Add Jorstad paper as a reference to cortical neuron CL terms

[AvolaAmg]

Fixes #2337

• Adds Jorstad paper as a reference to cortical neurons.
• Substitutes references doi ID for PMID:
  doi:10.1016/j.cell.2021.04.021 → PMID:34004146
  doi:10.1101/2022.11.06.515349 → PMID:37824655

[AvolaAmg]

#gogoeditdiff

[github-actions]

Here's a diff of how these changes impact the classified ontology (on -simple file):

Ontology comparison

Left

• Ontology IRI: http://purl.obolibrary.org/obo/cl/cl-simple.owl
• Version IRI: http://purl.obolibrary.org/obo/cl/releases/2024-04-17/cl-simple.owl
• Loaded from: file:/__w/cell-ontology/cell-ontology/src/ontology/cl-simple-master.owl/cl-simple.owl

Right

• Ontology IRI: http://purl.obolibrary.org/obo/cl/cl-simple.owl
• Version IRI: http://purl.obolibrary.org/obo/cl/releases/2024-04-17/cl-simple.owl
• Loaded from: file:/__w/cell-ontology/cell-ontology/src/ontology/cl-simple-pr.owl/cl-simple.owl

Ontology imports

Ontology annotations

L2/3 intratelencephalic projecting glutamatergic neuron http://purl.obolibrary.org/obo/CL_4030059

Removed

• L2/3 intratelencephalic projecting glutamatergic neuron definition "An intratelencephalic-projecting glutamatergic neuron with a soma found in cortical layer 2/3."

  • database_cross_reference "PMID:37292694"

  • database_cross_reference "PMID:34004146"

Added

• L2/3 intratelencephalic projecting glutamatergic neuron definition "An intratelencephalic-projecting glutamatergic neuron with a soma found in cortical layer 2/3."

  • database_cross_reference "PMID:37292694"

  • database_cross_reference "PMID:37824655"

  • database_cross_reference "PMID:34004146"

L2/3 intratelencephalic projecting glutamatergic neuron of the primary motor cortex http://purl.obolibrary.org/obo/CL_4023047

Removed

• L2/3 intratelencephalic projecting glutamatergic neuron of the primary motor cortex has exact synonym "L2/3 IT MOp"

• L2/3 intratelencephalic projecting glutamatergic neuron of the primary motor cortex definition "An intratelencephalic-projecting glutamatergic neuron with a soma found in cortical layer 2/3 of the primary motor cortex."

  • database_cross_reference "DOI:10.1101/2020.10.19.343129"

• L2/3 intratelencephalic projecting glutamatergic neuron of the primary motor cortex has exact synonym "L2/3 IT M1"

Added

• L2/3 intratelencephalic projecting glutamatergic neuron of the primary motor cortex has exact synonym "L2/3 IT MOp"

  • database_cross_reference "PMID:34616075"

• L2/3 intratelencephalic projecting glutamatergic neuron of the primary motor cortex has exact synonym "L2/3 IT M1"

  • database_cross_reference "PMID:34616075"

• L2/3 intratelencephalic projecting glutamatergic neuron of the primary motor cortex definition "An intratelencephalic-projecting glutamatergic neuron with a soma found in cortical layer 2/3 of the primary motor cortex."

  • database_cross_reference "PMID:34616075"

L4 intratelencephalic projecting glutamatergic neuron http://purl.obolibrary.org/obo/CL_4030063

Removed

• L4 intratelencephalic projecting glutamatergic neuron definition "An intratelencephalic-projecting glutamatergic neuron with a soma found in cortical layer 4."
  • database_cross_reference "PMID:37292694"

Added

• L4 intratelencephalic projecting glutamatergic neuron definition "An intratelencephalic-projecting glutamatergic neuron with a soma found in cortical layer 4."

  • database_cross_reference "PMID:37292694"

  • database_cross_reference "PMID:37824655"

L5 extratelencephalic projecting glutamatergic cortical neuron http://purl.obolibrary.org/obo/CL_4023041

Removed

• L5 extratelencephalic projecting glutamatergic cortical neuron has exact synonym "Pyramidal tract-like (PT-l)"

  • database_cross_reference "DOI:10.1016/j.cell.2019.09.023"

  • comment "pyramidal tract-like is used because, unlike pyramidal tract neurons in the motor cortex, neurons in the structures like the auditory cortex do not project to the spinal cord."

