Add 'resorptive cell' (CL:9900001) and 'fibrillar cell' (CL:9900002) NTR - Issue #3688 by ai4c-agent[bot] · Pull Request #3738 · obophenotype/cell-ontology

ai4c-agent · 2026-09-09T10:31:44Z

Summary

Adds two new cell types of the decapod crustacean hepatopancreas tubule, as requested:

CL:9900001 resorptive cell — primary site of nutrient absorption and storage.
CL:9900002 fibrillar cell — synthesizes and secretes digestive enzymes.

These are siblings of the previously added CL:0020076 blister-like cell (#3687 / PR #3696) and follow the same modelling pattern.

New Term Details

`CL:9900001` resorptive cell

Definition: "An epithelial cell of the decapod crustacean hepatopancreas tubule. Resorptive cells are the primary site of nutrient absorption and storage." [PMID:35096009]
Synonym: "R-cell" (related, abbreviation — OMO:0003000) [PMID:35096009]
Axioms:
- SubClassOf CL:0000066 (epithelial cell)
- part_of some UBERON:0010266 (arthropod hepatopancreas)
- in_taxon some NCBITaxon:6683 (Decapoda)

`CL:9900002` fibrillar cell

Definition: "An epithelial cell of the decapod crustacean hepatopancreas tubule. Fibrillar cells synthesize and secrete digestive enzymes." [PMID:35096009]
Synonym: "F-cell" (related, abbreviation — OMO:0003000) [PMID:35096009]
Axioms:
- SubClassOf CL:0000066 (epithelial cell)
- part_of some UBERON:0010266 (arthropod hepatopancreas)
- in_taxon some NCBITaxon:6683 (Decapoda)

Metadata (both terms)

term_tracker_item → issue [NTR] resorptive cells (R-cells) and fibrillarcells (F-cells) #3688
terms:creator "Claude"
terms:contributor https://orcid.org/0009-0002-8634-7138
terms:date 2026-09-09

Notes

Both terms use temporary IDs in the CL_99xxxxx range (idrange:81); please reassign to stable IDs at merge.
R-cell / F-cell are added as related synonyms with abbreviation type (OMO:0003000) rather than exact, matching the convention used across CL for cell-type acronyms (e.g. HSC, PLI, PC).
Taxon constraint uses the in taxon predicate (RO:0002162), matching @dosumis's guidance on the sibling term.

Validation

robot convert passes.
robot reason --reasoner ELK passes (no unsatisfiable classes).

Test plan

Reviewer confirms definitions and axioms are correct.
Confirm 'R-cell' / 'F-cell' should be related abbreviation synonyms (vs. exact).
Reassign CL:9900001 and CL:9900002 to stable IDs before/at merge.

🤖 Generated by @ai4c-agent

Model: claude-opus-4-7
Agent harness: claude-code
Triggered by: @dosumis
Run: View workflow run

🤖 Generated with Claude Code

…- Issue #3688 Adds two new decapod crustacean hepatopancreas tubule cell types: - CL:9900001 'resorptive cell' (synonym R-cell, abbreviation) Primary site of nutrient absorption and storage. PMID:35096009 - CL:9900002 'fibrillar cell' (synonym F-cell, abbreviation) Synthesizes and secretes digestive enzymes. PMID:35096009 Both terms share: - parent CL:0000066 (epithelial cell) - part_of some UBERON:0010266 (arthropod hepatopancreas) - in_taxon some NCBITaxon:6683 (Decapoda) — taxon constraint as requested - term_tracker_item linking back to issue #3688 - contributor ORCID 0009-0002-8634-7138 - creator "Claude" Follows the pattern established for the sibling term CL:0020076 'blister-like cell' (from #3687 / PR #3696). robot convert and robot reason --reasoner ELK both pass. Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

dosumis · 2026-09-09T10:34:35Z

@ai4c-agent please include 'hepatopancreas' in the name of each of these cell types. The current names sound way too generic.

ai4c-agent · 2026-09-09T10:34:53Z

🤖 Working on it...

