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basal cell of olfactory epithelium (CL:0002169): positional vs lineage sense, synonym scope, globose cell placement #3700
Description
Three linked problems on this term. All need an editor decision rather than a mechanical fix, so filing for discussion rather than proposing a PR.
1. "basal cell" is being used in two different senses
CL:0002169 is positional — a cell in the basal region of the olfactory epithelium — and is correctly not a subclass of CL:0000646 basal cell. But CL:0002187 basal cell of epidermis uses the identical naming template and is one. Nothing in the labels distinguishes the senses:
| term | sense | under CL:0000646? |
|---|---|---|
CL:0002187 basal cell of epidermis |
lineage/type (KRT5/TP63⁺ progenitor) | yes |
CL:0002169 basal cell of olfactory epithelium |
positional | no |
CL:0002341 basal cell of prostate epithelium |
positional | no |
CL:0002493 strial basal cell |
neither — name collision | no |
A curator or a mapping pipeline reading these labels has no way to tell which is meant.
2. Synonym scope looks inverted
synonym: "horizontal basal cell" BROAD
HBCs are one of (at least) two basal populations in the olfactory epithelium, and CL already models the other (CL:0002171 globose cell of olfactory epithelium) as a child of CL:0002169. So "horizontal basal cell" is narrower than the term, not broader — the scope should be NARROW, or HBC should become its own class sibling to CL:0002171 rather than a synonym of their shared parent.
3. Globose cell inherits a differentia its own definition contradicts
CL:0002171 is is_a CL:0002169, so it inherits the positional differentia. Its own definition says globose cells:
"form a distinct basal zone spaced slightly from the basal surface of the epithelium."
Biologically that is right — GBCs are the ASCL1/NEUROG1⁺ neurogenic transit-amplifying population sitting above the HBCs, en route to olfactory sensory neurons. So CL contradicts itself across two adjacent stanzas.
The same applies to CL:0002184 basal proper cell of olfactory epithelium, also is_a CL:0002169.
Options
- Rename
CL:0002169positionally, e.g. cell of basal region of olfactory epithelium, so it stops reading as aCL:0000646subtype. - Demote the HBC synonym to NARROW, or split HBC out as a proper class.
- Revisit whether
CL:0002171should remain a child, given it is not on the basal lamina.
Related: the relation used by this term is a separate, mechanical bug — see #3699 / #3704. Part of the epithelial hierarchy cleanup (#3703).
@cmungall drove the agent, checked its reasoning, and is accountable for its output.
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