[Electron-transport] one more addition

Mon Mar 17 08:30:21 PDT 2008

Now I'm confused.

It looks like there are two problems. One is to go downwards in the ontology 
to make is_a relationships between 'electron transport' and some specific 
kinds of electron transport found in photosynthesis (and, at the same time, 
perhaps, do the same for mitochondrial electron transport processes), and it 
looks like Jen's plan solves that one.

The other problem, though, is to go upwards to find a workable is_a parent 
that in turn links is_a fashion all the way up to 'biological process'. The 
'transport' is_a child of biological process looks like a poor fit in terms 
of the actual biology, but GO:0044237: cellular metabolic process still 
looks like a plausible is_a parent of 'electron transport'. Note, for what 
it's worth that 'cellular metabolic process' already has GO:0015979: 
photosynthesis and GO:0006091: generation of precursor metabolites and 
energy as is_a children. The second term is relevant here because it in turn 
has the old electron transport term, GO:0006118: electron transport, as an 
is_a child!

So is any term obsoletion needed?

Peter

----- Original Message ----- 
From: "Jennifer Deegan (nee Clark)" <jdeegan at ebi.ac.uk>
To: "Jim Hu" <jimhu at tamu.edu>
Cc: <electron-transport at genome.stanford.edu>
Sent: Monday, March 17, 2008 11:06 AM
Subject: Re: [Electron-transport] one more addition

> Hi Jim,
>
> That's exactly whatI was asking. :-) The thing that is missing there is
> that we hoped that the user interface of our browser would hid the is_a
> links that are there just for is_a completeness, but they don't yet.
>
> I think the suggestion that you make for the photosystem terms would do
> very well. The difficulty with the other two is that they should have
> is_a links to functions and they can't as they are in process. Really we
> should obsolete them, but we decided to save that for the next step in
> editing. Maybe for the commit on wednesday I could just change these
> relationships back to is_a and then we could deal with them further down
> the line. This might be better than cluttering the ontology with
> unnecessary relationships.
>
> On wednesday morning I will commit our changes to the live ontology file
> and everyone will get to see what we have done, so it will be pretty
> exciting to see what all the users say.
>
> Jen
>
> Jim Hu wrote:
>
>> Hi Jen,
>>
>> So, if I understand it correctly, the problem is that you have part_of
>> relationships to photosynthetic electron transport chain but can't use
>> is_a relationships because a part is not an instance of a thing?  And
>> because we added chain to the electron transport, it can only be is_a to
>> chain if it is a series of reactions.
>>
>> It seems to me that you could make the electron transport in photosystem
>> I and photosystem II are both is_a children of electron transport chain,
>> since they are each smaller chains that when linked up make the overall
>> photosynthetic electron transport chain.  I'm not sure about some of the
>> others, as they are in that grey area we discussed as being between
>> process and function.  Is one link still a chain?
>>
>> This is one of those places where I dislike the whole is_a complete
>> business.  Doing the above takes the hierarchy we worked so hard to
>> define and reflattens it for the sake of abstract philosophical
>> consistency.  But this flattening makes the graph nature of the ontology
>> confusing to humans, which suggests  to me that the ontological
>> principles for reasoning are not modeling how we actually think very
>> well. But that's a whole different discussion that I'm sure the
>> consortium has beaten to death long before I joined!
>>
>> Jim
>>
>>
>> On Mar 17, 2008, at 9:42 AM, Jennifer Deegan (nee Clark) wrote:
>>
>>> Hi,
>>>
>>> Thank you for your comments. Clearly that was not the way to go, so I
>>> will go back a few steps and explain the problem that I am trying to
>>> solve, and maybe you will have better ideas.
>>>
>>> I need to find an is_a path to the root (by tomorrow lunchtime GMT) for
>>> the following terms:
>>>
>>> photosynthetic electron transport in cytochrome b6/f ; GO:0009775
>>> (undefined)
>>>
>>> photosynthetic electron transport in photosystem I ; GO:0009773
>>> def: Electrons move from the primary electron acceptor (Quinone, X)
>>> through a chain of electron transport molecules in the thylakoid
>>> membrane until they reach ferredoxin which passes the electron to the
>>> ultimate electron acceptor; NADP.
>>>
>>> photosynthetic electron transport in photosystem II ; GO:0009772
>>> def: Electrons move from the primary electron acceptor (Quinone, Q)
>>> through a chain of electron transport molecules in the thylakoid
>>> membrane until they reach the ultimate electron acceptor of Photosystem
>>> II, which is plastocyanin (PC). The electron is then passed to the P700
>>> chlorophyll a molecules of the reaction centre of photosystem I.
>>>
>>> photosynthetic electron transport in plastocyanin ; GO:0009776
>>> (undefined)
>>>
>>> photosynthetic electron transport in plastoquinone ; GO:0009774
>>> (undefined)
>>>
>>> Does anybody have any good ideas for how I could do that? I just need to
>>> make an is_a relationship from the terms up to another term that has a
>>> direct is_a path up to the term 'biological_process'.
>>>
>>> I am working in the file go/scratch/electron_transport.obo
>>> http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/scratch/electron_transport.obo
>>>
>>> Thanks,
>>>
>>> Jen
>>>
>>>
>>> _______________________________________________
>>> Electron-transport mailing list
>>> Electron-transport at geneontology.org
>>> http://fafner.stanford.edu/mailman/listinfo/electron-transport
>>
>>
>> =====================================
>>
>> Jim Hu
>>
>> Associate Professor
>>
>> Dept. of Biochemistry and Biophysics
>>
>> 2128 TAMU
>>
>> Texas A&M Univ.
>>
>> College Station, TX 77843-2128
>>
>> 979-862-4054
>>
>>
>>
>
> -- 
> Jennifer Deegan (nee Clark)
> EMBL-European Bioinformatics Institute
> Gene Ontology Consortium
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> Electron-transport at geneontology.org
> http://fafner.stanford.edu/mailman/listinfo/electron-transport
> 