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@AvolaAmg AvolaAmg commented Feb 7, 2025

Fixes #2342

@AvolaAmg AvolaAmg self-assigned this Feb 7, 2025
@dosumis dosumis requested a review from gouttegd February 21, 2025 15:41
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No issues with the definitions, but CL:0000109 should not be purely removed from the ontology, it must be properly obsoleted instead.

AnnotationAssertion(rdfs:label obo:CL_0000108 "cholinergic neuron")
EquivalentClasses(obo:CL_0000108 ObjectIntersectionOf(obo:CL_0000540 ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0014055)))

# Class: obo:CL_0000109 (adrenergic neuron)
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Is that term removed because it “should be a synonym of noradrenergic neuron” (as stated in this comment)?

Terms should never be entirely removed like that. They should be obsoleted instead – kept around, but clearly marked as obsolete with a owl:deprecated annotation.



<!-- Generated by the OWL API (version 4.5.29) https://github.com/owlcs/owlapi -->
<!-- Generated by the OWL API (version 4.5.26.2023-07-17T20:34:13Z) https://github.com/owlcs/owlapi -->
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Has this file been modified with Protégé?

This file is automatically generated from the mappings between CL and foreign ontologies. It should not be manually edited.

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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.

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dosumis commented Apr 28, 2025

#gogoeditdiff

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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/2025-04-28/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/2025-04-28/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 long range interneuron http://purl.obolibrary.org/obo/CL_0000410

Added

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

Added

Mauthner neuron http://purl.obolibrary.org/obo/CL_0000246

Added

R1 photoreceptor cell http://purl.obolibrary.org/obo/CL_0000687

Added

  • R1 photoreceptor cell IAO_0000115 "A photoreceptor cell in the Drosophila visual system. The R1 photoreceptor is capable of detecting UV light and blue-green light with its sensitivity peaking at ∼360 nm and ∼490 nm. This photoreceptor expresses the opsin Rh1 which is responsible for light detection. This photoreceptor cell is arranged in the outer edges of the Drosophila ommatidia and it forms a trapezoidal pattern together with other photoreceptors. This photoreceptor innervates the laminate in the Drosophila optic lobe."

  • R1 photoreceptor cell IAO_0000028 "R1"

R2 photoreceptor cell http://purl.obolibrary.org/obo/CL_0000690

Added

  • R2 photoreceptor cell IAO_0000115 "A photoreceptor cell in the Drosophila visual system. The R2 photoreceptor is capable of detecting UV light and blue-green light with its sensitivity peaking at ∼360 nm and ∼490 nm. This photoreceptor expresses the opsin Rh1 which is responsible for light detection. This photoreceptor cell is arranged in the outer edges of the Drosophila ommatidia and it forms a trapezoidal pattern together with other photoreceptors. This photoreceptor innervates the laminate in the Drosophila optic lobe."

  • R2 photoreceptor cell IAO_0000028 "R2"

R3 photoreceptor cell http://purl.obolibrary.org/obo/CL_0000694

Added

  • R3 photoreceptor cell IAO_0000028 "R3"

  • R3 photoreceptor cell IAO_0000115 "A photoreceptor cell in the Drosophila visual system. The R3 photoreceptor is capable of detecting UV light and blue-green light with its sensitivity peaking at ∼360 nm and ∼490 nm. This photoreceptor expresses the opsin Rh1 which is responsible for light detection. This photoreceptor cell is arranged in the outer edges of the Drosophila ommatidia and it forms a trapezoidal pattern together with other photoreceptors. This photoreceptor innervates the laminate in the Drosophila optic lobe."

R4 photoreceptor cell http://purl.obolibrary.org/obo/CL_0000697

Added

  • R4 photoreceptor cell IAO_0000115 "A photoreceptor cell in the Drosophila visual system. The R4 photoreceptor is capable of detecting UV light and blue-green light with its sensitivity peaking at ∼360 nm and ∼490 nm. This photoreceptor expresses the opsin Rh1 which is responsible for light detection. This photoreceptor cell is arranged in the outer edges of the Drosophila ommatidia and it forms a trapezoidal pattern together with other photoreceptors. This photoreceptor innervates the laminate in the Drosophila optic lobe."

