Adjust hierarchy of somatosensory neurons (sensu Teleostei) #2751

AvolaAmg · 2024-11-13T13:48:37Z

Fixes #2727

…(sensu-Teleostei)

Caroline-99 · 2024-11-22T13:20:11Z

#gogoeditdiff

github-actions · 2024-11-22T13:26:22Z

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/2024-11-22/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/2024-11-22/cl-base.owl
Loaded from: file:/__w/cell-ontology/cell-ontology/src/ontology/cl-base-pr.owl/cl-base.owl

Ontology imports

Ontology annotations

CAP motoneuron `http://purl.obolibrary.org/obo/CL_0000532`

Added

CAP motoneuron IAO_0000115 "A primary motor neuron with its soma in the caudal region of a spinal cord. The axon of this motoneuron exit the spinal cord from one single point and innervates muscles from its lateral region."
- hasDbXref "PMID:35431796"
- hasDbXref "PMID:17971221"
CAP motoneuron hasRelatedSynonym "cap cell"
- hasDbXref "PMID:17971221"
CAP motoneuron hasRelatedSynonym "caudal primary motor neuron"
- hasDbXref "PMID:18077593"
CAP motoneuron hasExactSynonym "CaP motorneuron"
- hasDbXref "PMID:3746410"

UBERON_0010313 `http://purl.obolibrary.org/obo/UBERON_0010313`

Added

Class: UBERON_0010313

middle primary motoneuron `http://purl.obolibrary.org/obo/CL_4042037`

Added

middle primary motoneuron IAO_0000115 "A type of primary motor neuron located in the middle region of the spinal cord. This primary motor neuron type is characterized by their distinct axonal pathways that innervate the middle trunk muscles."
- hasDbXref "PMID:35431796"
- hasDbXref "PMID:3746410"
middle primary motoneuron hasRelatedSynonym "MiP"
- hasDbXref "PMID:3746410"
- hasSynonymType OMO_0003000
middle primary motoneuron contributor 0000-0002-0098-8958
middle primary motoneuron label "middle primary motoneuron"@en
middle primary motoneuron date "2024-11-13T13:39:28Z"^^dateTime
middle primary motoneuron hasDbXref "ZFA:0005179"
Class: middle primary motoneuron
middle primary motoneuron SubClassOf primary motor neuron (sensu Teleostei)

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 spinal cord interneuron

primary motor neuron (sensu Teleostei) `http://purl.obolibrary.org/obo/CL_0000533`

Removed

primary motor neuron (sensu Teleostei) SubClassOf motor neuron

Added

primary motor neuron (sensu Teleostei) SubClassOf spinal cord motor neuron

primary neuron (sensu Teleostei) `http://purl.obolibrary.org/obo/CL_0000530`

Added

primary neuron (sensu Teleostei) SubClassOf RO_0002100 some UBERON_0002240

rostral primary motorneuron `http://purl.obolibrary.org/obo/CL_4042038`

Added

rostral primary motorneuron IAO_0000115 "A type of primary motor neuron situated in the rostral region of the spinal cord. RoP neurons extend their axons to innervate the dorsal trunk musculature."
- hasDbXref "PMID:35431796"
- hasDbXref "PMID:3746410"
rostral primary motorneuron contributor 0000-0002-0098-8958
rostral primary motorneuron date "2024-11-13T13:42:01Z"^^dateTime
rostral primary motorneuron label "rostral primary motorneuron"@en
rostral primary motorneuron hasRelatedSynonym "RoP"
- hasDbXref "PMID:3746410"
- hasSynonymType OMO_0003000
Class: rostral primary motorneuron
rostral primary motorneuron SubClassOf primary motor neuron (sensu Teleostei)

secondary motor neuron (sensu Teleostei) `http://purl.obolibrary.org/obo/CL_0000536`

Removed

secondary motor neuron (sensu Teleostei) SubClassOf motor neuron

Added

secondary motor neuron (sensu Teleostei) SubClassOf spinal cord motor neuron

secondary neuron (sensu Teleostei) `http://purl.obolibrary.org/obo/CL_0000535`

Removed

secondary neuron (sensu Teleostei) SubClassOf BFO_0000002

Added

secondary neuron (sensu Teleostei) SubClassOf RO_0002100 some UBERON_0002240
secondary neuron (sensu Teleostei) SubClassOf UBERON_0010313

github-actions · 2024-11-22T13:26:24Z

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

CAP motoneuron `http://purl.obolibrary.org/obo/CL_0000532`

Added

CAP motoneuron definition "A primary motor neuron with its soma in the caudal region of a spinal cord. The axon of this motoneuron exit the spinal cord from one single point and innervates muscles from its lateral region."
- database_cross_reference "PMID:35431796"
- database_cross_reference "PMID:17971221"
CAP motoneuron has_related_synonym "cap cell"
- database_cross_reference "PMID:17971221"
CAP motoneuron has_related_synonym "caudal primary motor neuron"
- database_cross_reference "PMID:18077593"
CAP motoneuron has_exact_synonym "CaP motorneuron"
- database_cross_reference "PMID:3746410"