• L5 extratelencephalic projecting glutamatergic cortical neuron definition "A glutamatergic neuron, with a soma found in the deeper portion of L5, that has long-range axonal projections including deep subcortical targets outside of the telencephalon and, in some cases, the spinal cord. While the L5 ET neuron projections are not limited to ET targets, they are clearly differentiated from the neuron subclasses whose projections are constrained to intratelencephalic (IT) targets. L5 ET neurons are generally the largest excitatory cortical neurons, typically having a thick apical dendrite with a prominent dendritic tuft in layer 1 and displaying burst-firing physiological characteristics."

  • database_cross_reference "DOI:10.1101/2020.10.19.343129"

Added

• L5 extratelencephalic projecting glutamatergic cortical neuron has exact synonym "Pyramidal tract-like (PT-l)"

  • comment "pyramidal tract-like is used because, unlike pyramidal tract neurons in the motor cortex, neurons in the structures like the auditory cortex do not project to the spinal cord."

  • database_cross_reference "PMID:31626774"

• L5 extratelencephalic projecting glutamatergic cortical neuron definition "A glutamatergic neuron, with a soma found in the deeper portion of L5, that has long-range axonal projections including deep subcortical targets outside of the telencephalon and, in some cases, the spinal cord. While the L5 ET neuron projections are not limited to ET targets, they are clearly differentiated from the neuron subclasses whose projections are constrained to intratelencephalic (IT) targets. L5 ET neurons are generally the largest excitatory cortical neurons, typically having a thick apical dendrite with a prominent dendritic tuft in layer 1 and displaying burst-firing physiological characteristics."

  • database_cross_reference "PMID:34616075"

  • database_cross_reference "PMID:37824655"

L5 intratelencephalic projecting glutamatergic neuron http://purl.obolibrary.org/obo/CL_4030064

Removed

• L5 intratelencephalic projecting glutamatergic neuron definition "An intratelencephalic-projecting glutamatergic neuron with a soma found in cortical layer 5."

  • database_cross_reference "PMID:37609206"

  • database_cross_reference "PMID:37292694"

Added

• L5 intratelencephalic projecting glutamatergic neuron definition "An intratelencephalic-projecting glutamatergic neuron with a soma found in cortical layer 5."

  • database_cross_reference "PMID:37609206"

  • database_cross_reference "PMID:37292694"

  • database_cross_reference "PMID:37824655"

L5/6 near-projecting glutamatergic neuron http://purl.obolibrary.org/obo/CL_4030067

Removed

• L5/6 near-projecting glutamatergic neuron definition "A near-projecting glutamatergic neuron with a soma found in cortical layer 5/6."

  • database_cross_reference "PMID:37292694"

  • database_cross_reference "PMID:34004146"

Added

• L5/6 near-projecting glutamatergic neuron definition "A near-projecting glutamatergic neuron with a soma found in cortical layer 5/6."

  • database_cross_reference "PMID:37292694"

  • database_cross_reference "PMID:37824655"

  • database_cross_reference "PMID:34004146"

L5/6 near-projecting glutamatergic neuron of the primary motor cortex http://purl.obolibrary.org/obo/CL_4023043

Removed

• L5/6 near-projecting glutamatergic neuron of the primary motor cortex definition "A near-projecting glutamatergic neuron with a soma found in layer 5/6 of the primary motor cortex."

  • database_cross_reference "DOI:10.1101/2020.10.19.343129"

  • database_cross_reference "PMID:31209381"

Added

• L5/6 near-projecting glutamatergic neuron of the primary motor cortex definition "A near-projecting glutamatergic neuron with a soma found in layer 5/6 of the primary motor cortex."

  • database_cross_reference "PMID:34616075"

  • database_cross_reference "PMID:31209381"

L6 corticothalamic-projecting glutamatergic cortical neuron http://purl.obolibrary.org/obo/CL_4023042

Removed

• L6 corticothalamic-projecting glutamatergic cortical neuron has exact synonym "L6 CT"

• L6 corticothalamic-projecting glutamatergic cortical neuron definition "A corticothalamic-projecting neuron with a soma found in cortical layer 6."

  • database_cross_reference "DOI:10.1101/2020.10.19.343129"

Added

• L6 corticothalamic-projecting glutamatergic cortical neuron has exact synonym "L6 CT"

  • database_cross_reference "PMID:34616075"

  • database_cross_reference "PMID:28625486"

• L6 corticothalamic-projecting glutamatergic cortical neuron definition "A corticothalamic-projecting neuron with a soma found in cortical layer 6."