Follow along: View workflow run

— @ai4c-agent

@dosumis

Per @dosumis's review on PR #3738, the generic labels "resorptive cell" and "fibrillar cell" were too generic. Renamed to: - CL:9900001 -> "hepatopancreas resorptive cell" - CL:9900002 -> "hepatopancreas fibrillar cell" Preserved the original short forms ("resorptive cell", "fibrillar cell") as related synonyms (referencing PMID:35096009) so the literature usage is still discoverable. Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

ai4c-agent · 2026-09-09T10:37:40Z

Renamed both terms to include 'hepatopancreas' (commit 902ee60):

CL:9900001 — hepatopancreas resorptive cell (was: "resorptive cell")
CL:9900002 — hepatopancreas fibrillar cell (was: "fibrillar cell")

The previous labels ("resorptive cell", "fibrillar cell") have been retained as related synonyms with the PMID:35096009 xref so the literature-standard short forms remain discoverable. The R-cell / F-cell abbreviation synonyms are unchanged.

Let me know if you'd prefer a different naming pattern — e.g. resorptive cell of hepatopancreas, or something more taxon-explicit like decapod hepatopancreas resorptive cell.

🤖 Generated by @ai4c-agent

Model: claude-opus-4-7
Agent harness: claude-code
Triggered by: @dosumis
Run: View workflow run

dosumis · 2026-09-17T09:37:12Z

#gogoeditdiff

dosumis · 2026-09-17T09:37:27Z

/clara

github-actions · 2026-09-17T09:39:42Z

Claude finished @dosumis's task in 4m 41s —— View job

CLARA routed-target verification — done

Ran the routed CLARA verification (/clara) against routing.json, per clara_workflow_ref/clara_workflow/agent_instructions.md.

Read routing.json, changes.json, and clara_workflow_ref agent instructions
Process term group CL:9900001 (hepatopancreas resorptive cell) — 5 routed targets
Process term group CL:9900002 (hepatopancreas fibrillar cell) — 5 routed targets
Write runs/CL_9900001/{verdicts.json,tool_calls.jsonl,report.md}
Write runs/CL_9900002/{verdicts.json,tool_calls.jsonl,report.md}
Post final summary

Retrieval backend note: the Stage B tool named in the instructions (mcp__Asta_semanticscholar__snippet_search) isn't available in this environment, so I verified directly against Europe PMC full text (mcp__artl-mcp__get_europepmc_full_text) for PMID:35096009 instead — i.e. Stage C was used as the sole retrieval step. This is logged in each tool_calls.jsonl.

Result summary

Both term groups route only synonym (2 each) and relationship (3 each) targets — the text definitions themselves are in routing.json's ignored list (existing_term_text_not_yet_routed), so they weren't in scope for this pass.

Term	Synonyms	part_of hepatopancreas	is_a epithelial cell	in_taxon Decapoda
CL:9900001 hepatopancreas resorptive cell	✅ pass ("resorptive cell", "R-cell" both directly attested)	✅ pass	⚠️ uncertain	⚠️ uncertain
CL:9900002 hepatopancreas fibrillar cell	✅ pass ("fibrillar cell", "F-cell" both directly attested)	✅ pass	⚠️ uncertain	⚠️ uncertain

No contradictions (fail) on either term. The two uncertain items per term aren't flagged as defects — they're standard ontological modelling calls (epithelial classification, Decapoda taxon) that PMID:35096009 doesn't spell out verbatim, so per the "no pass from background knowledge alone" rule they can't be scored pass from this single reference alone. Full detail and quoted evidence is in each runs/<TERM_ID>/report.md.

Per the run's scope, only the runs/CL_9900001/ and runs/CL_9900002/ output bundles were written — no commits, pushes, or PR changes were made, and changes.json/routing.json were left untouched.
· Branch: ai4c-agent-issue-3688-run737

github-actions · 2026-09-17T09:43:35Z

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/2026-09-17/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/2026-09-17/cl-base.owl
Loaded from: file:/__w/cell-ontology/cell-ontology/src/ontology/cl-base-pr.owl/cl-base.owl

