[Ontology-editors] muscle relaxation

[Midori Harris]

Thanks, David,

The best way to bring this to David OS's attention is probably to put it 
in the SF item. Let me know if you want me to do it.

m

On Mon, 8 Jun 2009, David Hill wrote:

> I think the major question here is with respect to the relaxation and it's 
> relationship with contraction. Currently we have relaxation terms that are 
> 'negative regulation of muscle contraction'. Is this correct? If not, we need 
> to rearrange the ontology. If so, then we can add the new relaxation term as 
> another type of 'negative regulation' term. If we don't make it a negative 
> regulation term, how would it be related to contraction? Should it be 
> completely separate? I think it depends on how we view the role of the 
> calcium flux.
>
> As for the development question. If the fly community can use the cell-level 
> terms, we could simply remove the part_of relationship between the striated 
> muscle cell development term and its tissue/organ parents. We should ask 
> David OS if this would work for them.
>
> David
>
> 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
>>>>>> 
>>>>>> 
>>>> 
>>> 
>
>