Skip to content

Commit

Permalink
Added L4 IT MOp
Browse files Browse the repository at this point in the history 
Fixes #884
- Requires some input on what goes in/stays out, see ticket #884 for details.
- Not sure if morphological description is useful in this case too (given diverse morphologies)
  • Loading branch information
@shawntanzk
shawntanzk committed Mar 22, 2021
1 parent 2369cbf commit 8761b60
Showing 1 changed file with 21 additions and 40 deletions.
61 changes: 21 additions & 40 deletions src/ontology/cl-edit.owl
View file
Original file line number Diff line number Diff line change
Expand Up @@ -2458,9 +2458,7 @@ Declaration(Class(obo:CL_4023015))
Declaration(Class(obo:CL_4023016))
Declaration(Class(obo:CL_4023017))
Declaration(Class(obo:CL_4023018))

Declaration(Class(obo:CL_4023019))

Declaration(Class(obo:CL_4023022))
Declaration(Class(obo:CL_4023023))
Declaration(Class(obo:CL_4023024))
Expand All @@ -2471,24 +2469,11 @@ Declaration(Class(obo:CL_4023030))
Declaration(Class(obo:CL_4023031))
Declaration(Class(obo:CL_4023034))
Declaration(Class(obo:CL_4023036))





Declaration(Class(obo:CL_4023040))

Declaration(Class(obo:CL_4023038))



Declaration(Class(obo:CL_4023040))
Declaration(Class(obo:CL_4023041))


Declaration(Class(obo:CL_4023042))



Declaration(Class(obo:CL_4023051))
Declaration(Class(obo:CP_0000000))
Declaration(Class(obo:CP_0000025))
Declaration(Class(obo:CP_0000027))
Expand Down Expand Up @@ -27446,7 +27431,6 @@ SubClassOf(obo:CL_4023007 obo:CL_0000099)
SubClassOf(obo:CL_4023007 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0000956))
SubClassOf(obo:CL_4023007 ObjectSomeValuesFrom(obo:RO_0002162 obo:NCBITaxon_10090))
SubClassOf(obo:CL_4023007 ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0061534))

SubClassOf(obo:CL_4023007 ObjectSomeValuesFrom(obo:RO_0002292 obo:PR_P32648))

# Class: obo:CL_4023008 (intratelencephalic-projecting glutamatergic cortical neuron)
Expand All @@ -27471,7 +27455,6 @@ AnnotationAssertion(rdfs:label obo:CL_4023009 "extratelencephalic-projecting glu
SubClassOf(obo:CL_4023009 obo:CL_0000679)
SubClassOf(obo:CL_4023009 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0000956))


# Class: obo:CL_4023010 (alpha7 Lamp5 GABAergic cortical interneuron (Mus musculus))

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:30413647") Annotation(oboInOwl:hasDbXref "PMID:33184512") obo:IAO_0000115 obo:CL_4023010 "A Lamp5 GABAergic cortical interneuron that is strongly labelled for α7 nAChRs. These cells are located in L1 and have multipolar dendrites with vertically descending axonal collaterals that project deep into the column, usually branching and terminating in L5A. Unlike typical Lamp5 electrophysiology, they have Vip- and Sst-like firing properties, with active depolarizing hump at near-threshold membrane potentials, and larger hyperpolarization sag, stronger burst, and rebound firing.")
Expand Down Expand Up @@ -27561,7 +27544,6 @@ AnnotationAssertion(oboInOwl:created_by obo:CL_4023018 <http://orcid.org/0000-00
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_4023018 "ILX:0770154"^^xsd:string)
AnnotationAssertion(oboInOwl:inSubset obo:CL_4023018 <http://purl.obolibrary.org/obo/cl#BDS_subset>)
AnnotationAssertion(rdfs:label obo:CL_4023018 "pvalb GABAergic cortical interneuron")

EquivalentClasses(obo:CL_4023018 ObjectIntersectionOf(obo:CL_0000099 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0000956) ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0061534) ObjectSomeValuesFrom(obo:RO_0002292 obo:PR_000013502)))

# Class: obo:CL_4023019 (L5/6 CCK and Vip expressing cortical GABAergic interneuron (Mus musculus))
Expand All @@ -27577,7 +27559,6 @@ SubClassOf(obo:CL_4023019 ObjectSomeValuesFrom(obo:RO_0002162 obo:NCBITaxon_1009
SubClassOf(obo:CL_4023019 ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0061534))
SubClassOf(obo:CL_4023019 ObjectSomeValuesFrom(obo:RO_0002292 obo:PR_P32648))


