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Update S cell (CL_0002281) with detailed functional, morphological, and recent transcriptomic evidence#3551

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Update S cell (CL_0002281) with detailed functional, morphological, and recent transcriptomic evidence#3551
Copilot wants to merge 18 commits intomasterfrom
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Copilot AI commented Jan 8, 2026 •
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The existing S cell term (CL_0002281) lacked detailed functional and morphological information. Recent single-cell transcriptomic studies also challenge the traditional "one cell-one hormone" classification for enteroendocrine cells.

Changes

Definition expanded from basic secretion profile to comprehensive characterization:

  • Stimulus: pH-responsive secretion (luminal pH < ~4.5)
  • Morphology: Open-type cell with apical microvilli for luminal sensing
  • Function: Duodenal pH regulation via pancreatic bicarbonate stimulation, gastric acid inhibition
  • Distribution: Duodenojejunal epithelium, highest in duodenum

References updated: Added PMID:21518048, 30725969, 37240181 (preserved original PMID:15153415)

Editorial comment added: Documents PMID:38866945 findings showing SCT expression co-occurs across K, N, I, and L cell subtypes, contradicting discrete S cell population model

Synonym added: "S cell" for discoverability

Parent classes preserved: Maintains existing hierarchical relationships (enteroendocrine cell, peptide hormone secreting cell, serotonin secreting cell)

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Original prompt

This section details on the original issue you should resolve

<issue_title>[NTR] S cell</issue_title>
<issue_description>
Definition (free text, with reference(s), please. PubMed ID format is PMID:XXXXXX)

An enteroendocrine cell of the small intestine that secretes secretin into the bloodstream in response to decreased luminal pH (below ~4.5) (Parikh & Thevenin, 2023). This cell is an open-type cell, characterised by apical microvilli that extend to the intestinal lumen, allowing direct detection of luminal contents (Pandol, 2010; Atanga et al., 2023). This cell regulates duodenal pH by stimulating pancreatic bicarbonate secretion, inhibiting gastric acid secretion and gastric emptying, and promoting biliary secretion (Atanga et al., 2023). S cells are scattered throughout the duodenojejunal epithelium, with the highest density in the duodenum.

DONOT replace refrences - instead ss these to existing ones

PMID: 21518048
PMID: 37240181
https://www.ncbi.nlm.nih.gov/books/NBK54132/
PMID: 30725969

comments

Recent single-cell transcriptomic analyses in both mice and humans demonstrate that SCT expression is not restricted to a single distinct cell population but rather is co-expressed across multiple mature enteroendocrine cell subtypes, particularly K, N, I, and L cells, challenging the traditional "one cell-one hormone" classification.
PMID: 38866945

Parent cell type term (check the hierarchy here https://www.ebi.ac.uk/ols4/ontologies/cl)

enteroendocrine cell

Anatomical structure where the cell type is found (check Uberon for anatomical structures: https://www.ebi.ac.uk/ols4/ontologies/uberon)
small intestine epithelium

Poss additional
GO term for secretin secretion
GO term for pH detection
GO term for detection of chemical stimulus.

Additional notes or concerns

David's perplexity searches
https://www.perplexity.ai/search/give-me-details-of-the-structu-eFRGpDZlRbSxGuGk_j9bzg
https://www.perplexity.ai/search/system-role-you-are-a-knowledg-M_qeiaXmTvuWTZoCxpPJJw

</issue_description>

Comments on the Issue (you are @copilot in this section)

@dosumis UPDATE: RECENT PAPER QUESTIONS THIS CATEGORY (and other enteroendocrine categories too): https://www.nature.com/articles/s41598-024-63699-0 image @dosumis Turns out we do have this after all (Doh)

http://purl.obolibrary.org/obo/CL_0002281 - but note, nothing on what stimulates these cell types.</comment_new>

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Copilot AI and others added 2 commits January 8, 2026 14:00
@Caroline-99
Update S cell (CL_0002281) definition with detailed functional and mo…
3babe92 
…rphological information

- Enhanced definition to include stimulus (decreased luminal pH below ~4.5)
- Added open-type morphology details (apical microvilli extending to lumen)
- Added functional roles (pH regulation, bicarbonate secretion, inhibiting gastric acid)
- Added anatomical distribution (duodenojejunal epithelium, highest in duodenum)
- Added new references: PMID:21518048, PMID:30725969, PMID:37240181
- Added editorial comment about recent single-cell transcriptomic findings (PMID:38866945)
- Added "S cell" as exact synonym

Co-authored-by: Caroline-99 <116108977+Caroline-99@users.noreply.github.com>
@Caroline-99
Address code review feedback: use American spelling and clarify SCT a…
036c0a2 
…bbreviation

- Changed "characterised" to "characterized" for consistency
- Clarified SCT abbreviation as "(secretin)" in editorial comment

Co-authored-by: Caroline-99 <116108977+Caroline-99@users.noreply.github.com>
Copilot AI changed the title [WIP] Add definition for S cells in the small intestine Update S cell (CL_0002281) with detailed functional, morphological, and recent transcriptomic evidence Jan 8, 2026
Copilot AI requested a review from Caroline-99 January 8, 2026 14:05
@Caroline-99 Caroline-99 marked this pull request as ready for review January 16, 2026 11:21
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Caroline-99 commented Jan 16, 2026

