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obophenotype / cell-ontology

An ontology of cell types
https://obophenotype.github.io/cell-ontology/
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Add is_a edge between CL:0002453 and CL:0011115 #529

Closed mbernste closed 2 years ago

mbernste commented 5 years ago

I believe "oligodendrocyte precursor cell" should be a child of "precursor cell"

paolaroncaglia commented 2 years ago

@shawntanzk @dosumis would you have any objection to 'oligodendrocyte precursor cell' ("A progenitor cell of the central nervous system that can differentiate into oligodendrocytes or type-2 astrocytes...") being a subclass of 'precursor cell', as suggested above, or possibly even a subclass of 'progenitor cell' ("A precursor cell that has a tendency to differentiate into a specific type of cell. They are descendants of stem cells, only they are more constrained in their differentiation potential or capacity for self-renewal, and are often more limited in both senses.")? I'm happy to do the edit if you confirm. Thanks.

shawntanzk commented 2 years ago

I would rather we add 'capable of' some 'cell differentiation' on OPC -> that way it will automatically classify as a precursor cell. I think we might also have to relook into EA of progenitor cell, currently it is 'precursor cell' and ('develops from' some 'stem cell') which feels too broad, but im not 100% sure on that one.

paolaroncaglia commented 2 years ago

@shawntanzk

I would rather we add 'capable of' some 'cell differentiation' on OPC -> that way it will automatically classify as a precursor cell. I think we might also have to relook into EA of progenitor cell, currently it is 'precursor cell' and ('develops from' some 'stem cell') which feels too broad, but im not 100% sure on that one.

But if we make 'oligodendrocyte precursor cell' equivalent to 'neuron associated cell (sensu Vertebrata)' and 'capable of' some 'cell differentiation' wouldn't that translate into = all neuron associated cells give rise to oligodendrocytes (and not e.g. Merkel cells or perineuronal satellite cells)? Or did you mean subclass instead of equivalent? I'm not 100% sure about the progenitor equivalence either.

shawntanzk commented 2 years ago

I mean add a SubClassOf 'capable of' some 'cell differentiation' axiom to OPC, not an equivalent axiom. The auto-classification will happen cause precursor cell has a EA 'native cell' and ('capable of' some 'cell differentiation') -> OPC with that axiom will be classified rightly under precursor cell. If we want classification to progenitor cell, we can add (develops from' some 'stem cell' to OPC too, which is not wrong, just I don't feel comfortable with current progenitor equivalence.

paolaroncaglia commented 2 years ago

@shawntanzk I just tried and it classifies under progenitor, not precursor: Screenshot 2022-04-27 at 16 04 16 Haven't committed.

paolaroncaglia commented 2 years ago

(@shawntanzk adding you as co-assignee for your feedback, thanks.)

shawntanzk commented 2 years ago

oh nice, because of the develops from axiom in OPC, yeah that works, progenitor is under precursor so that basically fixes everything :) Thanks. Think you can commit that and get it thorugh