  • database_cross_reference "PMID:34616075"

  • database_cross_reference "PMID:37824655"

L6 intratelencephalic projecting Car3 glutamatergic neuron http://purl.obolibrary.org/obo/CL_4030068

Removed

• L6 intratelencephalic projecting Car3 glutamatergic neuron definition "An intratelencephalic-projecting glutamatergic neuron with a soma found in cortical layer 6 that expresses Car3."

  • database_cross_reference "doi:10.1016/j.cell.2021.04.021"

  • database_cross_reference "doi:10.1101/2022.11.06.515349"

  • database_cross_reference "doi:10.1101/2022.11.30.518285"

Added

• L6 intratelencephalic projecting Car3 glutamatergic neuron definition "An intratelencephalic-projecting glutamatergic neuron with a soma found in cortical layer 6 that expresses Car3."

  • database_cross_reference "PMID:37824655"

  • database_cross_reference "doi:10.1101/2022.11.30.518285"

  • database_cross_reference "PMID:34004146"

L6 intratelencephalic projecting glutamatergic neuron http://purl.obolibrary.org/obo/CL_4030065

Removed

• L6 intratelencephalic projecting glutamatergic neuron definition "An intratelencephalic-projecting glutamatergic neuron with a soma found in cortical layer 6."

  • database_cross_reference "PMID:37609206"

  • database_cross_reference "PMID:37292694"

Added

• L6 intratelencephalic projecting glutamatergic neuron definition "An intratelencephalic-projecting glutamatergic neuron with a soma found in cortical layer 6."

  • database_cross_reference "PMID:37609206"

  • database_cross_reference "PMID:37292694"

  • database_cross_reference "PMID:37824655"

L6b glutamatergic cortical neuron http://purl.obolibrary.org/obo/CL_4023038

Removed

• L6b glutamatergic cortical neuron definition "A glutamatergic neuron with a soma found in cortical layer 6b. They are transcriptomically related to corticothalamic-projecting neurons but have differential projections to the thalamus or anterior cingulate."

  • database_cross_reference "DOI:10.1101/2020.10.19.34312"

  • database_cross_reference "PMID:30382198"

Added

• L6b glutamatergic cortical neuron definition "A glutamatergic neuron with a soma found in cortical layer 6b. They are transcriptomically related to corticothalamic-projecting neurons but have differential projections to the thalamus or anterior cingulate."

  • database_cross_reference "DOI:10.1101/2020.10.19.34312"

  • database_cross_reference "PMID:37824655"

  • database_cross_reference "PMID:30382198"

chandelier cell http://purl.obolibrary.org/obo/CL_4023083

Removed

• chandelier cell definition "A GABAergic interneuron that selectively innervates the axon initial segment of pyramidal cells. Their local axonal clusters are formed by high-frequency branching at shallow angles, often ramifying around, above or below their somata with a high bouton density. The characteristic terminal portions of the axon form short vertical rows of boutons, resembling the candlesticks and candles of a chandelier. Chandelier cells can be multipolar or bitufted."

  • database_cross_reference "PMID:15378039"

  • database_cross_reference "PMID:27199673"

Added

• chandelier cell definition "A GABAergic interneuron that selectively innervates the axon initial segment of pyramidal cells. Their local axonal clusters are formed by high-frequency branching at shallow angles, often ramifying around, above or below their somata with a high bouton density. The characteristic terminal portions of the axon form short vertical rows of boutons, resembling the candlesticks and candles of a chandelier. Chandelier cells can be multipolar or bitufted."

  • database_cross_reference "PMID:15378039"

  • database_cross_reference "PMID:37824655"

  • database_cross_reference "PMID:27199673"

fibrous astrocyte http://purl.obolibrary.org/obo/CL_4042008

Removed

• fibrous astrocyte definition "A cell type located in the first layer of the neocortex with radial protrusions extending transversely into the deeper cortex layers, herby facilitating communication across neurons, astrocytes, capillaries, meninges and cerebrospinal fluid through contact with neurons, pia mater and capillaries."

