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[Gofriends] Mistake in GO structure?

Wacek Kusnierczyk waku at
Mon Jan 17 09:47:50 PST 2011

On 1/17/11 10:06 AM, David Hill wrote:
>> Consider these two examples:
>> (a) When you stop breathing (e.g., while diving), gaseous exchange 
>> continues, at least for some time.
>> (b) In conditions with abnormal ventilation-perfusion ratio ('wasted 
>> blood' or 'wasted air', e.g., in inefficient inflow of blood into the 
>> pulmonary circulation due to obstruction of a major artery or shunts, 
>> or emphysema) gas exchange decreases while breathing increases 
>> (precisely to accommodate for decreased gas exchange).
> Ah yes. I think I see your point.
> How about 'respiratory system process' part_of 'respiratory gaseous 
> exchange'?

For my part it does not solve anything, because gaseous exchange is 
still all-inclusive.

Let's give it a try with some parts of this subject -- here are some 
thought and suggestions:

(1) a respiratory process is a process which is performed by the 
respiratory system
this is a sheer genus-differentia exercise, but one that has the 
technical function of linking 'process' and 'respiratory system'

(2) respiration is a respiratory process
respiration here is specifically that in higher organisms, not cellular 
respiration; I see you'd have trouble calling it simply 'respiration' -- 
long live unique name assumption.

(2a) respiration is a sequence (sum, aggregate, name it) of respiratory 
processes that together lead to enriching the blood with oxygen and 
removing carbon dioxide from it
potential issues:
- too complicated?
- would imply that pulmonary circulation is part of respiration, etc.

(3) breathing is a respiratory process

(3a) breathing is part of respiration

(3b) breathing is the (respiratory) process of cyclically inhaling air 
into and exhaling air from the lungs
potential problems:
- air;  for example, we can breathe gas mixtures other than air, or even 
pure gasses such as helium (for whatever reason, e.g.[1]), though the 
latter to no respiratory effect;  we can also breathe air enriched in 
oxygen, to improve respiration, or in helium, as divers do, etc.  in 
general, breathing is the process of inhaling and exhaling breathing 
gasses -- are we going circular here?
- cyclically; in ataxic breathing, there is no apparent regularity
BUT we're in the realm of physiology, so the above are somewhat of out 
of scope.
- lungs; if you want to cover organisms that do not have lungs, you need 
to find a better formulation


(3b') breathing is the (respiratory) process of inhaling and exhaling 
gasses to and from the lungs


(3b'') breathing is the (respiratory) process of inhaling and exhaling 
gasses to and from the  respiratory organs where gas exchange takes place
BUT it's more complicated

(4) respiratory gas exchange is a respiratory process
isn't it?  on your reading probably not, but i think this is wrong
HOWEVER, you might want to acknowledge that the circulatory system plays 
an important role in gas exchange (but so does the nervous one, again)

(4a) respiratory gas exchange is part of respiration
follows logically from that it is a respiratory process and that 
respiration is the sequence of respiratory processes (ah, yes, 
respiration includes itself?)

(4b) respiratory gas exchange is the (respiratory) process of exchange 
of oxygen and carbon dioxide between the gas mixture in the alveoli and 
the blood in the alveolar capillaries
potential problems:
- does not clarify the directionality, which is essential in the 
physiological gas exchange
- refers to anatomical entities,  which may not accurate for all 
organisms intended to be covered by the term

(#) ventilation
You might want to say that ventilation *is* breathing, but this would go 
too far, I think.  You may have artificial ventilation, when the patient 
does not breath.  Breathing is the process of inhaling and exhaling air 
performed with the aid of respiratory muscles (the diaphragm and muscles 
of the thoracic cage).  Ventilation is merely the process of replacement 
(I'm purposefully avoiding the word 'exchange') of the air within the 
lungs.  Within the GO, I think there is no need for 'ventilation'.

So the hierarchy would look like (where 'X subsumes Y' equals 'Y is a X'):

respiratory process:
- subsumes: respiration
- subsumes: breathing
- subsumes: gas exchange

- has part: breathing
- has part: gas exchange

Again, all this with 'respiration' in the higher-organisms context.

I think this should be close to the understanding that the original 
poster (Peter Robinson, cc:ed) had in mind when complaining about 
'respiratory system process' being subclass of 'respiratory gaseous 

While you're into restructuring this part of the GO in this or any other 
way, you will need to carefully examine all annotations, as some of them 
may be the result of confused interpretation of the current terms, or 
correct interpretation of the currently confused terms.



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