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

[Jennifer Deegan (nee Clark)]

Hi Peter,

Thanks for your comments.

> 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.

Yes this is a good point. In this case it would just make sense to 
replace the obsoleted 'photosynthetic electron transport chain' term 
with a new term that specifically discusses the complexes as in the 
'mitochondrial electron transport system' term. We can do that if it is 
required. The current term talks about reactions rather than complexes.


> 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.
> 

The working group are very much in agreement with this point, and we 
have a proposal coming along to solve this problem.

The working group is meeting every two weeks just now to look through 
all electron transport terms and improve them. Anyone who would like to 
join us would be very welcome.

Thanks,

Jennifer