  • database_cross_reference "PMID:31435019"

  • database_cross_reference "PMID:34616062"

  • database_cross_reference "PMID:28280934"

  • database_cross_reference "PMID:19279265"

  • database_cross_reference "PMID:22144298"

Added

• fibrous astrocyte definition "A cell type located in the first layer of the neocortex with radial protrusions extending transversely into the deeper cortex layers, herby facilitating communication across neurons, astrocytes, capillaries, meninges and cerebrospinal fluid through contact with neurons, pia mater and capillaries."

  • database_cross_reference "PMID:31435019"

  • database_cross_reference "PMID:34616062"

  • database_cross_reference "PMID:37824655"

  • database_cross_reference "PMID:28280934"

  • database_cross_reference "PMID:19279265"

  • database_cross_reference "PMID:22144298"

lamp5 GABAergic cortical interneuron http://purl.obolibrary.org/obo/CL_4023011

Removed

• lamp5 GABAergic cortical interneuron definition "A GABAergic neuron located in the cerebral cortex that expresses Lamp5"
  • database_cross_reference "PMID:30382198"

Added

• lamp5 GABAergic cortical interneuron definition "A GABAergic neuron located in the cerebral cortex that expresses Lamp5"

  • database_cross_reference "PMID:37824655"

  • database_cross_reference "PMID:30382198"

pvalb GABAergic cortical interneuron http://purl.obolibrary.org/obo/CL_4023018

Removed

• pvalb GABAergic cortical interneuron definition "A GABAergic interneuron located in the cerebral cortex that expresses Parvalbumin."
  • database_cross_reference "PMID:27477017"

Added

• pvalb GABAergic cortical interneuron definition "A GABAergic interneuron located in the cerebral cortex that expresses Parvalbumin."

  • database_cross_reference "PMID:37824655"

  • database_cross_reference "PMID:27477017"

sncg GABAergic cortical interneuron http://purl.obolibrary.org/obo/CL_4023015

Removed

• sncg GABAergic cortical interneuron definition "A GABAergic neuron located in the cerebral cortex that expresses Gamma-synuclein"
  • database_cross_reference "PMID:33186530"

Added

• sncg GABAergic cortical interneuron definition "A GABAergic neuron located in the cerebral cortex that expresses Gamma-synuclein"

  • database_cross_reference "PMID:37824655"

  • database_cross_reference "PMID:33186530"

sst GABAergic cortical interneuron http://purl.obolibrary.org/obo/CL_4023017

Removed

• sst GABAergic cortical interneuron definition "A GABAergic neuron located in the cerebral cortex that expresses somatostatin (sst)"
  • database_cross_reference "PMID:27477017"

Added

• sst GABAergic cortical interneuron definition "A GABAergic neuron located in the cerebral cortex that expresses somatostatin (sst)"

  • database_cross_reference "PMID:37824655"

  • database_cross_reference "PMID:27477017"

sst chodl GABAergic cortical interneuron http://purl.obolibrary.org/obo/CL_4023121

Removed

• sst chodl GABAergic cortical interneuron definition "A sst GABAergic cortical interneuron that also expresses Chodl. These neurons are rare and correspond to the only known cortical interneurons with long-range projection."

  • database_cross_reference "PMID:33372656"

  • database_cross_reference "PMID:15845086"

  • database_cross_reference "PMID:31209381"

Added

• sst chodl GABAergic cortical interneuron definition "A sst GABAergic cortical interneuron that also expresses Chodl. These neurons are rare and correspond to the only known cortical interneurons with long-range projection."

  • database_cross_reference "PMID:33372656"

  • database_cross_reference "PMID:15845086"

  • database_cross_reference "PMID:37824655"

  • database_cross_reference "PMID:31209381"

vascular leptomeningeal cell http://purl.obolibrary.org/obo/CL_4023051

Removed

• vascular leptomeningeal cell definition "A type of mesothelial fibroblast that is derived from the neural crest, is localized on blood vessels, and is a key component of the pia and arachnoid membranes surrounding the brain."

  • database_cross_reference "PMID:27284195"

  • database_cross_reference "PMID:30096314"

  • database_cross_reference "PMID:29443965"

Added

• vascular leptomeningeal cell definition "A type of mesothelial fibroblast that is derived from the neural crest, is localized on blood vessels, and is a key component of the pia and arachnoid membranes surrounding the brain."

