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Add definitions to terms for neurons that lack them #2937

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47 changes: 38 additions & 9 deletions src/ontology/cl-edit.owl
Original file line number Diff line number Diff line change
Expand Up @@ -156,7 +156,6 @@ Declaration(Class(obo:CL_0000105))
Declaration(Class(obo:CL_0000106))
Declaration(Class(obo:CL_0000107))
Declaration(Class(obo:CL_0000108))
Declaration(Class(obo:CL_0000109))
Declaration(Class(obo:CL_0000110))
Declaration(Class(obo:CL_0000111))
Declaration(Class(obo:CL_0000112))
Expand Down Expand Up @@ -4668,13 +4667,6 @@ AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000108 "WBbt:0006840")
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.


AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000109 "MESH:D059331")
AnnotationAssertion(rdfs:label obo:CL_0000109 "adrenergic neuron")
SubClassOf(obo:CL_0000109 obo:CL_0000540)
SubClassOf(obo:CL_0000109 obo:CL_4033050)

# Class: obo:CL_0000110 (peptidergic neuron)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:23040809") Annotation(oboInOwl:hasDbXref "doi:10.1016/B978-012589762-4/50021-9") obo:IAO_0000115 obo:CL_0000110 "A neuron that uses neuropeptides as transmitters.")
Expand Down Expand Up @@ -5187,7 +5179,6 @@ AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000162 "BTO:0001780")
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000162 "FMA:62901")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:29263912") oboInOwl:hasExactSynonym obo:CL_0000162 "gastric parietal cell")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "Wikipedia:Parietal_cell") oboInOwl:hasExactSynonym obo:CL_0000162 "oxyntic cell")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "Wikipedia:Parietal_cell") oboInOwl:hasExactSynonym obo:CL_0000162 "oxyntic cell")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:29263912") Annotation(oboInOwl:hasDbXref "PMID:31613538") rdfs:comment obo:CL_0000162 "Parietal cells have dynamic, actin-supported microvilli that increase in number during active secretion, playing a crucial role in secreting hydrochloric acid and intrinsic factor. The structure and regulation of these microvilli are influenced by proteins such as ASAP3, which modulates Arf6 activity and actin assembly, thereby controlling microvilli formation and parietal cell function.")
AnnotationAssertion(rdfs:label obo:CL_0000162 "parietal cell")
SubClassOf(obo:CL_0000162 obo:CL_0000151)
Expand Down Expand Up @@ -5575,6 +5566,8 @@ EquivalentClasses(obo:CL_0000203 ObjectIntersectionOf(obo:CL_0000006 ObjectSomeV

# Class: obo:CL_0000204 (acceleration receptive cell)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:15342736") Annotation(oboInOwl:hasDbXref "PMID:18831600") obo:IAO_0000115 obo:CL_0000204 "A type of neuronal receptor cells that is responsive to changes of speed over time in a central nervous system.")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:15342736") Annotation(oboInOwl:hasDbXref "PMID:18831600") rdfs:comment obo:CL_0000204 "These neurons have been widely studied in pigeon brains. They were found in the pretectal nucleus in the brain of pigeons and they are characterised by plates-shaped firing rates sensitive to speed.")
AnnotationAssertion(rdfs:label obo:CL_0000204 "acceleration receptive cell")
SubClassOf(obo:CL_0000204 obo:CL_0000006)

Expand Down Expand Up @@ -5945,8 +5938,10 @@ AnnotationAssertion(owl:deprecated obo:CL_0000245 "true"^^xsd:boolean)

# Class: obo:CL_0000246 (Mauthner neuron)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:11163687") obo:IAO_0000115 obo:CL_0000246 "A reticulospinal neuron with soma location in the hindbrain of fish and amphibians. This neuron type is responsible for the rapid escape response known as C-start escape.")
AnnotationAssertion(rdfs:label obo:CL_0000246 "Mauthner neuron")
SubClassOf(obo:CL_0000246 obo:CL_0000099)
SubClassOf(obo:CL_0000246 obo:CL_4023107)

# Class: obo:CL_0000247 (Rohon-Beard neuron)

Expand Down Expand Up @@ -6900,6 +6895,7 @@ SubClassOf(obo:CL_0000378 obo:CL_0000630)

