[Electron-transport] one more addition

[Peter D'Eustachio]

Hi, Jen,

I understand that I'm jumping in late and may be asking to un-do carefully 
worked-out rearrangements. In that case, ignore this message.

However, I think the old term, GO:0006118, was correct in not being a kind 
of transport, but rather a kind of cellular metabolism - at least in humans, 
normal electron transport is actually a series of oxidation-reduction 
metabolic reactions taking place in very specific locations within a single 
cell. Indeed, making those intra-mitochondrial locations freely accessible 
even from elsewhere in the same cell disrupts the process.

Photosynthesis, as far as I know (but extremely limited knowledge here) is 
likewise an obligately cellular process (and indeed GO:0015979: 
photosynthesis is a child of GO:0044237: cellular metabolic process).

So, would the new term "electron transport" itself work better as a child of 
GO:0044237? All the other parts of the plan look OK, and everything would 
get an is_a path to root, I think.

At a minimum, the "into", "out of" and "between" cells part of the standard 
transport definition are wrong, or at least not generally true for electron 
transport.

Peter

----- Original Message ----- 
From: "Jennifer Deegan (nee Clark)" <jdeegan at ebi.ac.uk>
To: <electron-transport at genome.stanford.edu>
Sent: Monday, March 17, 2008 7:27 AM
Subject: [Electron-transport] one more addition


> Hi,
>
> I am making last minute preparations for the commit of our electron
> transport work, which will take place on wednesday.
>
> I found that some of the terms that are parts of photosynthetic electron
> transport don't have an is_a path to the root (which they must have
> before I can commit). To solve this problem I have made a new term
> 'electron transport', which is a direct child of the process 'transport'.
>
> This means that in the commit we will be obsoleting the old term
> 'electron transport' that used to roughly represent the respiratory
> electron transport chain, and replacing it with:
>
> [i]electron transport chain ; GO:new
> ---[i]respiratory electron transport chain ; GO:new
> ---[i]photosynthetic electron transport chain ; GO:new
>
> and that we will also be creating a new child of transport:
>
> [i]transport ; GO:0006810
> ---[i]electron transport ; GO:new
>
> electron transport ; GO:new
> def: The directed movement of electrons into, out of, within or between
> cells.
>
> The terms under photosynthetic electron transport chain ; GO:new
> that did not previously have an is_a path to the root will then have an
> is_a path to the root via
> electron transport ; GO:new.
>
> Does this all seem okay with everyone?
>
> Thanks,
>
> Jen
>
>
>
> -- 
> Jennifer Deegan (nee Clark)
> EMBL-European Bioinformatics Institute
> Gene Ontology Consortium
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