#gogoeditdiff

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github-actions bot commented Jan 16, 2026 •
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Here's a diff of how these changes impact the classified ontology (on -base file):

Ontology comparison

Left

  • Ontology IRI: http://purl.obolibrary.org/obo/cl/cl-base.owl
  • Version IRI: http://purl.obolibrary.org/obo/cl/releases/2026-03-12/cl-base.owl
  • Loaded from: file:/__w/cell-ontology/cell-ontology/src/ontology/cl-base-master.owl/cl-base.owl

Right

  • Ontology IRI: http://purl.obolibrary.org/obo/cl/cl-base.owl
  • Version IRI: http://purl.obolibrary.org/obo/cl/releases/2026-03-12/cl-base.owl
  • Loaded from: file:/__w/cell-ontology/cell-ontology/src/ontology/cl-base-pr.owl/cl-base.owl

Ontology imports

Ontology annotations

GO_0009593 http://purl.obolibrary.org/obo/GO_0009593

Added

type S enteroendocrine cell http://purl.obolibrary.org/obo/CL_0002281

Removed

Added

  • type S enteroendocrine cell hasExactSynonym "S cell"

  • type S enteroendocrine cell comment "Recent single-cell transcriptomic analyses in both mice and humans demonstrate that SCT (secretin) expression is not restricted to a single distinct cell population but rather is co-expressed across multiple mature enteroendocrine cell subtypes, particularly K, N, I, and L cells, challenging the traditional 'one cell-one hormone' classification."

  • type S enteroendocrine cell IAO_0000115 "An enteroendocrine cell of the small intestine that secretes secretin into the bloodstream in response to decreased luminal pH (below ~4.5) (Parikh & Thevenin, 2023). This cell is an open-type cell, characterised by apical microvilli that extend to the intestinal lumen, allowing direct detection of luminal contents (Pandol, 2010; Atanga et al., 2023). This cell regulates duodenal pH by stimulating pancreatic bicarbonate secretion, inhibiting gastric acid secretion and gastric emptying, and promoting biliary secretion (Atanga et al., 2023). S cells are scattered throughout the duodenojejunal epithelium, with the highest density in the duodenum."

  • type S enteroendocrine cell SubClassOf RO_0002215 some GO_0009593

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github-actions bot commented Jan 16, 2026 •
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Here's a diff of your edit file (unreasoned)

Ontology comparison

Left

  • Ontology IRI: http://purl.obolibrary.org/obo/cl.owl
  • Version IRI: None
  • Loaded from: file:/__w/cell-ontology/cell-ontology/master/src/ontology/cl-edit.owl

Right

  • Ontology IRI: http://purl.obolibrary.org/obo/cl.owl
  • Version IRI: None
  • Loaded from: file:/__w/cell-ontology/cell-ontology/branch/src/ontology/cl-edit.owl

Ontology imports

Ontology annotations

detection of mechanical stimulus involved in sensory perception http://purl.obolibrary.org/obo/GO_0050974

Added

type S enteroendocrine cell http://purl.obolibrary.org/obo/CL_0002281

Removed

Added

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Caroline-99 commented Jan 16, 2026

#gogoeditdiff

@Caroline-99 Caroline-99 requested review from RiveraAndrea83 and removed request for Caroline-99 January 16, 2026 12:00
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RiveraAndrea83 commented Feb 5, 2026

#gogoeditdiff

@RiveraAndrea83
Merge branch 'master' into copilot/add-s-cell-definition
091c686
@RiveraAndrea83
Merge branch 'master' into copilot/add-s-cell-definition
654d480
@RiveraAndrea83
Added GO term for detection of chemical stimulus
51622e1 
-Added capable of some 'detection of chemical stimuli';
-refreshed imports
@RiveraAndrea83
Fixed obsoleted GO terms
12f0e2f 
Fixed obsoleted GO terms on some terms

-Refreshed imports
@RiveraAndrea83
Merge branch 'master' into copilot/add-s-cell-definition
52c5bd7
@RiveraAndrea83
Fixed axiomatisation
71bc03b 
A GO term was mistakingly assigned as a child of a cell.

Fixed the issue
@RiveraAndrea83
Fixed GO terms
9eb66c5 
-replaced obsoleted detection of electrical stimuli involved in electroception with 'electroception'
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github-actions bot commented Feb 17, 2026

http://purl.obolibrary.org/obo/CL_0002042 in taxon http://purl.obolibrary.org/obo/NCBITaxon_9606 SubClassOf Nothing

Axiom Impact

Axioms used 1 times

Ontologies used:

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dosumis commented Feb 17, 2026

Looks like the inconsistency is nothing to do with this branch. Assume this is on master. I wonder if I accidentally merged a commit yesterday before all tests had run.

@dosumis
Update hra_subset.owl
cf87886 
Hack to remove HRA axiom from component/hra_subset causing inconsistency. This will reappear when we update imports, so needs to be fixed upstrea.
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RiveraAndrea83 commented Feb 19, 2026

#gogoeditdiff

@RiveraAndrea83 RiveraAndrea83 self-assigned this Mar 11, 2026
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dosumis commented Mar 12, 2026

#gogoeditdiff

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Improve Type S enteroendocrine cell

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