# Class: obo:CL_0000379 (sensory processing neuron)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "Wikipedia:Sensory_neuron") Annotation(oboInOwl:hasDbXref "https://www.ncbi.nlm.nih.gov/books/NBK547656/") obo:IAO_0000115 obo:CL_0000379 "A neuron of the central nervous system capable of processing external sensory stimuli.")
AnnotationAssertion(rdfs:label obo:CL_0000379 "sensory processing neuron")
SubClassOf(obo:CL_0000379 obo:CL_0000540)
SubClassOf(obo:CL_0000379 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0001017))
Expand Down Expand Up @@ -7087,6 +7083,7 @@ AnnotationAssertion(owl:deprecated obo:CL_0000405 "true"^^xsd:boolean)

# Class: obo:CL_0000406 (CNS short range interneuron)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:23394773") obo:IAO_0000115 obo:CL_0000406 "A type of interneuron with its soma located in a central nervous system. This neuronal type extends their axons locally within the same circuit.")
AnnotationAssertion(rdfs:label obo:CL_0000406 "CNS short range interneuron")
SubClassOf(obo:CL_0000406 obo:CL_0000099)

Expand Down Expand Up @@ -7115,6 +7112,7 @@ AnnotationAssertion(owl:deprecated obo:CL_0000409 "true"^^xsd:boolean)

# Class: obo:CL_0000410 (CNS long range interneuron)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:34322002") Annotation(oboInOwl:hasDbXref "PMID:35392440") obo:IAO_0000115 obo:CL_0000410 "A type of interneuron with its soma located in a cerebral cortex. This neuronal type extends their axons to remote cortical and subcortical areas.")
AnnotationAssertion(rdfs:label obo:CL_0000410 "CNS long range interneuron")
SubClassOf(obo:CL_0000410 obo:CL_0000099)

Expand Down Expand Up @@ -7727,11 +7725,17 @@ SubClassOf(obo:CL_0000488 obo:CL_0000210)

# Class: obo:CL_0000489 (scotopic photoreceptor cell)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "https://www.ncbi.nlm.nih.gov/books/NBK542177/") obo:IAO_0000115 obo:CL_0000489 "A type of photoreceptor cell that is capable of detecting very low light levels (i.e. in darkness).")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:38589506") Annotation(oboInOwl:hasDbXref "https://www.ncbi.nlm.nih.gov/books/NBK542177/") oboInOwl:hasRelatedSynonym obo:CL_0000489 "rod cell")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:38589506") Annotation(oboInOwl:hasDbXref "https://www.ncbi.nlm.nih.gov/books/NBK542177/") oboInOwl:hasRelatedSynonym obo:CL_0000489 "rod photoreceptor")
AnnotationAssertion(rdfs:label obo:CL_0000489 "scotopic photoreceptor cell")
SubClassOf(obo:CL_0000489 obo:CL_0000210)

# Class: obo:CL_0000490 (photopic photoreceptor cell)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "https://www.ncbi.nlm.nih.gov/books/NBK542177/") obo:IAO_0000115 obo:CL_0000490 "A type of photoreceptor cell that is capable of detecting light under well light and bright condition (i.e. daylight). This cell type is responsible for colour vision.")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:38589506") Annotation(oboInOwl:hasDbXref "https://www.ncbi.nlm.nih.gov/books/NBK542177/") oboInOwl:hasRelatedSynonym obo:CL_0000490 "cone cell")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "https://www.ncbi.nlm.nih.gov/books/NBK542177/") oboInOwl:hasRelatedSynonym obo:CL_0000490 "cone photoreceptor")
AnnotationAssertion(rdfs:label obo:CL_0000490 "photopic photoreceptor cell")
SubClassOf(obo:CL_0000490 obo:CL_0000488)

Expand Down Expand Up @@ -8173,6 +8177,8 @@ AnnotationAssertion(owl:deprecated obo:CL_0000543 "true"^^xsd:boolean)

# Class: obo:CL_0000544 (slowly adapting mechanoreceptor cell)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:19625527") Annotation(oboInOwl:hasDbXref "https://www.kenhub.com/en/library/physiology/peripheral-mechanosensory-receptors") Annotation(oboInOwl:hasDbXref "wikipedia:Mechanoreceptor") obo:IAO_0000115 obo:CL_0000544 "A type of mechanoreceptor cell that responds to a sustained stimulus with reduced sensitivity. This mechanoreceptor cell is capable of being responsive to ongoing stimuli.")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:19625527") oboInOwl:hasRelatedSynonym obo:CL_0000544 "SA mechanoreceptor cell")
AnnotationAssertion(rdfs:label obo:CL_0000544 "slowly adapting mechanoreceptor cell")
SubClassOf(obo:CL_0000544 obo:CL_0000199)

