gocentral
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Let me try to attach the file agian. Might help if I check the box!
David
Original comment by: ukemi
Closed gocentral closed 9 years ago
gocentral
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Let me try to attach the file agian. Might help if I check the box!
David
Original comment by: ukemi
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David,
I like the switch of words from "regulation" to "control" in the term names, since these are real identifiable processes with multiple steps, rather than the indefinite regulatory effects that many regulation terms cover.
Yet, I wonder if we still need generic terms, such as positive regulation of blood pressure and negative regulation of blood pressure, to cover experiments where the only available data reflects either an increase or a decrease in blood pressure. I don't see these existing terms as part of your DAG? Where do they fit in?
-- Alex
Original comment by: addiehl
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Alex,
The change to "control" was exactly for the reason you point out.
I thought about the regulation terms and as usual they are problematic. My tendency is to get rid of them. Rationale:
An increase or a decrease in blood pressure is a phenotype. If a mutant causes a change in blood pressure, then the best we can infer from the experiment is that the gene is involved in the control of blood pressure.
David
Original comment by: ukemi
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I'm going to have Harold make these changes since I have no more comments. For now I am going to leave the regulation terms in until as a whole group we decide how to address these issues.
David
Original comment by: ukemi
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Hi David,
Two quick Qs before this is implemented:
What's the phrasing (or phrasings) used in the literature for processes where blood pressure is modulated?
Are there processes that you imagine being annotated to a term 'regulation of blood pressure' which couldn't be annotated to 'control of blood pressure'?
I agree with the idea of making a difference between defined regulatory processes and any old regulation, but I'm just a bit wary of using 'control' rather than the standard word 'regulation'...
Sorry for chiming in so late!
Original comment by: girlwithglasses
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Blood pressure regulation is used frequently and should be a synonym (pubmed count 11892).Blood pressure control (pubmed 58204).Blood pressure modulation (pubmed 2443).
No, I really can't think of any. The issue here is that what we try to do is keep our blood pressure from changing and keep it at healthy levels. Unfortunately, there are many physiological processes that as a side effect cause blood pressure to rise or fall and we have to bring it back to normal. This regulation or control is the process itself. It is not regulating a process called blood pressure.
Original comment by: ukemi
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I have had several e-mail discussions with Jane and Amelia about this item. As a result of those, I have revised the graph a bit to show some additional relationships with other parts of GO. I attached the revised graph in OBO edit format. This file can be opened directly with OBO edit.
Here is a summary of our e-mail thread:
From Amelia: I was discussing it with Jane and the only thing we thought was that these terms might represent homeostatic processes
From David: I was proposing that it would replace regulation of blood pressure in the circulation part of the graph. This is a part_of relationship. I thought about homeostasis too. The def of homeostasis is: "Any of the processes involved in the maintenance of an internal equilibrium within an organism or cell." I think we could put the control of blood pressure there as an is_a if we think of the actual pressure of the circulatory machinery vs the pressure of the fluid being in equilibrium. We have used equilibrium in this sense to describe thermoregulation, where rather than refering to a chemical equilibrium, we are referring to a physical equilibrium. I think homeostasis would make the correct is_a parent.
from Amelia: I guess that one way to distinguish the processes you are representing from those which have a regulatory effect on blood pressure without being directly involved
From David: That is just it. There is nothing that I can think of that regulates blood pressure outside of the control of blood pressure. It is the change in pressure/flow that we respond to directly, no middle man, no outside influence. It's like a reflex, it just happens. There are lots of nonphysiological things that change blood pressure, including side effects of other physiological processes, but the goal of the control of blood pressure is to keep those things from letting blood pressure get physiologically unhealthy. In that way, control of blood pressure is more like a response to a change in blood pressure. Just as an aside, one of the cool things I'm learning about this is that some of the same processes are used for things like thermoregulation and other stuff too and there is this delicate balance between all kind of things. The biology is just mind-blowing.
So just for kicks, I went and asked one of the people here who is also an MD whether we regulate or control our blood pressure. She said, if I'm doing it by myself then I'm regulating it. If I'm doing it with a drug then I'm controlling it. This cracks me up because what the drugs are doing is compensating for an inablility for our bodies to do the process correctly. If I look up regulate and control in Webster's, they are given as synonymous. My real issue here is that if we use the word regulates, it is not really the same as how we use regulates elsewhere in GO. For those issues, there is a regulates relationship between processes, in this case there is not. I think that we need to pick one word "regulation" or "control" and then we certainly have to make the other term an exact synonym. If we use regulates, we have to remember that this is not one of the cases where the use of regulates rears its ugly head when we decide how to deal with the issues of one process regulating another.
