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Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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NTR: Extrasynaptic Membrane #13306

Closed cross12tamu closed 4 years ago

cross12tamu commented 7 years ago

Potential GO term name: Extrasynaptic Membrane

Definition: An area of the dendritic or somatic membrane that is perisynaptic or distal to the synapse in which presynaptic release of neurotransmitters do not significantly affect signaling.

Aspect: Cellular Component

Relationships: Parent term would be Plasma Membrane Region

References: 17023503 16162835 15542076 9464994 14627650

jimhu-tamu commented 7 years ago

I suspect this is a CACAO request.

ukemi commented 7 years ago

@dosumis Any comments, since this is is in the synapse realm?

pgaudet commented 6 years ago

@ukemi This seems to be defined negatively (anything that is not in the synaptic membrane); should we create such terms ? I would be inclined to close this without creating the term.

Pascale

ukemi commented 6 years ago

These kinds of terms are generally hard to maintain. They are equivalent to creating classes like nucleus and then a term like 'the rest of the cell'. Then any time you want to add another component it would need to be a child of 'the rest of the cell'. So although this request doesn't mean exactly (anything that is not in the synaptic membrane), it is along the same vein.

jimhu-tamu commented 6 years ago

I understand the problem @ukemi raises, but with my limited knowledge of neurobiology plus scanning a few abstracts, it appears that various cells in neurons do have distinct classes of receptors that evolved to act either in the synaptic membrane (GO:0097060) or outside the synaptic region. It seems to me that this is a place where NOT would be useful, but can't be used under our current model for what a NOT annotation is.

Note also that plasma membrane region (GO:0098590) is a do not annotate term.

I don't like Curtis' definition, though. Can this be modeled on GO:0005576 extracellular region?

dosumis commented 6 years ago

IIRC the terms 'extrasynaptic membrane' and 'perisynaptic membrane' are generally used to refer to parts of the presynapse that are not involved in release - not to the whole PM apart from the synaptic membrane.

After discussion, the synapse group decided not to add these but I don't recall the reasons. We probably have the discussion on some tickets. @pimmelorus may remember details.

dosumis commented 6 years ago

BTW - don't like the NOT solution here. Very hard to do anything useful with the resulting annotation.

pgaudet commented 4 years ago

Nobody could find a good definition. Closing.