  • database_cross_reference "PMID:27284195"

  • database_cross_reference "PMID:30096314"

  • database_cross_reference "PMID:37824655"

  • database_cross_reference "PMID:29443965"

vip GABAergic cortical interneuron http://purl.obolibrary.org/obo/CL_4023016

Removed

• vip GABAergic cortical interneuron definition "A GABAergic neuron located in the cerebral cortex that expresses vasoactive intestinal polypeptide"
  • database_cross_reference "PMID:33186530"

Added

• vip GABAergic cortical interneuron definition "A GABAergic neuron located in the cerebral cortex that expresses vasoactive intestinal polypeptide"

  • database_cross_reference "PMID:37824655"

  • database_cross_reference "PMID:33186530"

[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

L2/3 intratelencephalic projecting glutamatergic neuron http://purl.obolibrary.org/obo/CL_4030059

Removed

• L2/3 intratelencephalic projecting glutamatergic neuron definition "An intratelencephalic-projecting glutamatergic neuron with a soma found in cortical layer 2/3."

  • database_cross_reference "PMID:37292694"

  • database_cross_reference "PMID:34004146"

Added

• L2/3 intratelencephalic projecting glutamatergic neuron definition "An intratelencephalic-projecting glutamatergic neuron with a soma found in cortical layer 2/3."

  • database_cross_reference "PMID:37292694"

  • database_cross_reference "PMID:37824655"

  • database_cross_reference "PMID:34004146"

L2/3 intratelencephalic projecting glutamatergic neuron of the primary motor cortex http://purl.obolibrary.org/obo/CL_4023047

Removed

• L2/3 intratelencephalic projecting glutamatergic neuron of the primary motor cortex has exact synonym "L2/3 IT MOp"

• L2/3 intratelencephalic projecting glutamatergic neuron of the primary motor cortex definition "An intratelencephalic-projecting glutamatergic neuron with a soma found in cortical layer 2/3 of the primary motor cortex."

  • database_cross_reference "DOI:10.1101/2020.10.19.343129"

• L2/3 intratelencephalic projecting glutamatergic neuron of the primary motor cortex has exact synonym "L2/3 IT M1"

Added

• L2/3 intratelencephalic projecting glutamatergic neuron of the primary motor cortex has exact synonym "L2/3 IT MOp"

  • database_cross_reference "PMID:34616075"

• L2/3 intratelencephalic projecting glutamatergic neuron of the primary motor cortex has exact synonym "L2/3 IT M1"

  • database_cross_reference "PMID:34616075"

• L2/3 intratelencephalic projecting glutamatergic neuron of the primary motor cortex definition "An intratelencephalic-projecting glutamatergic neuron with a soma found in cortical layer 2/3 of the primary motor cortex."

  • database_cross_reference "PMID:34616075"

L4 intratelencephalic projecting glutamatergic neuron http://purl.obolibrary.org/obo/CL_4030063

Removed

• L4 intratelencephalic projecting glutamatergic neuron definition "An intratelencephalic-projecting glutamatergic neuron with a soma found in cortical layer 4."
  • database_cross_reference "PMID:37292694"

Added

• L4 intratelencephalic projecting glutamatergic neuron definition "An intratelencephalic-projecting glutamatergic neuron with a soma found in cortical layer 4."

  • database_cross_reference "PMID:37292694"

  • database_cross_reference "PMID:37824655"

L5 extratelencephalic projecting glutamatergic cortical neuron http://purl.obolibrary.org/obo/CL_4023041

Removed

• L5 extratelencephalic projecting glutamatergic cortical neuron has exact synonym "Pyramidal tract-like (PT-l)"

  • database_cross_reference "DOI:10.1016/j.cell.2019.09.023"

  • comment "pyramidal tract-like is used because, unlike pyramidal tract neurons in the motor cortex, neurons in the structures like the auditory cortex do not project to the spinal cord."

• L5 extratelencephalic projecting glutamatergic cortical neuron definition "A glutamatergic neuron, with a soma found in the deeper portion of L5, that has long-range axonal projections including deep subcortical targets outside of the telencephalon and, in some cases, the spinal cord. While the L5 ET neuron projections are not limited to ET targets, they are clearly differentiated from the neuron subclasses whose projections are constrained to intratelencephalic (IT) targets. L5 ET neurons are generally the largest excitatory cortical neurons, typically having a thick apical dendrite with a prominent dendritic tuft in layer 1 and displaying burst-firing physiological characteristics."

  • database_cross_reference "DOI:10.1101/2020.10.19.343129"

Added

• L5 extratelencephalic projecting glutamatergic cortical neuron has exact synonym "Pyramidal tract-like (PT-l)"

  • comment "pyramidal tract-like is used because, unlike pyramidal tract neurons in the motor cortex, neurons in the structures like the auditory cortex do not project to the spinal cord."