# Class: obo:CL_4023022 (canopy Lamp5 GABAergic cortical interneuron (Mus musculus))

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:30413647") obo:IAO_0000115 obo:CL_4023022 "A Lamp5 GABAergic cortical interneuron that has extended axons in the surface of L1. Canopy Lamp5 cells resemble neurogliaform cells in having elongated horizontal axonal arbors largely confined to L1; but the dendritic arbors are wider and have fewer branches, while the axon is less tortuous and extends further from the soma")
Expand All @@ -27601,10 +27582,8 @@ SubClassOf(obo:CL_4023023 obo:CL_0000099)
SubClassOf(obo:CL_4023023 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0000956))
SubClassOf(obo:CL_4023023 ObjectSomeValuesFrom(obo:RO_0002162 obo:NCBITaxon_10090))
SubClassOf(obo:CL_4023023 ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0061534))

SubClassOf(obo:CL_4023023 ObjectSomeValuesFrom(obo:RO_0002292 obo:PR_Q9D387))


# Class: obo:CL_4023024 (Neurogliaform Lamp5 GABAergic cortical interneuron (Mus musculus))

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:27477017") obo:IAO_0000115 obo:CL_4023024 "A Lamp5 GABAergic cortical interneuron with layer-adapting morphology. NGC Lamp5 cells have a small round soma, short dendrites, and a wide dense axonal arbor that tends to establish a dense axonal mesh with high connection probability both to themselves and L2 pyramidal cells. NGC Lamp5 cells have unique synaptic properties that distinguish them from other GABAergic interneurons, including the release of GABA to the extracellular space via volume transmission, and the ability to produce GABA-B responses in connected postsynaptic targets.")
Expand All @@ -27616,10 +27595,8 @@ SubClassOf(obo:CL_4023024 obo:CL_0000099)
SubClassOf(obo:CL_4023024 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0000956))
SubClassOf(obo:CL_4023024 ObjectSomeValuesFrom(obo:RO_0002162 obo:NCBITaxon_10090))
SubClassOf(obo:CL_4023024 ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0061534))

SubClassOf(obo:CL_4023024 ObjectSomeValuesFrom(obo:RO_0002292 obo:PR_Q9D387))


# Class: obo:CL_4023025 (Long-range projecting Sst GABAergic cortical interneuron (Mus musculus))

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:26727548") obo:IAO_0000115 obo:CL_4023025 "A Sst GABAergic cortical interneuron that is both an interneuron and a projecting neuron. They are found in all layers from upper L2/3 down to the bottom of L6. They have long-range projections, some with axons fading into white matter. These cells have low rebound potential, low hyperpolarization sag, and high variability in membrane time constant.")
Expand Down Expand Up @@ -27712,8 +27689,15 @@ SubClassOf(obo:CL_4023036 ObjectSomeValuesFrom(obo:RO_0002162 obo:NCBITaxon_1009
SubClassOf(obo:CL_4023036 ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0061534))
SubClassOf(obo:CL_4023036 ObjectSomeValuesFrom(obo:RO_0002292 obo:PR_P32848))

# Class: obo:CL_4023038 (L6b glutamatergic cortical neuron)


AnnotationAssertion(Annotation(oboInOwl:hasDbXref "DOI:10.1101/2020.10.19.34312") Annotation(oboInOwl:hasDbXref "PMID:30382198") obo:IAO_0000115 obo:CL_4023038 "A glutamatergic neuron located in cortical layer 6b. They are transcriptomically related to corticothalamic-projecting neurons but have differential projections to the thalamus or anterior cingulate.")
AnnotationAssertion(<http://purl.org/dc/elements/1.1/creator> obo:CL_4023038 <http://orcid.org/0000-0001-7258-9596>)
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_4023038 "ILX:0770163")
AnnotationAssertion(oboInOwl:inSubset obo:CL_4023038 <http://purl.obolibrary.org/obo/cl#BDS_subset>)
AnnotationAssertion(rdfs:label obo:CL_4023038 "L6b glutamatergic cortical neuron")
SubClassOf(obo:CL_4023038 obo:CL_0000679)
SubClassOf(obo:CL_4023038 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0000956))