Expand Down Expand Up @@ -8451,6 +8457,7 @@ SubClassOf(obo:CL_0000566 ObjectSomeValuesFrom(obo:RO_0002202 obo:CL_0000134))

# Class: obo:CL_0000567 (polymodal nocireceptor)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:21041958") Annotation(oboInOwl:hasDbXref "PMID:37006298") Annotation(oboInOwl:hasDbXref "PMID:38806708") Annotation(oboInOwl:hasDbXref "https://www.ncbi.nlm.nih.gov/books/NBK551562/") obo:IAO_0000115 obo:CL_0000567 "A type of pain receptor cell with soma in the peripheral nervous system. This cell type responds to a multiple type of noxious stimuli and its soma is located in the trigeminal root ganglia in the facial nerves and in the dorsal root ganglia in the rest of the body.")
AnnotationAssertion(rdfs:label obo:CL_0000567 "polymodal nocireceptor")
SubClassOf(obo:CL_0000567 obo:CL_0000198)

Expand Down Expand Up @@ -9554,6 +9561,8 @@ SubClassOf(obo:CL_0000686 ObjectSomeValuesFrom(obo:RO_0002202 obo:CL_0000333))

# Class: obo:CL_0000687 (R1 photoreceptor cell)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:37128740") obo:IAO_0000028 obo:CL_0000687 "R1")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:19623243") Annotation(oboInOwl:hasDbXref "PMID:31207209") Annotation(oboInOwl:hasDbXref "PMID:34003117") Annotation(oboInOwl:hasDbXref "PMID:37128740") obo:IAO_0000115 obo:CL_0000687 "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.")
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0000687 "R1 cell")
AnnotationAssertion(rdfs:label obo:CL_0000687 "R1 photoreceptor cell")
SubClassOf(obo:CL_0000687 obo:CL_0000488)
Expand All @@ -9574,6 +9583,8 @@ SubClassOf(obo:CL_0000689 obo:CL_0000163)

# Class: obo:CL_0000690 (R2 photoreceptor cell)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:37128740") obo:IAO_0000028 obo:CL_0000690 "R2")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:19623243") Annotation(oboInOwl:hasDbXref "PMID:31207209") Annotation(oboInOwl:hasDbXref "PMID:34003117") Annotation(oboInOwl:hasDbXref "PMID:37128740") obo:IAO_0000115 obo:CL_0000690 "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.")
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0000690 "R2 cell")
AnnotationAssertion(rdfs:label obo:CL_0000690 "R2 photoreceptor cell")
SubClassOf(obo:CL_0000690 obo:CL_0000488)
Expand Down Expand Up @@ -9608,6 +9619,8 @@ EquivalentClasses(obo:CL_0000693 ObjectIntersectionOf(obo:CL_0000099 ObjectSomeV

# Class: obo:CL_0000694 (R3 photoreceptor cell)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:37128740") obo:IAO_0000028 obo:CL_0000694 "R3")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:19623243") Annotation(oboInOwl:hasDbXref "PMID:31207209") Annotation(oboInOwl:hasDbXref "PMID:34003117") Annotation(oboInOwl:hasDbXref "PMID:37128740") obo:IAO_0000115 obo:CL_0000694 "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.")
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0000694 "R3 cell")
AnnotationAssertion(rdfs:label obo:CL_0000694 "R3 photoreceptor cell")
SubClassOf(obo:CL_0000694 obo:CL_0000488)
Expand Down Expand Up @@ -9636,6 +9649,8 @@ SubClassOf(obo:CL_0000696 obo:CL_0000167)

# Class: obo:CL_0000697 (R4 photoreceptor cell)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:37128740") obo:IAO_0000028 obo:CL_0000697 "R4")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:19623243") Annotation(oboInOwl:hasDbXref "PMID:31207209") Annotation(oboInOwl:hasDbXref "PMID:34003117") Annotation(oboInOwl:hasDbXref "PMID:37128740") obo:IAO_0000115 obo:CL_0000697 "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.")
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0000697 "R4 cell")
AnnotationAssertion(rdfs:label obo:CL_0000697 "R4 photoreceptor cell")
SubClassOf(obo:CL_0000697 obo:CL_0000488)
Expand Down Expand Up @@ -9673,6 +9688,8 @@ SubClassOf(obo:CL_0000701 obo:CL_0000630)