  • database_cross_reference "PMID:31626774"

• L5 extratelencephalic projecting glutamatergic cortical neuron definition "A glutamatergic neuron, with a soma found in the deeper portion of L5, that has long-range axonal projections including deep subcortical targets outside of the telencephalon and, in some cases, the spinal cord. While the L5 ET neuron projections are not limited to ET targets, they are clearly differentiated from the neuron subclasses whose projections are constrained to intratelencephalic (IT) targets. L5 ET neurons are generally the largest excitatory cortical neurons, typically having a thick apical dendrite with a prominent dendritic tuft in layer 1 and displaying burst-firing physiological characteristics."

  • database_cross_reference "PMID:34616075"

  • database_cross_reference "PMID:37824655"

L5 intratelencephalic projecting glutamatergic neuron http://purl.obolibrary.org/obo/CL_4030064

Removed

• L5 intratelencephalic projecting glutamatergic neuron definition "An intratelencephalic-projecting glutamatergic neuron with a soma found in cortical layer 5."

  • database_cross_reference "PMID:37609206"

  • database_cross_reference "PMID:37292694"

Added

• L5 intratelencephalic projecting glutamatergic neuron definition "An intratelencephalic-projecting glutamatergic neuron with a soma found in cortical layer 5."

  • database_cross_reference "PMID:37609206"

  • database_cross_reference "PMID:37292694"

  • database_cross_reference "PMID:37824655"

L5/6 near-projecting glutamatergic neuron http://purl.obolibrary.org/obo/CL_4030067

Removed

• L5/6 near-projecting glutamatergic neuron definition "A near-projecting glutamatergic neuron with a soma found in cortical layer 5/6."

  • database_cross_reference "PMID:37292694"

  • database_cross_reference "PMID:34004146"

Added

• L5/6 near-projecting glutamatergic neuron definition "A near-projecting glutamatergic neuron with a soma found in cortical layer 5/6."

  • database_cross_reference "PMID:37292694"

  • database_cross_reference "PMID:37824655"

  • database_cross_reference "PMID:34004146"

L5/6 near-projecting glutamatergic neuron of the primary motor cortex http://purl.obolibrary.org/obo/CL_4023043

Removed

• L5/6 near-projecting glutamatergic neuron of the primary motor cortex definition "A near-projecting glutamatergic neuron with a soma found in layer 5/6 of the primary motor cortex."

  • database_cross_reference "DOI:10.1101/2020.10.19.343129"

  • database_cross_reference "PMID:31209381"

Added

• L5/6 near-projecting glutamatergic neuron of the primary motor cortex definition "A near-projecting glutamatergic neuron with a soma found in layer 5/6 of the primary motor cortex."

  • database_cross_reference "PMID:34616075"

  • database_cross_reference "PMID:31209381"

L6 corticothalamic-projecting glutamatergic cortical neuron http://purl.obolibrary.org/obo/CL_4023042

Removed

• L6 corticothalamic-projecting glutamatergic cortical neuron has exact synonym "L6 CT"

• L6 corticothalamic-projecting glutamatergic cortical neuron definition "A corticothalamic-projecting neuron with a soma found in cortical layer 6."

  • database_cross_reference "DOI:10.1101/2020.10.19.343129"

Added

• L6 corticothalamic-projecting glutamatergic cortical neuron has exact synonym "L6 CT"

  • database_cross_reference "PMID:34616075"

  • database_cross_reference "PMID:28625486"

• L6 corticothalamic-projecting glutamatergic cortical neuron definition "A corticothalamic-projecting neuron with a soma found in cortical layer 6."

  • database_cross_reference "PMID:34616075"

  • database_cross_reference "PMID:37824655"

L6 intratelencephalic projecting Car3 glutamatergic neuron http://purl.obolibrary.org/obo/CL_4030068

Removed

• L6 intratelencephalic projecting Car3 glutamatergic neuron definition "An intratelencephalic-projecting glutamatergic neuron with a soma found in cortical layer 6 that expresses Car3."

  • database_cross_reference "doi:10.1016/j.cell.2021.04.021"

  • database_cross_reference "doi:10.1101/2022.11.06.515349"

  • database_cross_reference "doi:10.1101/2022.11.30.518285"

Added

• L6 intratelencephalic projecting Car3 glutamatergic neuron definition "An intratelencephalic-projecting glutamatergic neuron with a soma found in cortical layer 6 that expresses Car3."