# Class: obo:CL_4023040 (L2/3-6 intratelencephalic projecting glutamatergic cortical neuron)

Expand All @@ -27723,7 +27707,8 @@ AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_4023040 "L2/3-6 IT projectin
AnnotationAssertion(oboInOwl:inSubset obo:CL_4023040 <http://purl.obolibrary.org/obo/cl#BDS_subset>)
AnnotationAssertion(rdfs:label obo:CL_4023040 "L2/3-6 intratelencephalic projecting glutamatergic cortical neuron")
SubClassOf(obo:CL_4023040 obo:CL_4023008)

SubClassOf(obo:CL_4023040 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0001384))
SubClassOf(obo:CL_4023040 ObjectSomeValuesFrom(obo:RO_0002162 obo:NCBITaxon_10090))

# Class: obo:CL_4023041 (L5 extratelencephalic projecting glutamatergic cortical neuron)

Expand All @@ -27738,7 +27723,6 @@ AnnotationAssertion(oboInOwl:inSubset obo:CL_4023041 <http://purl.obolibrary.org
AnnotationAssertion(rdfs:label obo:CL_4023041 "L5 extratelencephalic projecting glutamatergic cortical neuron")
SubClassOf(obo:CL_4023041 obo:CL_4023009)


# Class: obo:CL_4023042 (L6 corticothalamic-projecting projecting glutamatergic cortical neuron)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "DOI:10.1101/2020.10.19.343129") obo:IAO_0000115 obo:CL_4023042 "A corticothalamic-projecting neuron located in cortical layer 6.")
Expand All @@ -27748,18 +27732,15 @@ AnnotationAssertion(oboInOwl:inSubset obo:CL_4023042 <http://purl.obolibrary.org
AnnotationAssertion(rdfs:label obo:CL_4023042 "L6 corticothalamic-projecting projecting glutamatergic cortical neuron")
SubClassOf(obo:CL_4023042 obo:CL_4023013)

# Class: obo:CL_4023051 (L4 intratelencephalic projecting glutamatergic neuron of the primary motor cortex (Mus musculus))


# Class: obo:CL_4023038 (L6b glutamatergic cortical neuron)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "DOI:10.1101/2020.10.19.34312") Annotation(oboInOwl:hasDbXref "PMID:30382198") obo:IAO_0000115 obo:CL_4023038 "A glutamatergic neuron located in cortical layer 6b. They are transcriptomically related to corticothalamic-projecting neurons but have differential projections to the thalamus or anterior cingulate.")
AnnotationAssertion(<http://purl.org/dc/elements/1.1/creator> obo:CL_4023038 <http://orcid.org/0000-0001-7258-9596>)
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_4023038 "ILX:0770163")
AnnotationAssertion(oboInOwl:inSubset obo:CL_4023038 <http://purl.obolibrary.org/obo/cl#BDS_subset>)
AnnotationAssertion(rdfs:label obo:CL_4023038 "L6b glutamatergic cortical neuron")
SubClassOf(obo:CL_4023038 obo:CL_0000679)
SubClassOf(obo:CL_4023038 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0000956))

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:33184512") obo:IAO_0000115 obo:CL_4023051 "An intratelencephalic-projecting glutamatergic neuron that is located in the boundary between L2/3 and L5 of the primary motor cortex. These cells have diverse morphologies with some pyramidal and some stellate cells.")
AnnotationAssertion(<http://purl.org/dc/elements/1.1/creator> obo:CL_4023051 <http://orcid.org/0000-0001-7258-9596>)
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_4023051 "ILX:0770172")
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_4023051 "L4 IT MOp (Mus)")
AnnotationAssertion(oboInOwl:inSubset obo:CL_4023051 <http://purl.obolibrary.org/obo/cl#BDS_subset>)
AnnotationAssertion(rdfs:label obo:CL_4023051 "L4 intratelencephalic projecting glutamatergic neuron of the primary motor cortex (Mus musculus)")
SubClassOf(obo:CL_4023051 obo:CL_4023040)

# Class: obo:CP_0000000 (neutrophillic cytoplasm)

Expand Down Expand Up @@ -27857,4 +27838,4 @@ SubClassOf(obo:D96882F1-8709-49AB-BCA9-772A67EA6C33 obo:GO_0005634)


SubClassOf(Annotation(oboInOwl:hasDbXref <https://github.com/obophenotype/cell-ontology/issues/757>) ObjectIntersectionOf(obo:CL_0000540 ObjectSomeValuesFrom(obo:RO_0002162 obo:NCBITaxon_7742)) ObjectSomeValuesFrom(obo:RO_0002202 obo:CL_0000031))
)
)

0 comments on commit 8761b60

Please sign in to comment.