Fixed #3552 hierarchy for listed cells

[RiveraAndrea83]

Fixes #3552

Added relevant parent to OB FRMD7 GABA GABAergic neuron (Primate) SN GATA3-PVALB GABA GABAergic neuron (Primate)
SN SOX6 Dopa substantia nigra dopaminergic neuron (Primate)
SN-VTR CALB1 Dopa substantia nigra dopaminergic neuron (Primate)
SN-VTR GAD2 Dopa dopaminergic neuron (Primate)
STRd D1/D2-hybrid medium spiny neuron (Primate)
STRd D2 Striomat hybrid medium spiny neuron (Primate)

• Added subclass Gabaergic interneuron to: GABAergic interneuron of the anterior substantia nigra pars reticulata.

[dosumis]

#gogoeditdiff

Let's see if we can fix pipeline and re-run. If not we will use this as a temporary patch fix.

[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/2026-01-27/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/2026-01-27/cl-base.owl
• Loaded from: file:/__w/cell-ontology/cell-ontology/src/ontology/cl-base-pr.owl/cl-base.owl

Ontology imports

Ontology annotations

GABAergic interneuron of the anterior substantia nigra pars reticulata http://purl.obolibrary.org/obo/CL_4042026

Added

• GABAergic interneuron of the anterior substantia nigra pars reticulata SubClassOf GABAergic interneuron

OB FRMD7 GABA GABAergic neuron (Primate) http://purl.obolibrary.org/obo/CL_4310148

Removed

• OB FRMD7 GABA GABAergic neuron (Primate) EquivalentTo cell and (RO_0015001 value CS20250428_GROUP_0068)

• OB FRMD7 GABA GABAergic neuron (Primate) SubClassOf cell

Added

• OB FRMD7 GABA GABAergic neuron (Primate) SubClassOf GABAergic neuron

SN GATA3-PVALB GABA GABAergic neuron (Primate) http://purl.obolibrary.org/obo/CL_4310113

Removed

• SN GATA3-PVALB GABA GABAergic neuron (Primate) EquivalentTo cell and (RO_0015001 value CS20250428_GROUP_0033)

• SN GATA3-PVALB GABA GABAergic neuron (Primate) SubClassOf cell

Added

• SN GATA3-PVALB GABA GABAergic neuron (Primate) SubClassOf GABAergic interneuron of the anterior substantia nigra pars reticulata

SN SOX6 Dopa substantia nigra dopaminergic neuron (Primate) http://purl.obolibrary.org/obo/CL_4310115

Removed

• SN SOX6 Dopa substantia nigra dopaminergic neuron (Primate) EquivalentTo cell and (RO_0015001 value CS20250428_GROUP_0035)

• SN SOX6 Dopa substantia nigra dopaminergic neuron (Primate) SubClassOf cell

Added

• SN SOX6 Dopa substantia nigra dopaminergic neuron (Primate) SubClassOf substantia nigra dopaminergic neuron

SN-VTR CALB1 Dopa substantia nigra dopaminergic neuron (Primate) http://purl.obolibrary.org/obo/CL_4310109

Removed

• SN-VTR CALB1 Dopa substantia nigra dopaminergic neuron (Primate) EquivalentTo cell and (RO_0015001 value CS20250428_GROUP_0029)

• SN-VTR CALB1 Dopa substantia nigra dopaminergic neuron (Primate) SubClassOf cell

Added

• SN-VTR CALB1 Dopa substantia nigra dopaminergic neuron (Primate) SubClassOf substantia nigra dopaminergic neuron

SN-VTR GAD2 Dopa dopaminergic neuron (Primate) http://purl.obolibrary.org/obo/CL_4310111

Removed

• SN-VTR GAD2 Dopa dopaminergic neuron (Primate) EquivalentTo cell and (RO_0015001 value CS20250428_GROUP_0031)

• SN-VTR GAD2 Dopa dopaminergic neuron (Primate) SubClassOf cell

Added

• SN-VTR GAD2 Dopa dopaminergic neuron (Primate) SubClassOf substantia nigra dopaminergic neuron

STRd D1/D2-hybrid medium spiny neuron (Primate) http://purl.obolibrary.org/obo/CL_4310131

Removed

• STRd D1/D2-hybrid medium spiny neuron (Primate) EquivalentTo cell and (RO_0015001 value CS20250428_GROUP_0051)

• STRd D1/D2-hybrid medium spiny neuron (Primate) SubClassOf cell

Added

• STRd D1/D2-hybrid medium spiny neuron (Primate) SubClassOf D1/D2-hybrid medium spiny neuron

STRd D2 Striomat hybrid medium spiny neuron (Primate) http://purl.obolibrary.org/obo/CL_4310133

Removed

• STRd D2 Striomat hybrid medium spiny neuron (Primate) EquivalentTo cell and (RO_0015001 value CS20250428_GROUP_0053)

• STRd D2 Striomat hybrid medium spiny neuron (Primate) SubClassOf cell

Added

• STRd D2 Striomat hybrid medium spiny neuron (Primate) SubClassOf striatum neuron

[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

GABAergic interneuron of the anterior substantia nigra pars reticulata http://purl.obolibrary.org/obo/CL_4042026

Added

• GABAergic interneuron of the anterior substantia nigra pars reticulata SubClassOf GABAergic interneuron

OB FRMD7 GABA GABAergic neuron (Primate) http://purl.obolibrary.org/obo/CL_4310148

Added

• OB FRMD7 GABA GABAergic neuron (Primate) SubClassOf GABAergic neuron

SN GATA3-PVALB GABA GABAergic neuron (Primate) http://purl.obolibrary.org/obo/CL_4310113

Added

• SN GATA3-PVALB GABA GABAergic neuron (Primate) SubClassOf GABAergic interneuron of the anterior substantia nigra pars reticulata

SN SOX6 Dopa substantia nigra dopaminergic neuron (Primate) http://purl.obolibrary.org/obo/CL_4310115

Added

• SN SOX6 Dopa substantia nigra dopaminergic neuron (Primate) SubClassOf substantia nigra dopaminergic neuron

SN-VTR CALB1 Dopa substantia nigra dopaminergic neuron (Primate) http://purl.obolibrary.org/obo/CL_4310109

Added

• SN-VTR CALB1 Dopa substantia nigra dopaminergic neuron (Primate) SubClassOf substantia nigra dopaminergic neuron

SN-VTR GAD2 Dopa dopaminergic neuron (Primate) http://purl.obolibrary.org/obo/CL_4310111

Added

• SN-VTR GAD2 Dopa dopaminergic neuron (Primate) SubClassOf substantia nigra dopaminergic neuron

STRd D1/D2-hybrid medium spiny neuron (Primate) http://purl.obolibrary.org/obo/CL_4310131

Added

• STRd D1/D2-hybrid medium spiny neuron (Primate) SubClassOf D1/D2-hybrid medium spiny neuron

STRd D2 Striomat hybrid medium spiny neuron (Primate) http://purl.obolibrary.org/obo/CL_4310133

Added

• STRd D2 Striomat hybrid medium spiny neuron (Primate) SubClassOf striatum neuron

[dosumis]

@ubyndr - did you get any further investigating this bug? (see discussion on Slack)

[ubyndr]

I was planning to debug the robot command to check whether it removed some relations, but the BGO release was broken. I worked on getting it running again. It’s working now, and I’m focusing on this issue.

[github-actions]

This PR has not seen any activity in the past month; if nobody comments or reviews it in the next week, the PR editor will be allowed to proceed with merging without explicit approval, should they wish to do so.