From Jane: I've been thinking about this - I do think you have a point about the control v/s regulation thing but I'm having a hard time pinning the difference down. In the case of blood pressure, I guess there are different things at play - you have homeostatic systems that try and keep blood pressure constant, but then you also have other endogenous factors that might affcet blood pressure e.g. adrenaline which would increase the blood pressure, maybe in response to being scared! Then once the adrenaline wears off, presumably the homeostatic forces kick in again. So are they both controlling blood pressure? Or does adrenaline regulate blood pressure?
From David: Adrenaline controls blood pressure, but it is also one of the cool things that does lots of other stuff too! So, if you look in the ontology, there is a term "norepinepherine-epinepherine blood pressure control". Norepinepherin and epinepherine are other names for noradrenaline and adrenaline. Presumably when you get scared and adrenaline does its thing, the rise in blood pressure will be sensed and then other factors will begin to work to control blood pressure.
From Jane: I've been thinking about this - I do think you have a point about the control v/s regulation thing but I'm having a hard time pinning the difference down.
From David: I think in common usage of the words, there is really not a difference, but here is what I am trying to get at:
In one case we have a process that is woriking outside another process to have an effect on how that process is carried out. In the second case we have a process that is in fact the direct process that that is regulating something measurable but is not itself a process.
Regulation of transcription is a process that is separate from but has a (regulates) relationship with another process called transcription. Regulation of blood pressure is process that is a be all and end all. It does not have a regulates relationship with another process.
I just thought it would be useful to use two different words to describe these slight differences, regulation would be the first and control would be the second. Although I'm starting to think this might be contrived!
From Amelia: The terms where you've got regulation of [trait/phenotype] would be processes rather than "regulation" as we think of it.
e.g. regulation of cell size buoyancy regulation
From David: This is exactly right. I think when we adopt the regulates relationship we will have to look at cases. Another one is thremoregualtion. So to get down to the practical, do you think we should call the primary term "regulation of "or" control of"? The MD here votes for "regualtion of", I vote for "control of" just to distinguish it from the other regulates.
From Amelia: I think it's really the difference between an "intentional" regulatory mechanism, by which I mean the various pathways and controlling processes that are there specifically to ensure that process X proceeds as it should, versus other processes that affect process X "unintentionally" - i.e. their "goal" is to perform some other task, but this has an effect on process X. How that could be (a) translated into English, and (b) translated into GO structures, I don't know!
From David: This is also a good point. There is also a problem in science here. A lot of times when experiments aren't that great, people see an effect on a process and say "this gene must regulate this process" when in fact they have no idea what the gene is really doing.
From Jane: Yes, that was my thinking too - perhaps the broad rule could be that if the process is regulating a trait, it's a true process rather than a regulation and we could call it 'control of' as David suggests. Then we have the trickier case of regulating processes - could we say that where the process couldn't occur without the regulation, the regulation is part of that process, and is called 'control'? And where the process can occur happliy without the regulation, we call it regulation and it will eventually have a regulates relation to the process?
Just one more thing, I think we need to separate homoestatic processes from the regulatory processes - in the example we were talking about before, I don't think adrenaline could be thought of as homeostatic could it?
From David: You are right. One way to solve this issue would be to change the def of GO:0008217 and many of the others in the graph to ""THE PROCESS that modulates the force with which blood travels through the circulatory system." from "Any processes that modulates the force with which blood travels through the circulatory system." Then this term will be a part-of circulation and a type of homeostasis.
Then I think it might be worthwhile to go through my defs again and see how they relate to this. I suspect that many of the is_a relationships will become part_of relationships. I have been thinking about this general strategy for a while for some of the process parts of the graph. I'll send you guys an updated version.
Original comment by: ukemi
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I don't want to get too deeply involved here, but I do think there is a difference between processes involved in blood pressure homeostasis and control of blood pressure in response to stimulus via epinephrine or whatever. The stimulus causes a temporary raising or lowering of blood pressure and the homeostatic process returns it to a normal range.
-- Alex
Original comment by: addiehl
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Alex, "There is a difference between processes involved in blood pressure homeostasis and control of blood pressure in response to stimulus via epinephrine or whatever. The stimulus causes a temporary raising or lowering of blood pressure and the homeostatic process returns it to a normal range"
This is very true. The process I am trying to describe is the latter, trying to return blood pressure to a normal range. If I understand what I read correctly, adrenaline is used for this too.
I would say this is different from for example "the fight or flight response". Although my guess is the rise in blood pressure during this response is performed by the smae mechanism physiologically as the adrenaline-mediated rise in blood pressure that results from a drop in blood pressure.
David
Original comment by: ukemi
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18 years ago revised blood pressure
Original comment by: ukemi
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I'm going to try to reattach the new blood pressure file. Apparently I attached the wrong one on Firday.