Ontology imports

Ontology annotations

hepatopancreas fibrillar cell `http://purl.obolibrary.org/obo/CL_9900002`

Added

Class: hepatopancreas fibrillar cell
hepatopancreas fibrillar cell IAO_0000233 "[NTR] resorptive cells (R-cells) and fibrillarcells (F-cells) #3688"
hepatopancreas fibrillar cell contributor 0009-0002-8634-7138
hepatopancreas fibrillar cell creator "Claude"
hepatopancreas fibrillar cell date "2026-09-09T10:27:00Z"^^dateTime
hepatopancreas fibrillar cell IAO_0000115 "An epithelial cell of the decapod crustacean hepatopancreas tubule. Fibrillar cells synthesize and secrete digestive enzymes."
- hasDbXref "PMID:35096009"
hepatopancreas fibrillar cell hasRelatedSynonym "fibrillar cell"
- hasDbXref "PMID:35096009"
hepatopancreas fibrillar cell hasRelatedSynonym "F-cell"
- hasSynonymType OMO_0003000
- hasDbXref "PMID:35096009"
hepatopancreas fibrillar cell label "hepatopancreas fibrillar cell"
hepatopancreas fibrillar cell SubClassOf epithelial cell
hepatopancreas fibrillar cell SubClassOf BFO_0000050 some UBERON_0010266
hepatopancreas fibrillar cell SubClassOf RO_0002162 some NCBITaxon_6683

hepatopancreas resorptive cell `http://purl.obolibrary.org/obo/CL_9900001`

Added

Class: hepatopancreas resorptive cell
hepatopancreas resorptive cell IAO_0000233 "[NTR] resorptive cells (R-cells) and fibrillarcells (F-cells) #3688"
hepatopancreas resorptive cell contributor 0009-0002-8634-7138
hepatopancreas resorptive cell creator "Claude"
hepatopancreas resorptive cell date "2026-09-09T10:27:00Z"^^dateTime
hepatopancreas resorptive cell IAO_0000115 "An epithelial cell of the decapod crustacean hepatopancreas tubule. Resorptive cells are the primary site of nutrient absorption and storage."
- hasDbXref "PMID:35096009"
hepatopancreas resorptive cell hasRelatedSynonym "resorptive cell"
- hasDbXref "PMID:35096009"
hepatopancreas resorptive cell hasRelatedSynonym "R-cell"
- hasSynonymType OMO_0003000
- hasDbXref "PMID:35096009"
hepatopancreas resorptive cell label "hepatopancreas resorptive cell"
hepatopancreas resorptive cell SubClassOf epithelial cell
hepatopancreas resorptive cell SubClassOf BFO_0000050 some UBERON_0010266
hepatopancreas resorptive cell SubClassOf RO_0002162 some NCBITaxon_6683

github-actions · 2026-09-17T09:43:39Z

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

hepatopancreas fibrillar cell `http://purl.obolibrary.org/obo/CL_9900002`

Added

hepatopancreas fibrillar cell term tracker item "[NTR] resorptive cells (R-cells) and fibrillarcells (F-cells) #3688"
hepatopancreas fibrillar cell contributor 0009-0002-8634-7138
hepatopancreas fibrillar cell creator "Claude"
hepatopancreas fibrillar cell date "2026-09-09T10:27:00Z"^^dateTime
hepatopancreas fibrillar cell definition "An epithelial cell of the decapod crustacean hepatopancreas tubule. Fibrillar cells synthesize and secrete digestive enzymes."
- has cross-reference "PMID:35096009"
hepatopancreas fibrillar cell has_related_synonym "fibrillar cell"
- has cross-reference "PMID:35096009"
hepatopancreas fibrillar cell has_related_synonym "F-cell"
- has_synonym_type abbreviation
- has cross-reference "PMID:35096009"
hepatopancreas fibrillar cell label "hepatopancreas fibrillar cell"
hepatopancreas fibrillar cell SubClassOf epithelial cell
hepatopancreas fibrillar cell SubClassOf part of some arthropod hepatopancreas
hepatopancreas fibrillar cell SubClassOf in taxon some Decapoda