  • database_cross_reference "PMID:37824655"

  • database_cross_reference "doi:10.1101/2022.11.30.518285"

  • database_cross_reference "PMID:34004146"

L6 intratelencephalic projecting glutamatergic neuron http://purl.obolibrary.org/obo/CL_4030065

Removed

• L6 intratelencephalic projecting glutamatergic neuron definition "An intratelencephalic-projecting glutamatergic neuron with a soma found in cortical layer 6."

  • database_cross_reference "PMID:37609206"

  • database_cross_reference "PMID:37292694"

Added

• L6 intratelencephalic projecting glutamatergic neuron definition "An intratelencephalic-projecting glutamatergic neuron with a soma found in cortical layer 6."

  • database_cross_reference "PMID:37609206"

  • database_cross_reference "PMID:37292694"

  • database_cross_reference "PMID:37824655"

L6b glutamatergic cortical neuron http://purl.obolibrary.org/obo/CL_4023038

Removed

• L6b glutamatergic cortical neuron definition "A glutamatergic neuron with a soma found in cortical layer 6b. They are transcriptomically related to corticothalamic-projecting neurons but have differential projections to the thalamus or anterior cingulate."

  • database_cross_reference "DOI:10.1101/2020.10.19.34312"

  • database_cross_reference "PMID:30382198"

Added

• L6b glutamatergic cortical neuron definition "A glutamatergic neuron with a soma found in cortical layer 6b. They are transcriptomically related to corticothalamic-projecting neurons but have differential projections to the thalamus or anterior cingulate."

  • database_cross_reference "DOI:10.1101/2020.10.19.34312"

  • database_cross_reference "PMID:37824655"

  • database_cross_reference "PMID:30382198"

chandelier cell http://purl.obolibrary.org/obo/CL_4023083

Removed

• chandelier cell definition "A GABAergic interneuron that selectively innervates the axon initial segment of pyramidal cells. Their local axonal clusters are formed by high-frequency branching at shallow angles, often ramifying around, above or below their somata with a high bouton density. The characteristic terminal portions of the axon form short vertical rows of boutons, resembling the candlesticks and candles of a chandelier. Chandelier cells can be multipolar or bitufted."

  • database_cross_reference "PMID:15378039"

  • database_cross_reference "PMID:27199673"

Added

• chandelier cell definition "A GABAergic interneuron that selectively innervates the axon initial segment of pyramidal cells. Their local axonal clusters are formed by high-frequency branching at shallow angles, often ramifying around, above or below their somata with a high bouton density. The characteristic terminal portions of the axon form short vertical rows of boutons, resembling the candlesticks and candles of a chandelier. Chandelier cells can be multipolar or bitufted."

  • database_cross_reference "PMID:15378039"

  • database_cross_reference "PMID:37824655"

  • database_cross_reference "PMID:27199673"

fibrous astrocyte http://purl.obolibrary.org/obo/CL_4042008

Removed

• fibrous astrocyte definition "A cell type located in the first layer of the neocortex with radial protrusions extending transversely into the deeper cortex layers, herby facilitating communication across neurons, astrocytes, capillaries, meninges and cerebrospinal fluid through contact with neurons, pia mater and capillaries."

  • database_cross_reference "PMID:31435019"

  • database_cross_reference "PMID:34616062"

  • database_cross_reference "PMID:28280934"

  • database_cross_reference "PMID:19279265"

  • database_cross_reference "PMID:22144298"

Added

• fibrous astrocyte definition "A cell type located in the first layer of the neocortex with radial protrusions extending transversely into the deeper cortex layers, herby facilitating communication across neurons, astrocytes, capillaries, meninges and cerebrospinal fluid through contact with neurons, pia mater and capillaries."

