Add new CL term for hilar mossy cell with requested definition and axiomatization

[Copilot]

This PR adds a dedicated Cell Ontology term for hilar mossy cell to resolve the current gap where this excitatory dentate hilar population is only covered by the broader dentate gyrus neuron class. It encodes the ticket-provided textual definition and requested placement/logic for annotation use.

• Term addition

  • Added obo:CL_9900000 in src/ontology/cl-edit.owl as a new temporary NTR ID.
  • Added label: hilar mossy cell.

• Definition and references

  • Added the full requested text definition verbatim from the ticket.
  • Attached supporting xrefs in the definition annotation: PMID:23420672, PMID:26347618, PMID:28451637, PMID:34214666, PMID:33600026.

• Synonyms

  • Added exact synonym: mossy cell (PMID:23420672).
  • Added exact synonym: dentate hilar mossy cell (PMID:34214666).

• Logical placement and constraints

  • Added asserted parent: SubClassOf(obo:CL_4023062) (dentate gyrus neuron).
  • Added location axiom: RO:0002100 some UBERON:0002928 (dentate gyrus polymorphic layer).
  • Added function axiom: RO:0002215 some GO:0061535 (glutamate secretion, neurotransmission).

• Term metadata

  • Added term_tracker_item annotation to the NTR issue URL.
  • Added contributor ORCID annotation: https://orcid.org/0000-0002-5507-2103.
  • Added terms:date timestamp.

# Class: obo:CL_9900000 (hilar mossy cell)
AnnotationAssertion(rdfs:label obo:CL_9900000 "hilar mossy cell")
SubClassOf(obo:CL_9900000 obo:CL_4023062)
SubClassOf(obo:CL_9900000 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0002928))
SubClassOf(obo:CL_9900000 ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0061535))

[RiveraAndrea83]

#gogoeditdiff

[RiveraAndrea83]

/clara

[RiveraAndrea83]

#gogoeditdiff

[github-actions]

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/2026-05-21/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/2026-05-21/cl-base.owl
• Loaded from: file:/__w/cell-ontology/cell-ontology/src/ontology/cl-base-pr.owl/cl-base.owl

Ontology imports

Ontology annotations

UBERON_0002928 http://purl.obolibrary.org/obo/UBERON_0002928

Added

• Class: UBERON_0002928

hilar mossy cell http://purl.obolibrary.org/obo/CL_9900000

Added

• Class: hilar mossy cell

• hilar mossy cell IAO_0000233 3648

• hilar mossy cell contributor 0000-0002-5507-2103

• hilar mossy cell date "2026-05-21T10:51:40Z"^^dateTime

• hilar mossy cell hasExactSynonym "mossy cell"

  • hasDbXref "PMID:23420672"

• hilar mossy cell IAO_0000115 "A dentate gyrus neuron with soma in the polymorphic layer (UBERON:0002928) (Scharfman & Myers, 2012), capable of glutamate secretion as a neurotransmitter (Scharfman & Bernstein, 2015). Distinguished by a large multipolar soma, thorny excrescences on proximal dendrites, and commissural/associational axon projections terminating in the inner molecular layer of the dentate gyrus (Scharfman & Myers, 2012). Electrophysiologically characterised by a depolarised resting membrane potential, prominent hyperpolarisation-activated cation current (Ih), and firing accommodation (Scharfman & Myers, 2012). In rodents, serves as a major excitatory neuron of the dentate hilus providing feedback excitation to granule cells (Sun et al., 2017)."

  • hasDbXref "PMID:28451637"

  • hasDbXref "PMID:23420672"

  • hasDbXref "PMID:34214666"

  • hasDbXref "PMID:33600026"

  • hasDbXref "PMID:26347618"

• hilar mossy cell hasExactSynonym "dentate hilar mossy cell"

  • hasDbXref "PMID:34214666"

• hilar mossy cell label "hilar mossy cell"

• hilar mossy cell SubClassOf glutamatergic neuron

• hilar mossy cell SubClassOf dentate gyrus neuron

• hilar mossy cell SubClassOf RO_0002100 some UBERON_0002928

[github-actions]

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

hilar mossy cell http://purl.obolibrary.org/obo/CL_9900000

Added

• Class: hilar mossy cell

• hilar mossy cell term tracker item 3648

• hilar mossy cell contributor 0000-0002-5507-2103

• hilar mossy cell date "2026-05-21T10:51:40Z"^^dateTime

• hilar mossy cell has exact synonym "mossy cell"

  • database_cross_reference "PMID:23420672"

• hilar mossy cell definition "A dentate gyrus neuron with soma in the polymorphic layer (UBERON:0002928) (Scharfman & Myers, 2012), capable of glutamate secretion as a neurotransmitter (Scharfman & Bernstein, 2015). Distinguished by a large multipolar soma, thorny excrescences on proximal dendrites, and commissural/associational axon projections terminating in the inner molecular layer of the dentate gyrus (Scharfman & Myers, 2012). Electrophysiologically characterised by a depolarised resting membrane potential, prominent hyperpolarisation-activated cation current (Ih), and firing accommodation (Scharfman & Myers, 2012). In rodents, serves as a major excitatory neuron of the dentate hilus providing feedback excitation to granule cells (Sun et al., 2017)."

