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NTR: crypt top colonocyte (closes #3756) - #3757

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NTR: crypt top colonocyte (closes #3756)#3757
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@ai4c-agent ai4c-agent Bot commented Sep 28, 2026

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Summary

Adds a new term as requested in #3756:

  • Label: crypt top colonocyte
  • Temporary ID: CL:9900001 (from the Temporary IDs idrange 9900000–9999999; expected to be replaced by a definitive ID during the standard reserialisation step)
  • Parent: colonocyte (CL:1000347)
  • Definition: "A mature, terminally differentiated colonic absorptive epithelial cell located at the top of the crypt (colonic surface epithelium), marked by high expression of AQP8 together with SLC26A3, CEACAM5, CEACAM7, GUCA2A, and TFF1. Represents the fully matured end-state of the colonocyte differentiation trajectory. Identified by sub-clustering analysis in the Human Gut Cell Atlas (HGCA) v1." [PMID:35530046]
  • Related synonyms: "colonocytes late", "surface colonocyte" (both with PMID:35530046 xref)
  • term_tracker_item: links back to [NTR] crypt top colonocyte #3756

Notes for the reviewer

  • Definition, synonyms, parent, and reference are all taken directly from the NTR in [NTR] crypt top colonocyte #3756 (the requester did not provide an ORCID, so no terms:contributor was added; terms:creator "Claude" is set as I authored the new term).
  • The requester noted that placement of the term "at the top of the crypt (colonic surface epithelium)" distinguishes it from crypt-base colonocytes; I have kept the anatomical relation implicit via the colonocyte parent (which is already part_of UBERON:0000397 colon) rather than fabricating a more specific UBERON class. Please advise if you'd like an explicit part_of axiom against a specific surface-epithelium UBERON term or a located_in relation.
  • The requester mentioned this is one of a batch of 7 related HGCA v1 differentiation-stage terms. Only the term explicitly requested in [NTR] crypt top colonocyte #3756 is added here — the other 6 will presumably arrive as their own NTR issues.
  • Validated with robot convert — no syntax errors.

Test plan

  • Reviewer confirms definition, reference (PMID:35530046), synonym choice, and parent placement are appropriate for the HGCA v1 use case.
  • robot reason on the ODK pipeline classifies the new term as expected.
  • Temporary CL:9900001 ID is replaced with a definitive ID during reserialisation.

Closes #3756.

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🤖 Generated with Claude Code

@github-actions @claude
Add new term: crypt top colonocyte (CL:9900001)
42f0de4 
Add a new term for crypt top colonocyte as requested in issue #3756.

- Label: crypt top colonocyte
- Parent: colonocyte (CL:1000347)
- Definition sourced from PMID:35530046 as provided by the requester,
  describing the mature, terminally differentiated colonic absorptive
  epithelial cell at the top of the crypt (colonic surface epithelium),
  marked by high expression of AQP8 together with SLC26A3, CEACAM5,
  CEACAM7, GUCA2A, and TFF1. Identified by sub-clustering analysis in
  the Human Gut Cell Atlas (HGCA) v1.
- Related synonyms: "colonocytes late", "surface colonocyte"
- Uses a temporary CL:9900001 ID (from the idranges Temporary IDs range)
  to be replaced with a definitive ID by the standard reserialisation
  process (see recent commit df153e1).

Signed-off-by: Claude

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
@ai4c-agent ai4c-agent Bot mentioned this pull request Sep 28, 2026
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@ct31-sanger

ct31-sanger commented Sep 28, 2026

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/clara

@ct31-sanger

ct31-sanger commented Sep 28, 2026

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#gogoeditdiff

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github-actions Bot commented Sep 28, 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/2026-09-28/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/2026-09-28/cl-base.owl
  • Loaded from: file:/__w/cell-ontology/cell-ontology/src/ontology/cl-base-pr.owl/cl-base.owl

Ontology imports

Ontology annotations

crypt top colonocyte http://purl.obolibrary.org/obo/CL_9900001

Added

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github-actions Bot commented Sep 28, 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

crypt top colonocyte http://purl.obolibrary.org/obo/CL_9900001

Added

This was referenced Sep 28, 2026
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ai4c-agent Bot commented Oct 2, 2026

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Closing in favor of #3777 (preferred by @ct31-sanger in #3776 (comment)). #3777 uses the richer #3776 definition that explicitly contrasts the term with CL:4047018 early colonocyte and CL:4047052 BEST4+ colonocyte, plus the late colonocyte / surface colonocyte synonyms.

Also closing the sister issue #3756 as a duplicate of #3776, which #3777 resolves.

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@ai4c-agent ai4c-agent Bot closed this Oct 2, 2026
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[NTR] crypt top colonocyte

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@ct31-sanger