Update CL_0004117: Rename to alpha retinal ganglion cell (Mmus) and revise definition

[Copilot]

Updates term CL_0004117 with revised nomenclature and comprehensive definition reflecting current understanding of alpha RGC biology.

Changes

• Label: retinal ganglion cell A → alpha retinal ganglion cell (Mmus)
• Definition: Replaced brief morphological description with detailed characterization including:
  • Morphology: large-bodied soma, wide monostratified dendritic arbors in defined IPL strata
  • Molecular: high neurofilament and osteopontin expression
  • Physiology: thick fast-conducting axon, short-latency non-direction-selective responses, large receptive fields, distinctive rapid AP waveform
  • Population: ~5% of mammalian RGCs, four conserved ON/OFF sustained/transient subtypes
  • Reference: PMID:28753612
• Synonym: Added retinal ganglion cell A as exact synonym (PMID:12209831) for backward compatibility

Validation

• Syntax valid (robot convert)
• Logically consistent (robot reason -r ELK)
• No impact on existing relationships or subclass hierarchy

Original prompt

---

This section details on the original issue you should resolve

<issue_title>[Text def] Revise textual definition of Retinal Ganglion Cell A into Alpha retinal ganglion cell</issue_title>
<issue_description>CL term
CL_0004117

Revised cell label
alpha retinal ganglion cell

Suggested revision of textual definition
A large-bodied retinal projection neuron with wide monostratified dendritic arbors in defined IPL strata, high neurofilament and osteopontin expression, and a thick, fast-conducting axon. It shows short-latency, non–direction-selective responses with large receptive fields and a distinctive rapid action potential waveform. In mammals it forms about five percent of RGCs and includes four conserved ON and OFF sustained and transient subtypes

PMID:28753612

exact synonym: Retinal ganglion cell A
PMID:12209831</issue_description>

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

• Fixes [Text def] Revise textual definition of Retinal Ganglion Cell A into Alpha retinal ganglion cell #3523

---

✨ Let Copilot coding agent set things up for you — coding agent works faster and does higher quality work when set up for your repo.

[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/2025-12-17/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/2025-12-17/cl-base.owl
• Loaded from: file:/__w/cell-ontology/cell-ontology/src/ontology/cl-base-pr.owl/cl-base.owl

Ontology imports

Ontology annotations

alpha retinal ganglion cell (Mmus) http://purl.obolibrary.org/obo/CL_0004117

Removed

• alpha retinal ganglion cell (Mmus) IAO_0000115 "A monostratified retinal ganglion cell with large soma and large dendritic field."

  • hasDbXref "PMID:12209831"

• alpha retinal ganglion cell (Mmus) label "retinal ganglion cell A"

Added

• alpha retinal ganglion cell (Mmus) hasExactSynonym "retinal ganglion cell A"

  • hasDbXref "PMID:12209831"

• alpha retinal ganglion cell (Mmus) IAO_0000115 "A large-bodied retinal projection neuron with wide monostratified dendritic arbors in defined IPL strata, high neurofilament and osteopontin expression, and a thick, fast-conducting axon. It shows short-latency, non-direction-selective responses with large receptive fields and a distinctive rapid action potential waveform. In mammals it forms about five percent of RGCs and includes four conserved ON and OFF sustained and transient subtypes."

  • hasDbXref "PMID:28753612"

• alpha retinal ganglion cell (Mmus) label "alpha retinal ganglion cell (Mmus)"

direct pathway medium spiny neuron http://purl.obolibrary.org/obo/CL_4023026

Removed

• direct pathway medium spiny neuron IAO_0000115 "A GABAergic medium spiny neuron located in the striatum that gives rise to the direct basal ganglia pathway. It projects directly to the GPi and SNr, where it inhibits tonically active GABAergic output neurons to disinhibit thalamic and brainstem motor targets (Gerfen. 2023). In mice and humans, this cell selectively expresses the D1 dopamine receptor (DRD1), which couples to stimulatory G-proteins (Gs/Gαolf) to increase cAMP and activate PKA-dependent signaling cascades (Gerfen et al., 1990; Kebabian & Calne, 1979). Functionally, activation of this cell promotes selected motor actions by disinhibiting thalamic and midbrain motor centers (Mink, 1996; Cui et al., 2013)."

  • hasDbXref "PMID:2147780"

  • hasDbXref "PMID:23354054"

  • hasDbXref "PMID:9004351"

  • hasDbXref "WikipediaVersioned:Medium_spiny_neuron&oldid=1109726850"

  • hasDbXref "PMID:34727523"

  • hasDbXref "PMID:215920"

  • hasDbXref "PMID:36741471"

• direct pathway medium spiny neuron comment "Despite the direct and indirect circuits are often described not only as functionally opposing but also as anatomically segregated there are several anatomical and functional studies that have challenged this notion of pure segregation based on extensive collateral projections between pathways, dual-projection neurons, simultaneous co-activation during behavior."

