[Ontology-editors] muscle relaxation

[David Hill]

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
>>>>>
>>>>>
>>>
>>

-- 
David P. Hill, Ph.D.
Bioinformatics Scientist: Ontology Development
Gene Ontology Consortium
The Jackson Laboratory
www.geneontology.org
www.informatics.jax.org
tel:207-288-6430