[Transport] GO transport terms.

[Jennifer Deegan (nee Clark)]

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

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