[Class hierarchy] Reclassifying basal cells as epithelial cells

[dillerm]

CL term
basal cell (CL:0000646)
epithelial cell (CL:0000066) (proposed parent)

Suggested revision of class hierarchy
Either reclassify 'basal cell' as a subclass of 'epithelial cell' or assert it to be part of some 'epithelium'. Alternatively, if you prefer to distinguish immature cells from mature cells of a certain type, you can create an 'epithelial lineage cell' that has both this and 'epithelial cell' as subclasses.

[cmungall]

At the least the current def needs to be made genus-differentia

id: CL:0000646
name: basal cell
def: "Undifferentiated; mitotic stem cell for other epithelial cell types; rounded or elliptical with little cytoplasm and few organelles; contain cytokeratin intermediate filament." [GOC:tfm, ISBN:0517223651]
xref: BTO:0000939
xref: FMA:62516
subset: human_reference_atlas
subset: mouse_subset
subset: human_subset
subset: cellxgene_subset
is_a: CL:0000036 ! epithelial fate stem cell

[cmungall]

Support option 1. Two things settle it from inside CL:

The layer directly above basal is already epithelial. CL:7770004 suprabasal cell — "An epithelial cell that resides in the layer(s) immediately above the basal layer in stratified or pseudostratified epithelia" — is asserted SubClassOf epithelial cell. And CL:4033048 respiratory tract suprabasal cell develops_from CL:0002633 respiratory basal cell, so CL currently has an epithelial cell developing from a non-epithelial cell within the same epithelium.

Four descendants are already classified both ways, via hand-asserted lineage parents (keratinocyte, urothelial cell, basal epithelial cell of tracheobronchial tree):

cl info [ .sub CL:0000036 .and .sub "epithelial cell" ]
CL:1000486 ! basal cell of urothelium
CL:2000033 ! limb basal cell of epidermis
CL:1000349 ! basal cell of epithelium of bronchus
CL:0002187 ! basal cell of epidermis

Four of eight. CL:0002633 respiratory basal cell is absent while its own child CL:1000349 is present; CL:1000447 is absent despite being labelled "epithelial cell of stratum germinativum of esophagus". So the classification is already half-done and arbitrary about which half — this makes it uniform.

Option 3 (epithelial lineage cell) is not needed: no member of CL:0000646 is pre-epithelial. All eight descendants are defined by position inside an epithelium, and the terms that look like counterexamples — CL:0002493 strial basal cell, CL:0002169 basal cell of olfactory epithelium, CL:0005017 obsolete plant basal cell — are name collisions, not members.

PR to follow, scoped to the SubClassOf edit alone. The definition rewrite is split to #3697 (the current text conflates position with stemness and needs its own discussion), and the related CL:0000036 rename to #3698. Index: #3703.

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[cmungall]

Attribution note for the comment above: @cmungall drove the agent, checked its reasoning, and is accountable for its output.

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