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

[Donghui Li]

I agree with the proposal to obsolete the cellular component term  
'photosynthetic electron transport chain' (GO:0009502).

First, I agree with the reason suggested by the working group that  
this term is confusing (component vs process);

The main reason: it appears that this term was created to  
'artificially' combine several protein complexes involved in the same  
process (photosynthetic electron transport) together - this is  
exactly what biological process term intend to be.  There are already  
more specific component terms that are probably more in agreement  
with the biological reality (i.e. such complex does exist).  For  
example, 'photosystem I' 'photosystem II'.

The fact that no genes in Arabidopsis were directly annotated to this  
component term GO:0009502 probably also suggests that the Arabidopsis/ 
wider plant biology community do not use this term as what is  
intended to be (as a component term to describe relevant gene  
products).  Of course this could also be due to our annotation  
practice at TAIR.

There are however annotations associated to the child term of GO: 
0009502:

cytochrome b6f complex ; GO:0009512

We could make this term a child of 'thylakoid part' (GO:0044436) and  
keep the existing annotations.

Overall my suggestion is that we annotate relevant gene products to  
the specific component terms (such as photosystem I) as well as to  
the process term photosynthetic electron transport (GO:0009767) and  
obsolete GO:0009502.

Donghui


On Feb 4, 2008, at 6:20 AM, Jennifer Deegan (nee Clark) wrote:

> 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



--
Donghui Li, PhD
TAIR Curator

Carnegie Institution
260 Panama Street
Stanford, CA 94305
U.S.A

donghui at stanford.edu
Tel (650) 325 1521 ext 356
Fax (650) 325 6857

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http://www.geneontology.org

Carnegie Institution - At the Frontiers of Science