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[Gofriends] Mistake in GO structure?

Wacek Kusnierczyk waku at
Mon Jan 17 10:19:11 PST 2011

On 1/17/11 10:31 AM, Wacek Kusnierczyk wrote:
> On 1/17/11 9:40 AM, David Hill wrote:
>> " The process of gaseous exchange between an organism and its 
>> environment. In plants, microorganisms, and many small animals, air 
>> or water makes direct contact with the organism's cells or tissue 
>> fluids, and the processes of diffusion supply the organism with 
>> dioxygen (O2) and remove carbon dioxide (CO2). In larger animals the 
>> efficiency of gaseous exchange is improved by specialized respiratory 
>> organs, such as lungs and gills, which are ventilated by breathing 
>> mechanisms.
>>> (b) in larger animals (that is?) gaseous exchange is improved by 
>>> respiratory organs, which a re ventilated by breathing mechanisms.
>>> From (a), it seems that the author wasn't able to give a clear 
>>> explanation of what precisely is meant by 'gaseous exchange'.  From 
>>> (b), it seems that ventilation by breathing improves gas exchange, 
>>> from which it is very hard to me to draw the conclusion that 
>>> breathing *is* respiratory gas exchange.
>> The second part of the definition explains why in larger organisms, 
>> simple diffusion does not suffice.
> I'm sorry, but there is no single part of the definition that would 
> explain that.  The only thing said is that efficiency of gaseous 
> exchange is improved by respiratory organs.  The term 'insufficient' 
> does not appear anywhere, lest be it explained what the source of 
> insufficiency is.  And insufficiency is certainly not a necessary 
> prerequisite for improvement; sufficient can be made better.  You're 
> reading between the lines; which is fine with me and you, but may be 
> not with the causal GO user (a computer scientist doing work on 
> ontology matching, say), and certainly not for an automated system 
> that would have to parse (omigosh) such definitions.

I also think the definition is not the right place for such 
'explanations'.  This would be comfortably placed in a comment field, or 
indeed an explanation field had the GO invented such, but a definition 
should be short, precise, and contain just the necessary and sufficient 
conditions, not distracting noise.

BTW., have a look at this definition, relevant in the context of this 

     respiratory system process
     A system process carried out by the organs and tissues of the 
respiratory system. The respiratory system is an organ system 
responsible for respiratory gaseous exchange.

The first sentence implies that any process carried out by the 
respiratory system is a respiratory system process, and that any process 
carried out by the respiratory system is a respiratory system process.  
The necessary and sufficient conditions are correct, if useful.

The second system is a distraction; it explains what respiratory system 
is, but this should be done in the definition of 'respiratory system', 
not here.  By referring to respiratory system in the first part, this 
definition provides sufficient means for establishing the meaning of 
'respiratory system' (though a cross-reference would be better).  The 
problem with the second part is not merely that it's inessential; it's 
that this add-on definition of another entity might (in principle) 
collide with the definition of that entity given in the right place.  
For that matter, FMA defines 'respiratory system' as "Functional system 
which consists of structures involved in respiration", which does not 
appeal to 'respiratory gaseous exchange'.  My guess is that the reason 
is, gaseous exchange is just a part of respiration.


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