middle primary motoneuron `http://purl.obolibrary.org/obo/CL_4042037`

Added

middle primary motoneuron definition "A type of primary motor neuron located in the middle region of the spinal cord. This primary motor neuron type is characterized by their distinct axonal pathways that innervate the middle trunk muscles."
- database_cross_reference "PMID:35431796"
- database_cross_reference "PMID:3746410"
middle primary motoneuron has_related_synonym "MiP"
- database_cross_reference "PMID:3746410"
- has_synonym_type abbreviation
middle primary motoneuron contributor 0000-0002-0098-8958
middle primary motoneuron label "middle primary motoneuron"@en
middle primary motoneuron date "2024-11-13T13:39:28Z"^^dateTime
middle primary motoneuron database_cross_reference "ZFA:0005179"
Class: middle primary motoneuron
middle primary motoneuron SubClassOf primary motor neuron (sensu Teleostei)

primary neuron (sensu Teleostei) `http://purl.obolibrary.org/obo/CL_0000530`

Removed

primary neuron (sensu Teleostei) SubClassOf has soma location some central nervous system

Added

primary neuron (sensu Teleostei) SubClassOf has soma location some spinal cord

rostral primary motorneuron `http://purl.obolibrary.org/obo/CL_4042038`

Added

rostral primary motorneuron definition "A type of primary motor neuron situated in the rostral region of the spinal cord. RoP neurons extend their axons to innervate the dorsal trunk musculature."
- database_cross_reference "PMID:35431796"
- database_cross_reference "PMID:3746410"
rostral primary motorneuron contributor 0000-0002-0098-8958
rostral primary motorneuron date "2024-11-13T13:42:01Z"^^dateTime
rostral primary motorneuron label "rostral primary motorneuron"@en
rostral primary motorneuron has_related_synonym "RoP"
- database_cross_reference "PMID:3746410"
- has_synonym_type abbreviation
Class: rostral primary motorneuron
rostral primary motorneuron SubClassOf primary motor neuron (sensu Teleostei)

secondary neuron (sensu Teleostei) `http://purl.obolibrary.org/obo/CL_0000535`

Removed

secondary neuron (sensu Teleostei) SubClassOf has soma location some central nervous system

Added

secondary neuron (sensu Teleostei) SubClassOf has soma location some spinal cord
secondary neuron (sensu Teleostei) SubClassOf develops from some neural crest

Caroline-99 · 2024-11-26T09:53:00Z

src/ontology/cl-edit.owl

+
+# Class: obo:CL_4042038 (rostral primary motorneuron)
+
+AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:35431796") Annotation(oboInOwl:hasDbXref "PMID:3746410") obo:IAO_0000115 obo:CL_4042038 "A type of primary motor neuron situated in the rostral region of the spinal cord. RoP neurons extend their axons to innervate the dorsal trunk musculature.")


Based on these references PMID: 35431796 and PMID: 3746410, RoP neurons extend their axons to innervate the ventral trunk musculature not the dorsal trunk musculature

Caroline-99 · 2024-11-26T10:45:50Z

src/ontology/cl-edit.owl

@@ -8029,6 +8031,10 @@ EquivalentClasses(obo:CL_0000531 ObjectIntersectionOf(obo:CL_0000101 obo:CL_0000

 # Class: obo:CL_0000532 (CAP motoneuron)

+AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:17971221") Annotation(oboInOwl:hasDbXref "PMID:35431796") obo:IAO_0000115 obo:CL_0000532 "A primary motor neuron with its soma in the caudal region of a spinal cord. The axon of this motoneuron exit the spinal cord from one single point and innervates muscles from its lateral region.")


I think CAP motoneuron innervating muscles from its **lateral region** needs more explanation. I found that this motornereron innervates the ventral portion of the axial musculature from its lateral region (PMID: 3746410, PMID: 3746409). If this is accurate, I would suggest adding The axon of this motoneuron exit the spinal cord from one single point and innervates the lateral surface of ventral axial muscles

Caroline-99 · 2024-11-26T10:46:34Z

I have made two suggestions. Everything else looks good.

