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geneontology / go-ontology

Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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Revise definition of GO:0001540 amyloid-beta binding #20109

Closed RLovering closed 3 years ago

RLovering commented 3 years ago

Hi

please would you revise the definition for this term GO:0001540 amyloid-beta binding as the term name is misleading. Many proteins bind amyloid precursor protein or one of the cleavage products, and they are not all binding amyloid-beta. However, the current definition would suggest that any protein binding the precursor would be annotated to this term.

current definition:Interacting selectively and non-covalently with amyloid-beta peptide/protein and/or its precursor.

Change definition to: Interacting selectively and non-covalently with amyloid-beta peptide/protein.

Thanks

Ruth @pgarmiri @magrane @slaulederkind

slaulederkind commented 3 years ago

And how about a amyloid-beta precursor binding term if the definition of term GO:0001540 "amyloid-beta binding" gets changed?

pgaudet commented 3 years ago

@RLovering - what do you think ?

RLovering commented 3 years ago

I think it is very odd that even though APP is a precursor of Amyloid-beta we haven't really assigned a MF term to the membrane protein. one of the cleavage products seems to be involved in transcription regulation (maybe as a coTF), the full proteins may act as an 'adhesion molecule' or signaling receptor. eg the uniprot record states: Functions as a cell surface receptor and performs physiological functions on the surface of neurons relevant to neurite growth, neuronal adhesion and axonogenesis.

APP has 2 paralogs APLP1 and APLP2 neither of which are given clear MF roles either.

So maybe it would be helpful to have a general term for binding these proteins, my problem is that because of their range of functions the term couldn't be included under anything other than protein binding. I think it might be better to annotate the binding of these three proteins (APP, APLP1, APLP2) based on how they are functioning, eg when they acts as a coreceptor to coreceptor binding and to include APP in the with field.

Or can you see a better way to do this

Best

Ruth