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Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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cardiac depolarization and repolarization terms #22617

Closed RLovering closed 2 years ago

RLovering commented 2 years ago

Hi I think David OS sorted these out but I don't really understand the logic behind this.

However, I think there should be more similarities between the depolarization and repolarization terms. Screenshot 2022-01-04 at 16 34 47

Currently regulation of depolarization has the parent term: ion homeostasis, but no link to regulation of ion transport. In contrast regulation of repolarization has the parent term: regulation of ion transport, but no link to ion homeostasis.

Ironically I think that depolarization is actually not 'ion homeostasis' as this is taking the ions away from the 'resting' polarized state whereas repolarization takes the membrane back to the resting polarized state.

What do you think?

More importantly I think either both or neither should have regulation of ion transport as parent terms.

What do you think?

I don't think GO:0051649 establishment of localization in cell should be a parent term for GO:0099622 cardiac muscle cell membrane repolarization. If this term is appropriate then it should be the parent to the more general term GO:0086009 membrane repolarization. And why not then add this as a parent to the equivalent depolarization terms?

Sorry about querying this, perhaps it does all make sense?

Ruth

raymond91125 commented 2 years ago

If there are no objections, I'll ADD membrane depolarization a child of ion transmembrane transport and REMOVE regulation of membrane depolarization a child of ion homeostasis.

establishment of localization in cell is very broadly defined as "Any process, occuring in a cell, that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation." The connection to is through inference, wrt the cardiac muscle cell part. There is no explicit mentioning of cell in membrane repolarization. @RLovering Do you think the changes are sufficient? Thanks.

pgaudet commented 2 years ago

Thanks @raymond91125

I wonder about transport - maybe we should use 'has part' some transport? I dont think depolarization/repolarization are types of transport, are they?

Thanks, Pascale

raymond91125 commented 2 years ago

de/repolarization is achieved via ion channels opening and closing. I don't think there are other parts. Thus transport is necessary and sufficient. In the case of cardiac muscle cells, depolarization opens up Ca2+ channels and the influx of Ca2+ further depolarizes as wells as causes contraction. Thus transport can have a purpose in addition to that of changing membrane potential.