  • R4 photoreceptor cell IAO_0000028 "R4"

R5 photoreceptor cell http://purl.obolibrary.org/obo/CL_0000702

Added

  • R5 photoreceptor cell IAO_0000115 "A photoreceptor cell in the Drosophila visual system. The R5 photoreceptor is capable of detecting UV light and blue-green light with its sensitivity peaking at ∼360 nm and ∼490 nm. This photoreceptor expresses the opsin Rh1 which is responsible for light detection. This photoreceptor cell is arranged in the outer edges of the Drosophila ommatidia and it forms a trapezoidal pattern together with other photoreceptors. This photoreceptor innervates the laminate in the Drosophila optic lobe."

  • R5 photoreceptor cell IAO_0000028 "R5"

R6 photoreceptor cell http://purl.obolibrary.org/obo/CL_0000705

Added

R7 photoreceptor cell http://purl.obolibrary.org/obo/CL_0000707

Added

R8 photoreceptor cell http://purl.obolibrary.org/obo/CL_0000709

Added

  • R8 photoreceptor cell IAO_0000115 "A photoreceptor cell in the Drosophila visual system. The R8 photoreceptor is capable of detecting UV light . This photoreceptor expresses the opsin Rh5 or Rh6 which detect light at their peak of 435 nm and 600 nm. This photoreceptor cell is arranged in the center of the Drosophila ommatidia and it innervates the medulla in the Drosophila optic lobe."

  • R8 photoreceptor cell IAO_0000028 "R8"

acceleration receptive cell http://purl.obolibrary.org/obo/CL_0000204

Added

adrenergic neuron http://purl.obolibrary.org/obo/CL_0000109

Removed

noradrenergic neuron http://purl.obolibrary.org/obo/CL_0008025

Added

photopic photoreceptor cell http://purl.obolibrary.org/obo/CL_0000490

Added

polymodal nocireceptor http://purl.obolibrary.org/obo/CL_0000567

Added

scotopic photoreceptor cell http://purl.obolibrary.org/obo/CL_0000489

Added

sensory processing neuron http://purl.obolibrary.org/obo/CL_0000379

Added

slowly adapting mechanoreceptor cell http://purl.obolibrary.org/obo/CL_0000544

Added

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

Added

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

Added

Mauthner neuron http://purl.obolibrary.org/obo/CL_0000246

Added

R1 photoreceptor cell http://purl.obolibrary.org/obo/CL_0000687

Added

R2 photoreceptor cell http://purl.obolibrary.org/obo/CL_0000690

Added

R3 photoreceptor cell http://purl.obolibrary.org/obo/CL_0000694

Added

R4 photoreceptor cell http://purl.obolibrary.org/obo/CL_0000697

Added

R5 photoreceptor cell http://purl.obolibrary.org/obo/CL_0000702

Added

R6 photoreceptor cell http://purl.obolibrary.org/obo/CL_0000705

Added

R7 photoreceptor cell http://purl.obolibrary.org/obo/CL_0000707

Added

R8 photoreceptor cell http://purl.obolibrary.org/obo/CL_0000709

Added

acceleration receptive cell http://purl.obolibrary.org/obo/CL_0000204

Added

adrenergic neuron http://purl.obolibrary.org/obo/CL_0000109

Removed

noradrenergic neuron http://purl.obolibrary.org/obo/CL_0008025

Added

photopic photoreceptor cell http://purl.obolibrary.org/obo/CL_0000490

Added

polymodal nocireceptor http://purl.obolibrary.org/obo/CL_0000567

Added

scotopic photoreceptor cell http://purl.obolibrary.org/obo/CL_0000489

Added

sensory processing neuron http://purl.obolibrary.org/obo/CL_0000379

Added

slowly adapting mechanoreceptor cell http://purl.obolibrary.org/obo/CL_0000544

Added

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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.

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Add definitions to terms for neurons that lack them

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