  • database_cross_reference "PMID:34214666"

  • database_cross_reference "PMID:26347618"

  • database_cross_reference "PMID:33600026"

  • database_cross_reference "PMID:23420672"

  • database_cross_reference "PMID:28451637"

• hilar mossy cell has exact synonym "dentate hilar mossy cell"

  • database_cross_reference "PMID:34214666"

• hilar mossy cell label "hilar mossy cell"

• hilar mossy cell SubClassOf dentate gyrus neuron

• hilar mossy cell SubClassOf has soma location some dentate gyrus polymorphic layer

• hilar mossy cell SubClassOf capable of some glutamate secretion, neurotransmission

[RiveraAndrea83]

/clara

[github-actions]

Claude finished @RiveraAndrea83's task in 9m 22s —— View job

---

CLARA Review — CL:9900000 hilar mossy cell

Term: hilar mossy cell (CL:9900000) · New term request · PR #3649

Overall result: ✅ PASS (13/15 core assertions pass, 0 fail, 2 uncertain)

---

Targets reviewed

Target	Route	Result
ntr:CL:9900000	ntr (definition + relationships)	✅ 11 pass · ⚠️ 1 uncertain
synonym:CL:9900000:1 — "mossy cell"	synonym	✅ pass
synonym:CL:9900000:2 — "dentate hilar mossy cell"	synonym	⚠️ uncertain

---

Assertion-level results

ID	Claim	Verdict	Key evidence
a1	Is a dentate gyrus neuron	✅ pass	PMID:28451637
a2	Soma in polymorphic layer (UBERON:0002928)	✅ pass	PMID:23420672
a3	Glutamate secretion as neurotransmitter	✅ pass	PMID:23420672
a4	Large multipolar soma	✅ pass	PMID:28451637
a5	Thorny excrescences on proximal dendrites	✅ pass	PMID:23420672
a6	Commissural/assoc. axons → inner molecular layer	✅ pass	PMID:23420672
a7	Depolarised resting membrane potential	✅ pass	PMID:23420672
a8	Prominent Ih (hyperpolarisation-activated cation current)	⚠️ uncertain	Not found in scoped refs
a9	Firing accommodation	✅ pass	PMID:23420672
a10	Major excitatory neuron, feedback excitation to GCs (rodents)	✅ pass	PMID:28451637
a11	SubClassOf dentate gyrus neuron (relationship axiom)	✅ pass	PMID:28451637
a12	has soma location: dentate gyrus polymorphic layer (relationship axiom)	✅ pass	PMID:23420672
a13	capable of glutamate secretion, neurotransmission (relationship axiom)	✅ pass	PMID:23420672
a14	"mossy cell" exact synonym	✅ pass	PMID:23420672
a15	"dentate hilar mossy cell" exact synonym	⚠️ uncertain	PMID:34214666 full text unavailable

---

Uncertainties requiring attention

a8 — Ih (hyperpolarisation-activated cation current):
No snippet or full-text passage from the five scoped references explicitly mentions a prominent Ih current in hilar mossy cells. The full text of PMID:23420672 (Scharfman & Myers, 2012) was reviewed across all electrophysiology sections; firing accommodation, depolarised RMP, and spontaneous synaptic activity are well-described, but Ih is absent. Full text of PMID:34214666 (Botterill et al., 2021) is unavailable via Europe PMC.
→ Recommendation: Add a reference that explicitly documents Ih in hilar mossy cells, e.g. Lübke et al. (1998) J. Neurophysiol. 79:1518 (cited within PMID:23420672 for specialised electrophysiological properties) or Jinno et al. (2003) Eur. J. Neurosci. 17:1338 (ionic currents in mossy cells).

a15 — "dentate hilar mossy cell" synonym:
PMID:34214666 (Botterill et al., 2021) is the sole cited reference. Available snippets use "hilar mossy cells (MCs)" but the exact phrase "dentate hilar mossy cell" was not confirmed. Full text unavailable.
→ Recommendation: Verify that the exact phrase appears in Botterill et al. (2021), or supply an additional reference.

---

Run artefacts

Output bundle written to runs/CL_9900000/ on branch copilot/add-hilar-mossy-cell-term:

• runs/CL_9900000/verdicts.json
• runs/CL_9900000/tool_calls.jsonl
• runs/CL_9900000/report.md

---

🤖 CLARA automated review · workflow ref

[github-actions]

CLARA review for PR #3649

• Base SHA: 5222c96d5ebffc9d4485a8c89bc85dd077f14b42
• Head SHA: 49c491681d2e16102cb5dd32b82374374a552e38
• Terms touched: 1
• Total extracted changes: 11
• Reviewable changes: 6
• Decomposable changes: 1
• Routed validation targets: 3
• Routed NTR bundles: 1
• Routed relationship targets: 0
• Routed synonym targets with refs: 2

Stage 2/3 verification ran for 1 routed term(s).

Routed verification results

• CL_9900000 — hilar mossy cell: UNCERTAIN (core: 15, fail: 0, uncertain: 2, background warnings: 0)

Artifacts uploaded:

• changes.json
• routing.json
• runs/