[Electron-transport] one more addition

[Jim Hu]

Hi Jen,

So, if I understand it correctly, the problem is that you have part_of  
relationships to photosynthetic electron transport chain but can't use  
is_a relationships because a part is not an instance of a thing?  And  
because we added chain to the electron transport, it can only be is_a  
to chain if it is a series of reactions.

It seems to me that you could make the electron transport in  
photosystem I and photosystem II are both is_a children of electron  
transport chain, since they are each smaller chains that when linked  
up make the overall photosynthetic electron transport chain.  I'm not  
sure about some of the others, as they are in that grey area we  
discussed as being between process and function.  Is one link still a  
chain?

This is one of those places where I dislike the whole is_a complete  
business.  Doing the above takes the hierarchy we worked so hard to  
define and reflattens it for the sake of abstract philosophical  
consistency.  But this flattening makes the graph nature of the  
ontology confusing to humans, which suggests  to me that the  
ontological principles for reasoning are not modeling how we actually  
think very well. But that's a whole different discussion that I'm sure  
the consortium has beaten to death long before I joined!

Jim


On Mar 17, 2008, at 9:42 AM, Jennifer Deegan (nee Clark) wrote:

> Hi,
>
> Thank you for your comments. Clearly that was not the way to go, so I
> will go back a few steps and explain the problem that I am trying to
> solve, and maybe you will have better ideas.
>
> I need to find an is_a path to the root (by tomorrow lunchtime GMT)  
> for
> the following terms:
>
> photosynthetic electron transport in cytochrome b6/f ; GO:0009775
> (undefined)
>
> photosynthetic electron transport in photosystem I ; GO:0009773
> def: Electrons move from the primary electron acceptor (Quinone, X)
> through a chain of electron transport molecules in the thylakoid
> membrane until they reach ferredoxin which passes the electron to the
> ultimate electron acceptor; NADP.
>
> photosynthetic electron transport in photosystem II ; GO:0009772
> def: Electrons move from the primary electron acceptor (Quinone, Q)
> through a chain of electron transport molecules in the thylakoid
> membrane until they reach the ultimate electron acceptor of  
> Photosystem
> II, which is plastocyanin (PC). The electron is then passed to the  
> P700
> chlorophyll a molecules of the reaction centre of photosystem I.
>
> photosynthetic electron transport in plastocyanin ; GO:0009776
> (undefined)
>
> photosynthetic electron transport in plastoquinone ; GO:0009774
> (undefined)
>
> Does anybody have any good ideas for how I could do that? I just  
> need to
> make an is_a relationship from the terms up to another term that has a
> direct is_a path up to the term 'biological_process'.
>
> I am working in the file go/scratch/electron_transport.obo
> http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/scratch/electron_transport.obo
>
> Thanks,
>
> Jen
>
>
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=====================================
Jim Hu
Associate Professor
Dept. of Biochemistry and Biophysics
2128 TAMU
Texas A&M Univ.
College Station, TX 77843-2128
979-862-4054


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