVEL Ruth Lovering is right: Relaxation of muscles is an
> active process.  Before a muscle can contract again calcium needs to be
> pumped back into the sarcoplasmic reticulum.  Consequently people with
> mutations in ATP2A1 take longer to relax their muscles, not because nothing
> is pulling the other way but because the calcium pump is not removing the
> calcium from the cytosol quick enough.
>
> However, at the ANATOMICAL LEVEL David Hill is not wrong: contraction of
> agonistic muscles is coupled by relaxation of antagonistic ones (e.g. biceps
> vs triceps).
>
> This is matter for muscle physiologists...
>
>
> I have something to ask you in the discussion about muscle development.
>
> If "Individual somatic (skeletal) muscles in Drosophila consist of a single
> cell" why drosophilists cannot use the terms muscle cell development or
> muscle fiber development to annotate their genes? I would simply change the
> current definition of muscle fiber development by adding "They can be
> classed as slow, intermediate/fast or fast IN VERTEBRATES", as I am not sure
> the same is true in insects.
>
> I sit a simplistic view?
>
> Paolo
>
>
>
>
>
> David Hill wrote:
>> Hopefully some of the muscle folks will respond.
>> 
>> Ruth Lovering wrote:
>>> I object to this decision.
>>> 
>>> Relaxation of muscles is an active process.  Before a muscle can contract 
>>> again calcium needs to be pumped back into the sarcoplasmic reticulum. 
>>> Consequently people with mutations in ATP2A1 take longer to relax their 
>>> muscles, not because nothing is pulling the other way but because the 
>>> calcium pump is not removing the calcium from the cytosol quick enough.
>>> 
>>> See SF item for reference to Brody's disease.
>>> 
>>> Ruth
>>> 
>>> On 4 Jun 2009, at 13:54, Midori Harris wrote:
>>> 
>>>> Hi David,
>>>> 
>>>> That makes sense, and would mean that we should rename GO:0060085 and 
>>>> GO:0060087, and merge GO:0055119 into GO:0055118.
>>>> 
>>>> Any objections?
>>>> 
>>>> Midori
>>>> 
>>>> On Thu, 4 Jun 2009, David Hill wrote:
>>>> 
>>>>> Hi Midori,
>>>>> 
>>>>> This is because muscles don't actively relax per se. The stop 
>>>>> contracting and then some other force causes the muscle tissue to 
>>>>> expand. In skeletal muscle this is done by having opposing pairs of 
>>>>> muscles like the biceps and the triceps. I think describing muscle 
>>>>> relaxation as a negative regulation of contraction is actually the way 
>>>>> it really works.
>>>>> 
>>>>> David
>>>>> 
>>>>> Midori Harris wrote:
>>>>>> Hello,
>>>>>> Prompted by a SourceForge request from Ruth, I've noticed that we 
>>>>>> haven't been consistent about representing muscle relaxation. We have 
>>>>>> three terms that use 'relaxation' in the names, but all have 
>>>>>> definitions that are worded much like regulation term defs (especially 
>>>>>> the latter two):
>>>>>> [Term]
>>>>>> id: GO:0055119
>>>>>> name: relaxation of cardiac muscle
>>>>>> namespace: biological_process
>>>>>> def: "The process whereby the extent of cardiac muscle contraction is 
>>>>>> reduced." [GOC:ed]
>>>>>> is_a: GO:0055118 ! negative regulation of cardiac muscle contraction
>>>>>> [Term]
>>>>>> id: GO:0060085
>>>>>> name: smooth muscle relaxation of the bladder outlet
>>>>>> namespace: biological_process
>>>>>> def: "Any process that stops, prevents or reduces the frequency, rate 
>>>>>> or extent of smooth muscle contraction in the bladder outlet that 
>>>>>> contributes to the expulsion of urine from the body." [GOC:dph, 
>>>>>> PMID:15827347]
>>>>>> synonym: "synaptic transmission involved in urination" EXACT []
>>>>>> is_a: GO:0045986 ! negative regulation of smooth muscle contraction
>>>>>> relationship: part_of GO:0060073 ! micturition
>>>>>> [Term]
>>>>>> id: GO:0060087
>>>>>> name: relaxation of vascular smooth muscle
>>>>>> namespace: biological_process
>>>>>> def: "Any process that stops, prevents or reduces the frequency, rate 
>>>>>> or extent of vascular smooth muscle contraction." [GOC:dph, 
>>>>>> PMID:15867178]
>>>>>> synonym: "vascular smooth muscle relaxation" EXACT []
>>>>>> is_a: GO:0045986 ! negative regulation of smooth muscle contraction
>>>>>> relationship: part_of GO:0042311 ! vasodilation
>>>>>> On the other hand, for uterine smooth muscle and the generic smooth 
>>>>>> muscle parent, 'relaxation' is a related synonym for the negative 
>>>>>> regulation of contraction term:
>>>>>> [Term]
>>>>>> id: GO:0045986
>>>>>> name: negative regulation of smooth muscle contraction
>>>>>> namespace: biological_process
>>>>>> def: "Any process that stops, prevents or reduces the frequency, rate 
>>>>>> or extent of smooth muscle contraction." [GOC:go_curators]
>>>>>> synonym: "smooth muscle relaxation" RELATED []
>>>>>> is_a: GO:0006940 ! regulation of smooth muscle contraction
>>>>>> is_a: GO:0045932 ! negative regulation of muscle contraction
>>>>>> relationship: negatively_regulates GO:0006939 ! smooth muscle 
>>>>>> contraction
>>>>>> [Term]
>>>>>> id: GO:0070473
>>>>>> name: negative regulation of uterine smooth muscle contraction
>>>>>> namespace: biological_process
>>>>>> def: "Any process that modulates the frequency, rate or extent of 
>>>>>> uterine smooth muscle contraction." [GOC:go_curators]
>>>>>> synonym: "uterine smooth muscle relaxation" RELATED [GOC:mah]
>>>>>> is_a: GO:0045986 ! negative regulation of smooth muscle contraction
>>>>>> is_a: GO:0070472 ! regulation of uterine smooth muscle contraction
>>>>>> relationship: negatively_regulates GO:0070471 ! uterine smooth muscle 
>>>>>> contraction
>>>>>> Not only is the term naming inconsistent, the related scope of the 
>>>>>> relaxation synonyms is at odds with the fact that GO:0045986 is an is_a 
>>>>>> parent of GO:0060085 and GO:0060087 (I would expect exact or narrow 
>>>>>> scope).
>>>>>> There is also no generic parent named 'muscle relaxation', although 
>>>>>> Ruth has requested one as part of the SF item, nor is 'muscle 
>>>>>> relaxation' a synonym for 'negative regulation of muscle contraction' 
>>>>>> (GO:0045932). I think we should make this area of the graph consistent 
>>>>>> before we add any new terms.
>>>>>> So, my question is: which way should we standardize, separate terms or 
>>>>>> synonyms for muscle relaxation? Any comments are welcome.
>>>>>> SF link:
>>>>>> https://sourceforge.net/tracker/?func=detail&aid=2800451&group_id=36855&atid=440764 
>>>>>> ccing ontdev list for archiving
>>>>>> cheers,
>>>>>> midori
>>>>> 
>>>>> 
>>> 
>> 
>