[Ontology-editors] muscle relaxation

[Midori Harris]

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
>> 
>> 
>
>