hepatopancreas resorptive cell `http://purl.obolibrary.org/obo/CL_9900001`

Added

hepatopancreas resorptive cell term tracker item "[NTR] resorptive cells (R-cells) and fibrillarcells (F-cells) #3688"
hepatopancreas resorptive cell contributor 0009-0002-8634-7138
hepatopancreas resorptive cell creator "Claude"
hepatopancreas resorptive cell date "2026-09-09T10:27:00Z"^^dateTime
hepatopancreas resorptive cell definition "An epithelial cell of the decapod crustacean hepatopancreas tubule. Resorptive cells are the primary site of nutrient absorption and storage."
- has cross-reference "PMID:35096009"
hepatopancreas resorptive cell has_related_synonym "resorptive cell"
- has cross-reference "PMID:35096009"
hepatopancreas resorptive cell has_related_synonym "R-cell"
- has_synonym_type abbreviation
- has cross-reference "PMID:35096009"
hepatopancreas resorptive cell label "hepatopancreas resorptive cell"
hepatopancreas resorptive cell SubClassOf epithelial cell
hepatopancreas resorptive cell SubClassOf part of some arthropod hepatopancreas
hepatopancreas resorptive cell SubClassOf in taxon some Decapoda

github-actions · 2026-09-17T09:44:40Z

CLARA review for PR #3738

Base SHA: e5bce66aef6807ef1e62e1f90e333eee904a9ecc
Head SHA: 1293d074e69a6e7cf91586d94cab081f16b6304c
Terms touched: 2
Total extracted changes: 22
Reviewable changes: 12
Decomposable changes: 2
Routed validation targets: 10
Routed NTR bundles: 0
Routed relationship targets: 6
Routed synonym targets with refs: 4

Stage 2/3 verification ran for 2 routed term(s).

Routed verification results

CL_9900001 — hepatopancreas resorptive cell: UNCERTAIN (core: 5, fail: 0, uncertain: 2, background warnings: 0)
CL_9900002 — hepatopancreas fibrillar cell: UNCERTAIN (core: 5, fail: 0, uncertain: 2, background warnings: 0)

Currently ignored by routing

Existing-term text changes not yet routed: 2
Synonym changes without refs: 0

Artifacts uploaded:

changes.json
routing.json
runs/

ai4c-agent Bot mentioned this pull request Sep 9, 2026

[NTR] resorptive cells (R-cells) and fibrillarcells (F-cells) #3688

Closed

Merge branch 'master' into ai4c-agent-issue-3688-run737

1293d07

dosumis approved these changes Sep 18, 2026

View reviewed changes

dosumis merged commit bd5ed85 into master Sep 18, 2026
3 checks passed

dosumis deleted the ai4c-agent-issue-3688-run737 branch September 18, 2026 10:59

Conversation

ai4c-agent Bot commented Sep 9, 2026

Summary

New Term Details

CL:9900001 resorptive cell

CL:9900002 fibrillar cell

Metadata (both terms)

Notes

Validation

Test plan

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dosumis commented Sep 9, 2026

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ai4c-agent Bot commented Sep 9, 2026

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ai4c-agent Bot commented Sep 9, 2026

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dosumis commented Sep 17, 2026

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dosumis commented Sep 17, 2026

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github-actions Bot commented Sep 17, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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CLARA routed-target verification — done

Result summary

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github-actions Bot commented Sep 17, 2026

Ontology comparison

Left

Right

Ontology imports

Ontology annotations

hepatopancreas fibrillar cell http://purl.obolibrary.org/obo/CL_9900002

Added

hepatopancreas resorptive cell http://purl.obolibrary.org/obo/CL_9900001

Added

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github-actions Bot commented Sep 17, 2026

Ontology comparison

Left

Right

Ontology imports

Ontology annotations

hepatopancreas fibrillar cell http://purl.obolibrary.org/obo/CL_9900002

Added

hepatopancreas resorptive cell http://purl.obolibrary.org/obo/CL_9900001

Added

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github-actions Bot commented Sep 17, 2026

CLARA review for PR #3738

Routed verification results

Currently ignored by routing

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`CL:9900001` resorptive cell

`CL:9900002` fibrillar cell

github-actions Bot commented Sep 17, 2026 •

edited

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hepatopancreas fibrillar cell `http://purl.obolibrary.org/obo/CL_9900002`

hepatopancreas resorptive cell `http://purl.obolibrary.org/obo/CL_9900001`

hepatopancreas fibrillar cell `http://purl.obolibrary.org/obo/CL_9900002`

hepatopancreas resorptive cell `http://purl.obolibrary.org/obo/CL_9900001`