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geneontology / go-ontology

Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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Is there a difference between GO:1990753 equatorial cell cortex/ GO:0031097 medial cortex #18498

Open ValWood opened 4 years ago

ValWood commented 4 years ago

equatorial cell cortex Definition (GO:1990753 GONUTS page) The region of the cell cortex in a mitotically dividing cell that flanks the central spindle and corresponds to the site of actomyosin ring formation that results in cleavage furrow formation and ingression. PMID:16352658 PMID:22552143 PMID:23750214 PMID:25898168

GO:0031097 medial cortex Definition (GO:0031097 GONUTS page) A medial cortical band overlaying the nucleus which acts as a landmark for contractile ring positioning and plays a role in cell cycle regulation. PMID:15572668 PMID:19474789

ValWood commented 4 years ago

(I know GO:1990753 speciifes mitotic, but

GO:0031097 medial cortex in PMID:15572668 PMID:19474789 is also mitotic

ukemi commented 4 years ago

It seems like what you call the medial cortex we call the equatorial cortex. My only concern is how does it play a role in cell cycle regulation and does that extend across the phyla?

ukemi commented 4 years ago

If we merge, does it make sense to keep the first definition. I like it better.

ValWood commented 4 years ago

  1. I don't really know why " plays a role in cell cycle regulation" is part of the second def. The medial cortex is the place that the cell cycle regulators localize to (wee1 etc) but I would not say that the cortex directly played a part in cell cycle regulation?

  2. These do seem to mean the same thing. I prefer aspects of both definitions.

cortical band overlaying the nucleus which acts as a landmark for contractile ring positioning in mitosis

is clearest and most accurate, because flanking the spindle depends on the time point and orientation of the spindle.

That said, what would we call it? "medial cortex" is very established for fission yeast. Equatorial band is never used fission yeast. I guess because the cell is cylindrical, not spherical.

ValWood commented 4 years ago

Ah I think "flanking the central spindle" is used in vertebrate term, because cells that undergo open mitosis have nuclear breakdown. For yeast the term is defined wrt the nucleus.

ValWood commented 3 years ago

we can keep these as separate terms for now, as it doesn't make anything incorrect. Logical defs should fix this down the line.

ValWood commented 2 years ago

I came across this again today. reopening. I will assign to me for when I begin editing.

ValWood commented 2 years ago
  1. note that "in a mitotically dividing cell " is not necessarily true. The medial cortex exists when the cell is not dividing (proteins begin accumulating at the medial cortex in interphase).
  2. I pefer the "medial cortex term and definition, and this is used in 1111 annotations whereas "equatorial cortex is only used in 7", I would check these 7 to make sure they fit a new more generic definition.
ValWood commented 2 years ago

A medial cortical band overlaying the nucleus which acts as a landmark for contractile ring positioning during mitotic M-phase.

seems to work for both