David
Original comment by: ukemi
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Terms added: GO:0001974 blood vessel remodeling GO:0001975 response to amphetamine GO:0001976 fast regulation of arterial pressure GO:0001977 renal blood volume regulation of blood pressure GO:0001978 baroreceptor feedback regulation of blood pressure GO:0001979 chemoreceptor regulation of blood pressure GO:0001980 ischemic regulation of blood pressure GO:0001981 barorecetor detection of arterial stretch GO:0001982 baroreceptor response to lowering of blood pressure GO:0001983 baroreceptor response to increased blood pressure GO:0001984 vasodailation of an artery buring baroreceptor response to increased blood pressure GO:0001985 negative control of heart contraction rate in baroreceptor response to increased blood pressure GO:0001986 decreased strength of heart contraction during baroreceptor response to increased blood pressure GO:0001987 vasoconsriction of an artery during the baroreceptor response to lowering of blood pressure GO:0001988 positive control of heart contraction rate in baroreceptor response to decreased blood pressure GO:0001989 increased strength of heart contraction during baroreceptor response to decreased blood pressure GO:0001990 hormonal regulation of blood pressure GO:0001991 circulatory renin-angiotensin blood pressure regulation GO:0001992 vasopressin regulation of blood pressure GO:0001993 norepinepherine-epinepherine blood pressure regulation GO:0001994 norepinepherine-epinepherine vasoconstriction during blood pressure regulation GO:0001995 norepinepherine-epinepherine catabolism in the blood stream GO:0001996 positive regulation of heart contraction rate by epinepherine- norepinepherine GO:0001997 increased strength of heart contraction by epinepherine- norepinepherine GO:0001998 angiotensin mediated vasoconstriction during blood pressure control GO:0001999 renal response to blood flow during renin-angiotensin control of blood pressure GO:0002000 detection of renal blood flow GO:0002001 renin release into the blood stream GO:0002002 control of angiotensin levels in blood GO:0002003 angiotensin maturation GO:0002004 secretion of vasopressin during fast control of blood pressure GO:0002005 angiotensin catabolism in the blood GO:0002006 vasopressin mediated vasoconstriction during blood pressure control GO:0002007 detection of hypoxic conditions in the blood by chemoreceptors GO:0002008 excitation of the vasomotor center by chemoreceptor signaling GO:0002010 excitation of the vasomotor center by baroreceptor signaling GO:0002012 vasoconsriction of arteries during the chemoreceptor response to lowering of blood pressure GO:0002013 detection of carbon dioxide by the vasomotor center GO:0002014 vasoconsriction of an artery during the ischemic response to lowering of blood pressure GO:0002015 atrial regulation of blood pressure GO:0002016 renin-angiotensin regulation of body fluid levels GO:0002017 aldosterone mediated control of body fluids GO:0002018 renin-angiotensin regulation of aldosterone production GO:0002019 angiotensin mediated regulation of renal output GO:0002021 response to dietary excess GO:0002022 detection of dietary excess GO:0002023 reduction of food intake in response to dietary excess GO:0002024 diet induced thermogenesis GO:0002025 norepinepherine-epinepherine vasodilation during blood pressure regulation GO:0002026 cardiac inotropy GO:0002027 cardiac chronotropy
Can this item be closed now?
Original comment by: girlwithglasses
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18 years ago Original comment by: girlwithglasses
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Yes, I have already been using these terms.
David
Original comment by: ukemi
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18 years ago Original comment by: girlwithglasses
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18 years ago Original comment by: girlwithglasses
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Reopening this because there are a few changes that need to be made:
- standardize term names (e.g. vasoconsriction of arteries during the chemoreceptor response to lowering of blood pressure vs. vasoconsriction of an artery during the ischemic response to lowering of blood pressure)
- correct spelling mistakes
- deploy standard defs where applicable
- clarify defs
Original comment by: girlwithglasses
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18 years ago Original comment by: girlwithglasses
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A load of super-picky comments about the terms in this node:
--
fast regulation of arterial pressure
- The terms underneath this are all blood pressure - should this be blood pressure too?
--
circulatory renin-angiotensin blood pressure regulation A process that controls the force with which blood passes through the circulatory system by the secretion of angiotensin II into the bloodstream.
vasopressin regulation of blood pressure A process that controls the force with which blood passes through the circulatory system by the secretion of vasopressin into the bloodstream.
- Should all terms representing processes whereby a substance secreted into the bloodstream controls blood pressure have "circulatory" in the term string?
--
norepinepherine-epinepherine blood pressure regulation A process that controls the force with which blood passes through the circulatory system by the secretion of norepinepherine or epinepherine into the bloodstream.
- Can this be split into two terms, one for norepinephrine and one for epinephrine? If not, should we have specific children?
- Also, I think the term string would be clearer if it were 'regulation of blood pressure by epinephrine or norepinephrine' - otherwise it sounds like it's a complex of norepinephrine and epinephrine which is doing the regulation!
