rhythmic behavior

[gocentral]

Hi,

I just noticed that circadian rhythm is a child of rhythmic behavior and I think would be a true path violation. Plants have circadian controlled processes that would not be called behaviors. e.g. the storage of malate in the vacuole during the night in CAM plants. I had a chat with Jane and she suggests that we make a new term called rhythmic process to take the terms that are currently children of rhythmic behavior:

[i]physiological process ---[i]rhythmic process ; GO:new ------[i]circadian rhythm ------[i]ultradian rhythm

The term rhythmic behavior has annotations and is fine as it stands so we could leave it to receive new children that are actually examples of rhythmic behavior.

Does anybody see any problems with that?

Thanks,

Jen

Reported by: jenclark

Original Ticket: "geneontology/ontology-requests/2114":https://sourceforge.net/p/geneontology/ontology-requests/2114

[gocentral]

Logged In: YES user_id=482748

hi Jen,

Removing 'circadian rhythm' from under behavior is ok with me. But can we have/keep a term 'circadian behavior'. ie something like:

physiological process --%rhythmic process ----%rhythmic behavior % behavior ------%circadian behavior --------%locomotor rhythm ----%circadian rhythm ------%circadian behavior ----%ultradian rhythm

circadian rhythm The biological processes in an organism that recur with a regularity of approximately 24 hours.

circadian behavior synonym: circadian rhythm behavior The specific actions or reactions of an organism that recur with a regularity of approximately 24 hours.

I think locomotor rhythm can stay under rhythmic behavior, since the locomotion terms are in the behavior node anyhow.

btw: should 'menstrual cycle ; GO:0042698' be given the new rhythmic process parent too, since it's a type of infradian rhythm? see http://www.23nlpeople.com/Rhythm.htm

just a suggestion. thanks Becky

Original comment by: beckyfoulger

[gocentral]

Logged In: YES user_id=735846

Hi Becky,

Yes that all looks good to me. David e-mailed and said he was happy with my suggestions too so I can probably go ahead and do that.

Jen

Original comment by: jenclark

[gocentral]

Logged In: YES user_id=735846

I just sent this to David Hill:

> Hi David, > > Would you mind if I merge > > response to circadian rhythm ; GO:0050895 > def: A physiological response to a circadian rhythm. > > into the 'circadian rhythm' term that we've already agreed: > > physiological process > --%rhythmic process > ----%rhythmic behavior % behavior > ------%circadian behavior > --------%locomotor rhythm > ----%circadian rhythm > ------%circadian behavior > ----%ultradian rhythm > > circadian rhythm > The biological processes in an organism that recur with a > regularity of approximately 24 hours. > > circadian behavior > synonym: circadian rhythm behavior > The specific actions or reactions of an organism that recur > with a regularity of approximately 24 hours. > > https://sourceforge.net/tracker/index.php? func=detail&aid=1065207&group_id=36855&atid=440764 > > > Thanks, > > Jen

He says that's fine.

Jen

Original comment by: jenclark

[gocentral]

Logged In: YES user_id=735846

I have done that now:

changed 'circadian rhythm' to be under 'physiological process' instead of under 'behavior'.

'response to circadian rhythm' GO:0050895 was merged into 'circadian rhythm' GO:0007623.

'circadian rhythm' GO:0007623 was redefined as a physiological process term instead of a behavior term. Changed definition from "The specific actions or reactions of an organism that recur with a regularity of approximately 24 hours." to "The biological processes in an organism that recur with a regularity of approximately 24 hours."

Two new terms were created called 'rhythmic process' and 'circadian behavior'. The children of 'circadian rhythm' were split between 'circadian rhythm' and 'circadian behavior' as appropriate.

circadian behavior ; GO:0048512 def: definition "The specific actions or reactions of an organism that recur with a regularity of approximately 24 hours."

rhythmic process ; GO:0048511 def: "Those processes pertinent to the generation and maintenance of rhythms in the physiology of an organism."

new structure:

physiological process --%rhythmic process ----%rhythmic behavior % behavior ------%circadian behavior --------%locomotor rhythm ----%circadian rhythm ; GO:0007623 ------%circadian behavior ----%ultradian rhythm

Jen

Original comment by: jenclark

[gocentral]

• status: open --> closed-accepted

Original comment by: jenclark