[Transport] GO transport terms.

[Jennifer Deegan (nee Clark)]

Hi Val,

> However, Jen, I think there may be an issiue wiuth the definition of 'pore complex'  in the component ontology
> 
> It is
> pore complex
> Definition 
> Any small opening in a membrane that allows the passage of gases and/or liquids
> (and it has some strange synonyms, including channel-forming toxin activity -related)?
> 
> Its children are
> GO:0005643 nuclear pore
> GO:0005579 membrane attack complex
> GO:0005757 mitochondrial permeability transit
> 
> So, it seems like the component terms do not mirror the meaning of the function terms described below.
> 
> For instance, I would not annotate "narrow pore channel activity" to "pore complex" but this would not be excluded by the current definition of pore complex

Yes I was thinking that we ought to look at that too. I am noting it on 
the 'to do' part of the transport section of the wiki.

Jen


> 
> 
> "Jennifer Deegan (nee Clark)" <jdeegan at ebi.ac.uk> wrote: 
> 
>>Dear Mike,
>>
>>This is a bit of tricky area, with some ambiguous language. The pore 
>>complex terms in the component ontology are defined as being holes in 
>>the membrane that allow substrates to flow through without any kind of 
>>activity required to open the holes or encourage transport. The channel 
>>complex terms, however, are defined as requiring some activity to cause 
>>them to open or to transport substrates. In your annotation it would be 
>>best if you could figure out whether the complexes that you are 
>>annotating are the sort that are open by default, or the sort that 
>>require opening (gating).
>>
>>There is a lot of very clear information about this in the definitions 
>>of the transport terms in the function ontology, as we have just 
>>overhauled these terms. The standard structure that we created is here:
>>http://wiki.geneontology.org/index.php/Docs
>>The standard definitions at the bottom of this page may help you.
>>
>>The minutes of our discussion are here:
>>http://wiki.geneontology.org/index.php/Tranporter_Activity_Meeting_Notes
>>
>>Our transport overhaul is still in progress, and I will note your 
>>comments so that we can come back and make any necessary improvements in 
>>the component ontology structure.
>>
>>If you are looking for further information, I found the transmembrane 
>>transport section of the Molecular Biology of the Cell very useful. The 
>>view presented here almost exactly corresponds to the structure that we 
>>ended up implementing in the function ontology.
>>
>>I hope this helps. I am cc'ing transport list in case others have 
>>further comments. Please do write again if you have further questions.
>>
>>Best wishes,
>>
>>Jennifer Deegan
>>GO Curator
>>
>>
>>
>>
>>
>>From:
>>Mike Bada <mike.bada at UCHSC.edu>
>>Date:
>>Thu, 24 Jul 2008 20:10:22 -0600
>>To:
>>gohelp at genome.stanford.edu
>>
>>Hello GO helpdesk,
>>
>>Quick question:  In the GO cellular-component subontology, should the 
>>channel complex terms be more directly related to pore complex, or is 
>>the current structure (with a lack of a more direct connection between 
>>the channel complex terms and pore complex) advertent?  I'm not at all 
>>an expert in this, but "pore" and "channel" seem to be quite 
>>interchangeable in the literature.  (We're using the GO to annotate 
>>biomedical literature for NLP applications and have been encountering 
>>"channel" a lot and wonder if we should annotate these mentions with 
>>"pore complex".)
>>
>>Thanks in advance,
>>Mike
>>
> 
> 

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