--
negative regulation of heart contraction rate in baroreceptor response to increased blood pressure Any process that stops, prevents or reduces the rate, frequency or extent of heart contraction as a result of the baroreceptor response to increased blood pressure
decreased strength of heart contraction during baroreceptor response to increased blood pressure Any process that decreases the force with which the cardiac muscles of the heart pump blood through the circulatory system as a result of the broreceptor response to increased blood pressure.
vasoconstriction of artery during baroreceptor response to lowering of blood pressure A process that is triggered by vasomotor excitation and results in a decrease in the diameter of an artery during the baroreceptor response to decreased blood pressure.
- Should all these terms have the string "during baroreceptor response" and the def string "... during the baroreceptor response to ..."?
--
norepinephrine-epinephrine vasoconstriction during blood pressure regulation A process that results in a decrease in the diameter of an artery during the norepinephrine-epinephrine response to decreased blood pressure.
- Would this term be better called "vasoconstriction during regulation of blood pressure by epinephrine or norepinephrine"? It's a bit clearer.
(angiotensin|vasopressin) mediated vasoconstriction during blood pressure control The decrease in blood vessel diameter as a result of the release of (angiotensin|vasopressin) into the blood stream.
- Is this analogous to the norepi/epi term above but with angiotensin/vasopressin? If so, can we standardize term strings and defs?
--
increased strength of heart contraction by epinephrine-norepinephrine Any process that increases the force with which the cardiac muscles of the heart pump blood through the circulatory system as a result of the presence of epinephrine or norepinephrine in the bloodstream.
- "increased strength" is a condition - could we make this term sound more like the process described in the def by calling it "positive regulation of strength of heart contraction by epinephrine or norepinephrine"?
--
excitation of vasomotor center by [...] signaling The process by which the molecular signal from [...] is relayed to the vasomotor center, causing it to signal an increase arterial pressure.
- Should that be "causing it to signal an increase in arterial pressure"?
--
vasoconstriction of artery during the ischemic response to lowering of blood pressure (et al) A process that is triggered by vasomotor excitation resulting from the detection of high carbon dioxide levels in the vasomotor center of the central nervous system.
vs
norepinepherine-epinepherine vasoconstriction during blood pressure regulation A process that results in a decrease in the diameter of an artery during the norepinepherine-epinepherine response to decreased blood pressure.
- Does the former term need to have 'artery' in it, since it seems to be implicit in the word 'vasoconstriction' (if the latter term is to be believed)?
--
brain renin-angiotensin system The process by which an angiotensin-mediated signaling system present in the brain regulates the force with which blood passes through the circulatory system.
- "brain renin-angiotensin system" doesn't sound like a process; could we change the term string? The def suggests it should be something like 'regulation of blood pressure by brain renin-angiotensin system'.
-- These are all rather specific and picky, but I like to make sure everything is consistent!
Cheers! Amelia.
Original comment by: girlwithglasses
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Also:
cardiac chronotropy shouldn't this have the children '+/- regulation of heart contraction rate by ...'?
Similarly, cardiac inotropy proposed children: '+/- strength of heart contraction'
--
renin-angiotensin regulation of aldosterone production The process by which an increase in active angiotensin stimulates the adrenal cortices to secrete aldosterone.
shouldn't the term name be something like 'induction of aldosterone production by angiotensin'?
Similarly with 'angiotensin mediated regulation of renal output' The process by which angiotensin directly decreases the rate of natriuresis and diuresis in the kidney.
--> neg reg of renal output by angiotensin
and 'aldosterone mediated regulation of body fluids' The process by which the hormone aldosterone decreases the rate of diuresis and natriuresis.
--> neg reg of body fluid levels by aldosterone
Why is the aldosterone term related to body fluids whilst the angiotensin one is renal output, when both terms are defined in terms of diuresis and natriuresis?
--
I think that's all on the pedantry front for now...
I've changed all the terms which had 'control' in the string into regulation terms - I assume they were just overlooked. Have also corrected the spelling errors in the term names.
Cheers! Amelia.
Original comment by: girlwithglasses
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17 years ago Logged In: YES user_id=436423 Originator: NO
Did this get finished? I thought it did but the item is still open ... m
Original comment by: mah11
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16 years ago Original comment by: tberardini
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16 years ago Original comment by: ukemi
I am about to embark upon the curation of a lot of genes involved in the control of blood pressure. I decided that before I do this, I should expand the node, so I got a medical physiology text book and came up with the new terms that are listed in the attached obo file. Note that you can open this in obo-edit and peruse the graph. The part that is here is only for blood pressure control, but some of these terms will obviously relate to other parts of the GO process graph as well. Since I am no expert on blood pressure control, it would be nice to get some feedback.
David
Reported by: ukemi
Original Ticket: "geneontology/ontology-requests/3046":https://sourceforge.net/p/geneontology/ontology-requests/3046