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[Class hierarchy] terminally differentiated cells #2922

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noamrotenberg opened this issue Jan 28, 2025 · 2 comments
Open

[Class hierarchy] terminally differentiated cells #2922

noamrotenberg opened this issue Jan 28, 2025 · 2 comments

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@noamrotenberg
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CL term
non-terminally differentiated cell (CL:0000055) and terminally differentiated osteoblast (CL:0001039)

Suggested revision of class hierarchy
Currently, "non-terminally differentiated cell" (CL:0000055) is an ancestor of "terminally differentiated osteoblast" (CL:0001039), which seems incorrect to me.
I think the issue is osteoblast (CL:0000062) isa Subclass of "non-terminally differentiated cell", even though there is a "non-terminally differentiated osteoblast" child of osteoblast. I'm not sure whether these 2 children of "osteoblast" should be deleted or the connection between "osteoblast" and "non-terminally differentiated cell" should be deleted.

@dosumis
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dosumis commented Feb 5, 2025

Seems to be based on the assumption that 'blast' indicated non-terminally differentiated.

Some possible fixes

Option 1

Merge

"terminally differentiated odontoblast" --> odontocyte
"terminally differentiated osteoblast" --> osteocyte

Merge "terminally differentiated odontoblast" --> odontoblast

etc.

However, from reading around it seems that existence of odontocytes is controversial & maybe not all osteoblasts end up as osteocytes.

Option 2:

Obsolete the general grouping term (I'm not sure how useful it is and it is incompletely populated right now anyway)

@addiehl
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addiehl commented Feb 5, 2025

I favor option 2, as cell differentiation is a lot more complicated than previously appreciated. Mature naive T cells might be considered fully differentiated, but clearly can undergo additional paths of differentiation once activated. Other cell types can dedifferentiate under the right conditions.

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