# Class: obo:CL_0000702 (R5 photoreceptor cell)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:37128740") obo:IAO_0000028 obo:CL_0000702 "R5")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:19623243") Annotation(oboInOwl:hasDbXref "PMID:31207209") Annotation(oboInOwl:hasDbXref "PMID:34003117") Annotation(oboInOwl:hasDbXref "PMID:37128740") obo:IAO_0000115 obo:CL_0000702 "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.")
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0000702 "R5 cell")
AnnotationAssertion(rdfs:label obo:CL_0000702 "R5 photoreceptor cell")
SubClassOf(obo:CL_0000702 obo:CL_0000488)
Expand All @@ -9693,8 +9710,11 @@ SubClassOf(obo:CL_0000704 obo:CL_0000071)

# Class: obo:CL_0000705 (R6 photoreceptor cell)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:37128740") obo:IAO_0000028 obo:CL_0000705 "R6")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:19623243") Annotation(oboInOwl:hasDbXref "PMID:31207209") Annotation(oboInOwl:hasDbXref "PMID:34003117") Annotation(oboInOwl:hasDbXref "PMID:37128740") obo:IAO_0000115 obo:CL_0000705 "A photoreceptor cell in the Drosophila visual system. The R6 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.")
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0000705 "R6 cell")
AnnotationAssertion(rdfs:label obo:CL_0000705 "R6 photoreceptor cell")
SubClassOf(obo:CL_0000705 obo:CL_0000028)
SubClassOf(obo:CL_0000705 obo:CL_0000488)
SubClassOf(obo:CL_0000705 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0000971))

Expand All @@ -9714,8 +9734,11 @@ SubClassOf(obo:CL_0000706 ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0033326))

# Class: obo:CL_0000707 (R7 photoreceptor cell)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:37128740") obo:IAO_0000028 obo:CL_0000707 "R7")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:19623243") Annotation(oboInOwl:hasDbXref "PMID:31207209") Annotation(oboInOwl:hasDbXref "PMID:34003117") Annotation(oboInOwl:hasDbXref "PMID:37128740") obo:IAO_0000115 obo:CL_0000707 "A photoreceptor cell in the Drosophila visual system. The R7 photoreceptor cell is a capable of detecting UV light at peak of 330nm wavelength, this cell type expresses the opsin gene Rh3 or Rh4 and it is located at the center of the drosophila ommatidia. Photoreceptor R7 innervates the M6 layer in the medulla in Drosophila the optic lobe.")
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0000707 "R7 cell")
AnnotationAssertion(rdfs:label obo:CL_0000707 "R7 photoreceptor cell")
SubClassOf(obo:CL_0000707 obo:CL_0000028)
SubClassOf(obo:CL_0000707 obo:CL_0000494)
SubClassOf(obo:CL_0000707 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0000971))

Expand All @@ -9730,6 +9753,8 @@ SubClassOf(Annotation(oboInOwl:is_inferred "true") obo:CL_0000708 obo:CL_0002320

# Class: obo:CL_0000709 (R8 photoreceptor cell)

AnnotationAssertion(obo:IAO_0000028 obo:CL_0000709 "R8")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:19623243") Annotation(oboInOwl:hasDbXref "PMID:31207209") Annotation(oboInOwl:hasDbXref "PMID:34003117") Annotation(oboInOwl:hasDbXref "PMID:37128740") obo:IAO_0000115 obo:CL_0000709 "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.")
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0000709 "R8 cell")
AnnotationAssertion(rdfs:label obo:CL_0000709 "R8 photoreceptor cell")
SubClassOf(obo:CL_0000709 obo:CL_0000488)
Expand Down Expand Up @@ -22686,8 +22711,12 @@ SubClassOf(obo:CL_0008024 obo:CL_0000163)
# Class: obo:CL_0008025 (noradrenergic neuron)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:dos") obo:IAO_0000115 obo:CL_0008025 "A neuron that release noradrenaline (noriphinephrine) as a neurotransmitter.")
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0008025 "MESH:D059331")
AnnotationAssertion(oboInOwl:hasRelatedSynonym obo:CL_0008025 "adrenergic neuron")
AnnotationAssertion(rdfs:label obo:CL_0008025 "noradrenergic neuron")
EquivalentClasses(obo:CL_0008025 ObjectIntersectionOf(obo:CL_0000540 ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0061533)))
SubClassOf(obo:CL_0008025 obo:CL_0000540)
SubClassOf(obo:CL_0008025 obo:CL_4033050)

# Class: obo:CL_0008026 (open tracheal system tracheocyte)

Expand Down
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