Merge cns interneuron interneuron term

[AvolaAmg]

Fixes #2685

[dosumis]

Refs/images here use 'interneuron' to name mesenteric neurons: #2702 - potential clash with this PR?

[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.

[Caroline-99]

#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/2024-12-16/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/2024-12-16/cl-base.owl
• Loaded from: file:/__w/cell-ontology/cell-ontology/src/ontology/cl-base-pr.owl/cl-base.owl

Ontology imports

Ontology annotations

CNS interneuron http://purl.obolibrary.org/obo/CL_0000402

Removed

• CNS interneuron IAO_0000115 "An interneuron that has its cell body in a central nervous system."

  • hasDbXref "doi:10.1016/B978-0-12-817424-1.00001-X"

• CNS interneuron hasDbXref "ZFA:0009191"

  • mapping_justification UnspecifiedMatching

• CNS interneuron comment "Interneurons are commonly described as being only found in the central nervous system. However, in CL we define 'interneuron' more broadly as any neuron that is neither a motor neuron nor a sensory neuron, regardless of its location, so we need this term to refer strictly to interneurons of the central nervous system."

• CNS interneuron label "CNS interneuron"

• CNS interneuron EquivalentTo interneuron and (RO_0002100 some UBERON_0001017)

• CNS interneuron SubClassOf interneuron

• CNS interneuron SubClassOf central nervous system neuron

Added

• CNS interneuron deprecated true

• CNS interneuron comment "Merge cns interneuron interneuron term #2686"

• CNS interneuron IAO_0100001 interneuron

CNS long range interneuron http://purl.obolibrary.org/obo/CL_0000410

Removed

• CNS long range interneuron SubClassOf CNS interneuron

Added

• CNS long range interneuron SubClassOf interneuron

CNS short range interneuron http://purl.obolibrary.org/obo/CL_0000406

Removed

• CNS short range interneuron SubClassOf CNS interneuron

Added

• CNS short range interneuron SubClassOf interneuron

TAC3-positive striatal interneuron http://purl.obolibrary.org/obo/CL_4042001

Removed

• TAC3-positive striatal interneuron SubClassOf CNS interneuron

bistratified retinal amacrine cell http://purl.obolibrary.org/obo/CL_0004250

Removed

• bistratified retinal amacrine cell SubClassOf CNS interneuron

cerebellar inhibitory GABAergic interneuron http://purl.obolibrary.org/obo/CL_4023057

Removed

• cerebellar inhibitory GABAergic interneuron SubClassOf CNS interneuron

cerebellum basket cell http://purl.obolibrary.org/obo/CL_2000027

Removed

• cerebellum basket cell SubClassOf CNS interneuron

cortical interneuron http://purl.obolibrary.org/obo/CL_0008031

Removed

• cortical interneuron SubClassOf CNS interneuron

Added

• cortical interneuron SubClassOf interneuron

interneuron http://purl.obolibrary.org/obo/CL_0000099

Removed

• interneuron SubClassOf neuron

Added

• interneuron hasRelatedSynonym "CNS interneuron"

• interneuron hasDbXref "ZFA:0009191"

  • mapping_justification UnspecifiedMatching

• interneuron SubClassOf central nervous system neuron

local interneuron http://purl.obolibrary.org/obo/CL_0004001

Removed

• local interneuron SubClassOf CNS interneuron

Added

• local interneuron SubClassOf interneuron

monostratified amacrine cell http://purl.obolibrary.org/obo/CL_0004226

Removed

• monostratified amacrine cell SubClassOf RO_0000053 some PATO_0070063

Added

• monostratified amacrine cell SubClassOf monostratified cell

olfactory bulb interneuron http://purl.obolibrary.org/obo/CL_1001434

Removed

• olfactory bulb interneuron SubClassOf CNS interneuron

Added

• olfactory bulb interneuron SubClassOf interneuron

primary interneuron (sensu Teleostei) http://purl.obolibrary.org/obo/CL_0000534

Removed

• primary interneuron (sensu Teleostei) SubClassOf CNS interneuron

Added

• primary interneuron (sensu Teleostei) SubClassOf interneuron

spinal cord interneuron http://purl.obolibrary.org/obo/CL_0005000

Removed

• spinal cord interneuron SubClassOf CNS interneuron
  • is_inferred "true"

Added

• spinal cord interneuron SubClassOf interneuron
  • is_inferred "true"

stellate interneuron http://purl.obolibrary.org/obo/CL_0000691

Removed

• stellate interneuron SubClassOf CNS interneuron

Added

• stellate interneuron SubClassOf interneuron

striatal pthlh-expressing interneuron http://purl.obolibrary.org/obo/CL_4042023

Removed

• striatal pthlh-expressing interneuron SubClassOf CNS interneuron

unipolar brush cell http://purl.obolibrary.org/obo/CL_4023161

Removed

• unipolar brush cell SubClassOf CNS interneuron

Added

• unipolar brush cell SubClassOf interneuron

[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

CNS interneuron http://purl.obolibrary.org/obo/CL_0000402

Removed

• CNS interneuron definition "An interneuron that has its cell body in a central nervous system."

  • database_cross_reference "doi:10.1016/B978-0-12-817424-1.00001-X"

• CNS interneuron comment "Interneurons are commonly described as being only found in the central nervous system. However, in CL we define 'interneuron' more broadly as any neuron that is neither a motor neuron nor a sensory neuron, regardless of its location, so we need this term to refer strictly to interneurons of the central nervous system."

• CNS interneuron label "CNS interneuron"

• Class: CNS interneuron

• CNS interneuron EquivalentTo interneuron and (has soma location some central nervous system)

CNS long range interneuron http://purl.obolibrary.org/obo/CL_0000410

Removed

• CNS long range interneuron SubClassOf CNS interneuron

Added

• CNS long range interneuron SubClassOf interneuron

CNS short range interneuron http://purl.obolibrary.org/obo/CL_0000406

Removed

• CNS short range interneuron SubClassOf CNS interneuron

Added

• CNS short range interneuron SubClassOf interneuron

interneuron http://purl.obolibrary.org/obo/CL_0000099

Added

• interneuron has_related_synonym "CNS interneuron"

• interneuron SubClassOf has soma location some central nervous system

local interneuron http://purl.obolibrary.org/obo/CL_0004001

Removed

• local interneuron SubClassOf CNS interneuron

Added

• local interneuron SubClassOf interneuron

spinal cord interneuron http://purl.obolibrary.org/obo/CL_0005000

Removed

• spinal cord interneuron SubClassOf CNS interneuron
  • is_inferred "true"

Added

• spinal cord interneuron SubClassOf interneuron
  • is_inferred "true"

[Caroline-99]

Everything looks good.