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

[Jennifer Deegan (nee Clark)]

Hi Donghui,

Thanks for your input on that. It's good to know that you are in agreement.

Jen

Donghui Li wrote:

> 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
> 
> http://www.arabidopsis.org
> http://www.geneontology.org
> 
> Carnegie Institution - At the Frontiers of Science
> 

-- 
Jennifer Deegan (nee Clark)
EMBL-European Bioinformatics Institute
Gene Ontology Consortium