  • hasDbXref "PMID:26018615"

  • hasDbXref "PMID:29737578"

• direct pathway medium spiny neuron hasRelatedSynonym "dSPN"

  • hasDbXref "PMID:30096299"

  • hasDbXref "PMID:36741471"

  • hasSynonymType OMO_0003000

• direct pathway medium spiny neuron hasRelatedSynonym "D1-MSN"

  • hasDbXref "PMID:34727523"

  • hasSynonymType OMO_0003000

Added

• direct pathway medium spiny neuron hasExactSynonym "dSPN"

  • hasDbXref "PMID:30096299"

  • hasSynonymType OMO_0003000

• direct pathway medium spiny neuron IAO_0000115 "A medium spiny neuron that expresses dopamine type 1 receptors and projects to the globus pallidus internus or the substantia nigra pars reticulata."

  • hasDbXref "WikipediaVersioned:Medium_spiny_neuron&oldid=1109726850"

  • hasDbXref "PMID:34727523"

• direct pathway medium spiny neuron hasExactSynonym "D1-MSN"

  • hasDbXref "PMID:34727523"

  • hasSynonymType OMO_0003000

[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

direct pathway medium spiny neuron http://purl.obolibrary.org/obo/CL_4023026

Removed

• direct pathway medium spiny neuron definition "A GABAergic medium spiny neuron located in the striatum that gives rise to the direct basal ganglia pathway. It projects directly to the GPi and SNr, where it inhibits tonically active GABAergic output neurons to disinhibit thalamic and brainstem motor targets (Gerfen. 2023). In mice and humans, this cell selectively expresses the D1 dopamine receptor (DRD1), which couples to stimulatory G-proteins (Gs/Gαolf) to increase cAMP and activate PKA-dependent signaling cascades (Gerfen et al., 1990; Kebabian & Calne, 1979). Functionally, activation of this cell promotes selected motor actions by disinhibiting thalamic and midbrain motor centers (Mink, 1996; Cui et al., 2013)."

  • has cross-reference "PMID:36741471"

  • has cross-reference "PMID:215920"

  • has cross-reference "PMID:34727523"

  • has cross-reference "PMID:23354054"

  • has cross-reference "PMID:9004351"

  • has cross-reference "PMID:2147780"

  • has cross-reference "WikipediaVersioned:Medium_spiny_neuron&oldid=1109726850"

• direct pathway medium spiny neuron comment "Despite the direct and indirect circuits are often described not only as functionally opposing but also as anatomically segregated there are several anatomical and functional studies that have challenged this notion of pure segregation based on extensive collateral projections between pathways, dual-projection neurons, simultaneous co-activation during behavior."

  • has cross-reference "PMID:26018615"

  • has cross-reference "PMID:29737578"

• direct pathway medium spiny neuron has_related_synonym "dSPN"

  • has cross-reference "PMID:36741471"

  • has_synonym_type abbreviation

  • has cross-reference "PMID:30096299"

• direct pathway medium spiny neuron has_related_synonym "D1-MSN"

  • has cross-reference "PMID:34727523"

  • has_synonym_type abbreviation

Added

• direct pathway medium spiny neuron has exact synonym "dSPN"

  • has_synonym_type abbreviation

  • has cross-reference "PMID:30096299"

• direct pathway medium spiny neuron definition "A medium spiny neuron that expresses dopamine type 1 receptors and projects to the globus pallidus internus or the substantia nigra pars reticulata."

  • has cross-reference "PMID:34727523"

  • has cross-reference "WikipediaVersioned:Medium_spiny_neuron&oldid=1109726850"

• direct pathway medium spiny neuron has exact synonym "D1-MSN"

  • has cross-reference "PMID:34727523"

  • has_synonym_type abbreviation

retinal ganglion cell A http://purl.obolibrary.org/obo/CL_0004117

Removed

• retinal ganglion cell A definition "A monostratified retinal ganglion cell with large soma and large dendritic field."

  • has cross-reference "PMID:12209831"

• retinal ganglion cell A label "retinal ganglion cell A"

Added

• retinal ganglion cell A has exact synonym "retinal ganglion cell A"

  • has cross-reference "PMID:12209831"

• retinal ganglion cell A definition "A large-bodied retinal projection neuron with wide monostratified dendritic arbors in defined IPL strata, high neurofilament and osteopontin expression, and a thick, fast-conducting axon. It shows short-latency, non-direction-selective responses with large receptive fields and a distinctive rapid action potential waveform. In mammals it forms about five percent of RGCs and includes four conserved ON and OFF sustained and transient subtypes."

  • has cross-reference "PMID:28753612"

• retinal ganglion cell A label "alpha retinal ganglion cell (Mmus)"

[RiveraAndrea83]

@copilot please change label to: alpha retinal ganglion cell (Mmus)

[Copilot]

@copilot please change label to: alpha retinal ganglion cell (Mmus)

Updated the label to "alpha retinal ganglion cell (Mmus)" in commit 120a536.

[Caroline-99]

#gogoeditdiff