  • database_cross_reference "PMID:31435019"

  • database_cross_reference "PMID:34616062"

  • database_cross_reference "PMID:37824655"

  • database_cross_reference "PMID:28280934"

  • database_cross_reference "PMID:19279265"

  • database_cross_reference "PMID:22144298"

lamp5 GABAergic cortical interneuron http://purl.obolibrary.org/obo/CL_4023011

Removed

• lamp5 GABAergic cortical interneuron definition "A GABAergic neuron located in the cerebral cortex that expresses Lamp5"
  • database_cross_reference "PMID:30382198"

Added

• lamp5 GABAergic cortical interneuron definition "A GABAergic neuron located in the cerebral cortex that expresses Lamp5"

  • database_cross_reference "PMID:37824655"

  • database_cross_reference "PMID:30382198"

pvalb GABAergic cortical interneuron http://purl.obolibrary.org/obo/CL_4023018

Removed

• pvalb GABAergic cortical interneuron definition "A GABAergic interneuron located in the cerebral cortex that expresses Parvalbumin."
  • database_cross_reference "PMID:27477017"

Added

• pvalb GABAergic cortical interneuron definition "A GABAergic interneuron located in the cerebral cortex that expresses Parvalbumin."

  • database_cross_reference "PMID:37824655"

  • database_cross_reference "PMID:27477017"

sncg GABAergic cortical interneuron http://purl.obolibrary.org/obo/CL_4023015

Removed

• sncg GABAergic cortical interneuron definition "A GABAergic neuron located in the cerebral cortex that expresses Gamma-synuclein"
  • database_cross_reference "PMID:33186530"

Added

• sncg GABAergic cortical interneuron definition "A GABAergic neuron located in the cerebral cortex that expresses Gamma-synuclein"

  • database_cross_reference "PMID:37824655"

  • database_cross_reference "PMID:33186530"

sst GABAergic cortical interneuron http://purl.obolibrary.org/obo/CL_4023017

Removed

• sst GABAergic cortical interneuron definition "A GABAergic neuron located in the cerebral cortex that expresses somatostatin (sst)"
  • database_cross_reference "PMID:27477017"

Added

• sst GABAergic cortical interneuron definition "A GABAergic neuron located in the cerebral cortex that expresses somatostatin (sst)"

  • database_cross_reference "PMID:37824655"

  • database_cross_reference "PMID:27477017"

sst chodl GABAergic cortical interneuron http://purl.obolibrary.org/obo/CL_4023121

Removed

• sst chodl GABAergic cortical interneuron definition "A sst GABAergic cortical interneuron that also expresses Chodl. These neurons are rare and correspond to the only known cortical interneurons with long-range projection."

  • database_cross_reference "PMID:33372656"

  • database_cross_reference "PMID:15845086"

  • database_cross_reference "PMID:31209381"

Added

• sst chodl GABAergic cortical interneuron definition "A sst GABAergic cortical interneuron that also expresses Chodl. These neurons are rare and correspond to the only known cortical interneurons with long-range projection."

  • database_cross_reference "PMID:33372656"

  • database_cross_reference "PMID:15845086"

  • database_cross_reference "PMID:37824655"

  • database_cross_reference "PMID:31209381"

vascular leptomeningeal cell http://purl.obolibrary.org/obo/CL_4023051

Removed

• vascular leptomeningeal cell definition "A type of mesothelial fibroblast that is derived from the neural crest, is localized on blood vessels, and is a key component of the pia and arachnoid membranes surrounding the brain."

  • database_cross_reference "PMID:27284195"

  • database_cross_reference "PMID:30096314"

  • database_cross_reference "PMID:29443965"

Added

• vascular leptomeningeal cell definition "A type of mesothelial fibroblast that is derived from the neural crest, is localized on blood vessels, and is a key component of the pia and arachnoid membranes surrounding the brain."

  • database_cross_reference "PMID:27284195"

  • database_cross_reference "PMID:30096314"

  • database_cross_reference "PMID:37824655"

  • database_cross_reference "PMID:29443965"

vip GABAergic cortical interneuron http://purl.obolibrary.org/obo/CL_4023016

Removed

• vip GABAergic cortical interneuron definition "A GABAergic neuron located in the cerebral cortex that expresses vasoactive intestinal polypeptide"
  • database_cross_reference "PMID:33186530"

Added

• vip GABAergic cortical interneuron definition "A GABAergic neuron located in the cerebral cortex that expresses vasoactive intestinal polypeptide"

  • database_cross_reference "PMID:37824655"

  • database_cross_reference "PMID:33186530"

[aleixpuigb]

It looks good. To keep track of all changes, can you edit the first comment of the PR to include this, please?

• Adds Jorstad paper as a reference to cortical neurons.
• Substitutes references doi ID for PMID:
  • doi:10.1016/j.cell.2021.04.021 → PMID:34004146
  • doi:10.1101/2022.11.06.515349 → PMID:37824655