Index for a set of small, related fixes to the epithelial branch, surfaced while reviewing #3692 (cycling epithelial cell). Each child is independently reviewable; this ticket exists only to record the dependency order.
The thread
basal cell (CL:0000646) is not classified as an epithelial cell. It sits under CL:0000036 epithelial fate stem cell ≡ somatic stem cell and capable_of some 'epithelial cell differentiation' — a "not yet epithelial" reading that no member of the class satisfies. Downstream, four of eight basal descendants are already classified as epithelial via hand-asserted lineage parents, and four are not, so the classification is half-done and arbitrary about which half.
Children
| issue |
what |
status |
| #3694 |
Reclassify CL:0000646 as epithelial cell (SubClassOf edit only) |
PR #3705 |
| #3697 |
Rewrite the CL:0000646 definition position-first — current text conflates position with stemness |
PR #3706, stacked on #3705 |
| #3698 |
Rename CL:0000036 → epithelial stem cell; fix the capable_of differentia |
blocked on #3694 |
| #3699 |
CL:0002169, CL:4033093 asserted part_of the acellular basal lamina |
PR #3704 |
| #3700 |
CL:0002169: positional vs lineage sense, HBC synonym scope, globose cell placement |
discussion, no PR |
| #3701 |
Two QC invariants (no cell part_of acellular structure; classification completeness) |
axiom in PR #3707 (draft) |
Order
#3694 / #3705 ── #3697 / #3706 (stacked, same stanza)
├──── #3698
└──── #3701 (check 2)
#3699 / #3704 ── #3707 (draft; blocked on upstream UBERON)
#3700 (discussion; #3704 fixes the relation, this decides what the class means)
Only #3705/#3706 and #3704/#3707 need stacking. Everything else touches disjoint regions of cl-edit.owl.
Upstream dependency
#3707 cannot merge until two UBERON axioms are fixed:
SubClassOf(UBERON:0002139 subcommissural organ, part_of some UBERON:0011357 Reissner's fiber)
SubClassOf(UBERON:0001993 reticular layer of dermis, part_of some UBERON:0008877 epidermal-dermal junction) [FMA]
These make CL:0008045, CL:4023181 and CL:2000096 violate the acellular-parthood constraint through inheritance, despite those three having correct CL axioms. Both also place a multicellular anatomical structure inside an acellular one, so they are defects on UBERON's own terms.
Noted and deliberately deferred
CL:0000066 epithelial cell is defined as "…usually found in a two-dimensional sheet with a free surface … apical part is directed towards the lumen…" — a simple-epithelium definition. No cell of a stratified or pseudostratified epithelium below the surface layer satisfies the apical clause, including suprabasal cell, keratinocyte, and urothelial cell, all of which CL already classifies as epithelial. The definition is applied loosely everywhere, so the reclassification in #3694 is consistent with existing practice; tightening CL:0000066 itself is a much larger discussion and is not in scope for this epic.
Also out of scope, tracked separately on the cell-state thread: #3702.
@cmungall drove the agent, checked its reasoning, and is accountable for its output.
Generated by Claude Code
Index for a set of small, related fixes to the epithelial branch, surfaced while reviewing #3692 (
cycling epithelial cell). Each child is independently reviewable; this ticket exists only to record the dependency order.The thread
basal cell(CL:0000646) is not classified as anepithelial cell. It sits underCL:0000036 epithelial fate stem cell≡somatic stem cell and capable_of some 'epithelial cell differentiation'— a "not yet epithelial" reading that no member of the class satisfies. Downstream, four of eight basal descendants are already classified as epithelial via hand-asserted lineage parents, and four are not, so the classification is half-done and arbitrary about which half.Children
CL:0000646asepithelial cell(SubClassOfedit only)CL:0000646definition position-first — current text conflates position with stemnessCL:0000036→epithelial stem cell; fix thecapable_ofdifferentiaCL:0002169,CL:4033093assertedpart_ofthe acellular basal laminaCL:0002169: positional vs lineage sense, HBC synonym scope, globose cell placementpart_ofacellular structure; classification completeness)Order
Only #3705/#3706 and #3704/#3707 need stacking. Everything else touches disjoint regions of
cl-edit.owl.Upstream dependency
#3707 cannot merge until two UBERON axioms are fixed:
These make
CL:0008045,CL:4023181andCL:2000096violate the acellular-parthood constraint through inheritance, despite those three having correct CL axioms. Both also place a multicellular anatomical structure inside an acellular one, so they are defects on UBERON's own terms.Noted and deliberately deferred
CL:0000066 epithelial cellis defined as "…usually found in a two-dimensional sheet with a free surface … apical part is directed towards the lumen…" — a simple-epithelium definition. No cell of a stratified or pseudostratified epithelium below the surface layer satisfies the apical clause, includingsuprabasal cell,keratinocyte, andurothelial cell, all of which CL already classifies as epithelial. The definition is applied loosely everywhere, so the reclassification in #3694 is consistent with existing practice; tighteningCL:0000066itself is a much larger discussion and is not in scope for this epic.Also out of scope, tracked separately on the cell-state thread: #3702.
@cmungall drove the agent, checked its reasoning, and is accountable for its output.
Generated by Claude Code