Adjust hierarchy of somatosensory neurons (sensu Teleostei)

a4640c1

Fixes #2727

AvolaAmg added new term request CL-classhierarchy BICAN labels Nov 13, 2024

AvolaAmg added this to the Milestone 25/11/2024 milestone Nov 13, 2024

AvolaAmg requested a review from Caroline-99 November 13, 2024 13:48

AvolaAmg self-assigned this Nov 13, 2024

AvolaAmg and others added 3 commits November 14, 2024 13:21

Merge branch 'master' into Adjust-hierarchy-of-somatosensory-neurons-…

70e1c7e

…(sensu-Teleostei)

Merge branch 'master' into Adjust-hierarchy-of-somatosensory-neurons-…

730adc5

…(sensu-Teleostei)

Merge branch 'master' into Adjust-hierarchy-of-somatosensory-neurons-…

436c572

…(sensu-Teleostei)

Caroline-99 requested changes Nov 26, 2024

View reviewed changes


		# Class: obo:CL_4042038 (rostral primary motorneuron)

		AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:35431796") Annotation(oboInOwl:hasDbXref "PMID:3746410") obo:IAO_0000115 obo:CL_4042038 "A type of primary motor neuron situated in the rostral region of the spinal cord. RoP neurons extend their axons to innervate the dorsal trunk musculature.")

		@@ -8029,6 +8031,10 @@ EquivalentClasses(obo:CL_0000531 ObjectIntersectionOf(obo:CL_0000101 obo:CL_0000

		# Class: obo:CL_0000532 (CAP motoneuron)

		AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:17971221") Annotation(oboInOwl:hasDbXref "PMID:35431796") obo:IAO_0000115 obo:CL_0000532 "A primary motor neuron with its soma in the caudal region of a spinal cord. The axon of this motoneuron exit the spinal cord from one single point and innervates muscles from its lateral region.")

Adjust hierarchy of somatosensory neurons (sensu Teleostei) #2751

Are you sure you want to change the base?

Adjust hierarchy of somatosensory neurons (sensu Teleostei) #2751

Conversation

AvolaAmg commented Nov 13, 2024

Caroline-99 commented Nov 22, 2024

github-actions bot commented Nov 22, 2024

Ontology comparison

Left

Right

Ontology imports

Ontology annotations

CAP motoneuron http://purl.obolibrary.org/obo/CL_0000532

Added

UBERON_0010313 http://purl.obolibrary.org/obo/UBERON_0010313

Added

middle primary motoneuron http://purl.obolibrary.org/obo/CL_4042037

Added

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

Removed

Added

primary motor neuron (sensu Teleostei) http://purl.obolibrary.org/obo/CL_0000533

Removed

Added

primary neuron (sensu Teleostei) http://purl.obolibrary.org/obo/CL_0000530

Added

rostral primary motorneuron http://purl.obolibrary.org/obo/CL_4042038

Added

secondary motor neuron (sensu Teleostei) http://purl.obolibrary.org/obo/CL_0000536

Removed

Added

secondary neuron (sensu Teleostei) http://purl.obolibrary.org/obo/CL_0000535

Removed

Added

github-actions bot commented Nov 22, 2024

Ontology comparison

Left

Right

Ontology imports

Ontology annotations

CAP motoneuron http://purl.obolibrary.org/obo/CL_0000532

Added

middle primary motoneuron http://purl.obolibrary.org/obo/CL_4042037

Added

primary neuron (sensu Teleostei) http://purl.obolibrary.org/obo/CL_0000530

Removed

Added

rostral primary motorneuron http://purl.obolibrary.org/obo/CL_4042038

Added

secondary neuron (sensu Teleostei) http://purl.obolibrary.org/obo/CL_0000535

Removed

Added

Caroline-99 Nov 26, 2024

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Caroline-99 Nov 26, 2024

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Caroline-99 commented Nov 26, 2024

CAP motoneuron `http://purl.obolibrary.org/obo/CL_0000532`

UBERON_0010313 `http://purl.obolibrary.org/obo/UBERON_0010313`

middle primary motoneuron `http://purl.obolibrary.org/obo/CL_4042037`

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

primary motor neuron (sensu Teleostei) `http://purl.obolibrary.org/obo/CL_0000533`

primary neuron (sensu Teleostei) `http://purl.obolibrary.org/obo/CL_0000530`

rostral primary motorneuron `http://purl.obolibrary.org/obo/CL_4042038`

secondary motor neuron (sensu Teleostei) `http://purl.obolibrary.org/obo/CL_0000536`

secondary neuron (sensu Teleostei) `http://purl.obolibrary.org/obo/CL_0000535`

CAP motoneuron `http://purl.obolibrary.org/obo/CL_0000532`

middle primary motoneuron `http://purl.obolibrary.org/obo/CL_4042037`

primary neuron (sensu Teleostei) `http://purl.obolibrary.org/obo/CL_0000530`

rostral primary motorneuron `http://purl.obolibrary.org/obo/CL_4042038`

secondary neuron (sensu Teleostei) `http://purl.obolibrary.org/obo/CL_0000535`