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[Gofriends] Mistake in GO structure?

David Hill dph at informatics.jax.org
Mon Jan 17 10:12:34 PST 2011


I think the major issue that I have with your proposal is that this is 
very specific to organisms that have a 'respiratory system'. The 
original intent of the 'respiratory gaseous exchange' term was to cover 
gaseous exchange in all organisms. We did intend gaseous exchange to be 
all inclusive, literally the exchange between an organism and its 
environment. The respiratory system term was meant to cover the gaseous 
exchange in organisms that have a 'respiratory system'. The function of 
the respiratory system would be either is_a or part_of the gaseous 
exchange process depending on where gaseous exchange begins and ends. I 
think you have made a good argument that gaseous exchange includes an 
aspect of the function of the circulatory system.

D

On 1/17/11 12:47 PM, Wacek Kusnierczyk wrote:
> 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
>
> Alternatively,
>
> (3b') breathing is the (respiratory) process of inhaling and exhaling 
> gasses to and from the lungs
>
> or
>
> (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
>
> respiration:
> - 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 
> exchange'.
>
> 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.
>
> vQ
>
> [1] http://www.theregister.co.uk/2007/01/03/2006_darwin_award/
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