[Ontology-editors] muscle relaxation

[David Hill]

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