[go] Alert: Proposal to obsolete GO:0009502 ; photosynthetic electron transport chain that impacts existing annotation - possible objection

[Peter D'Eustachio]

Two possible problems here -

The term is defined as a proper component: "A series of membrane-linked 
oxidation-reduction reactions in which electrons are transferred from an 
initial electron donor through a series of intermediates to a final electron 
acceptor (usually oxygen)." That is, chain here is being used in a literal 
rather than a metaphoric sense, so this is really a question for the plant 
biologists. Do they understand this to be a component rather than a process? 
If so, shouldn't GO tolerate that usage?

The other problem is that the exactly analogous term and definition exists 
for mitochondria. GO:0005746 mitochondrial respiratory chain "The protein 
complexes that form the mitochondrial electron transport system (the 
respiratory chain). Complexes I, III and IV can transport protons if 
embedded in an oriented membrane, such as an intact mitochondrial inner 
membrane." Again, chain has a literal rather than metaphoric meaning. Here, 
my sense from textbook discussions is that the biologists' usage is somewhat 
blurred - they are trying to capture both the physical organization of 
molecules that transports electrons and the fact that this organization 
enables the transport process.

The GO process ontology, meanwhile, has a term for  photosynthetic electron 
transport (GO:0009767). It lacks a term for mitochondrial eletron transport, 
but has both the parent  electron transport (GO:0006118) and many 
appropriate children, e.g.,  mitochondrial electron transport, NADH to 
ubiquinone (GO:0006120). There's no question that GO annotation should keep 
the structure and process distinct and unblurred but, with the creation of a 
single new process term, GO would have all the terms and relationships 
needed to distinguish the structures from the processes they mediate, no 
obsoletions needed.

Peter D'E
Reactome

----- Original Message ----- 
From: "Jennifer Deegan (nee Clark)" <jdeegan at ebi.ac.uk>
To: "go list" <go at genome.stanford.edu>
Sent: Monday, February 04, 2008 8:44 AM
Subject: [go] Alert: Proposal to obsolete GO:0009502 ; photosynthetic 
electron transport chain that impacts existing annotation


> Hi,
>
> The proposal has been made to obsolete GO:0009502 ; photosynthetic 
> electron transport chain.
>
> There exist today annotations to this term as follows (data from AmiGO):
>
>     * UniProtKB: 6 objects
>     * TAIR: 4 objects
>
> The reasons for this proposal are that the term is defined as a process 
> term but is in the cellular component ontology.
>
> UNLESS OBJECTIONS ARE RECEIVED BY 4th April WE WILL ASSUME THAT YOU AGREE 
> TO THIS CHANGE.
>
> Thanks,
>
> Jennifer
>
> -- 
> Jennifer Deegan (nee Clark)
> EMBL-European Bioinformatics Institute
> Gene Ontology Consortium
>