[Ontology-editors] muscle relaxation

[David Hill]

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