Text def Purkinje neuron

[AvolaAmg]

Fixes #2176

• Expand text definition and references
• Expand the comment section and references
• Add synonyms and references

[JABelfiore]

Suggest text amends to the following:
An inhibitory neuron and the sole output neuron of the cerebellar cortex, the Purkinje cell's soma is located between the granular and molecular layers of the cerebellum. It is one of the largest neural cells in the mammalian brain, ranging from 50 to 80 micrometres in diameter. Purkinje cells have planar, fan-shaped dendrites that branch extensively with little overlap. This cell type receives synaptic input from parallel fibres, which modulate high-frequency spike activity known as "simple spikes," and climbing fibres, which modulate infrequent calcium spike activity known as "complex spikes". Purkinje cells are involved in motor coordination, particularly in correcting movements in progress."

Looks good! just minor grammatical changes :)

[AvolaAmg]

Thank you @JABelfiore for your review, I will apply the changes. Could you also check the content (references, synonyms etc)? I will ask you to re-review after I change the body of text!

[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/2024-07-18/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/2024-07-18/cl-simple.owl
• Loaded from: file:/__w/cell-ontology/cell-ontology/src/ontology/cl-simple-pr.owl/cl-simple.owl

Ontology imports

Ontology annotations

Purkinje cell http://purl.obolibrary.org/obo/CL_0000121

Removed

• Purkinje cell has exact synonym "cerebellum Purkinje cell"

• Purkinje cell has exact synonym "Purkinje's cell"

• Purkinje cell definition "The output neuron of the cerebellar cortex."

  • database_cross_reference "MESH:D011689"

• Purkinje cell has exact synonym "cerebellar Purkinje cell"

• Purkinje cell has exact synonym "Purkinje neuron"

Added

• Purkinje cell has exact synonym "cerebellar Purkinje cell"

  • database_cross_reference "https://doi.org/10.1016/j.proghi.2004.07.002"

• Purkinje cell definition "An inhibitory neuron and the sole output neuron of the cerebellar cortex, the Purkinje cell's soma is located between the granular and molecular layers of the cerebellum. It is one of the largest neural cells in the mammalian brain, ranging from 50 to 80 micrometres in diameter. Purkinje cells have planar, fan-shaped dendrites that branch extensively with little overlap. This cell type receives synaptic input from parallel fibres, which modulate high-frequency spike activity known as "simple spikes," and climbing fibres, which modulate infrequent calcium spike activity known as "complex spikes". Purkinje cells are involved in motor coordination, particularly in correcting movements in progress."

  • database_cross_reference "PMID:33288911"

  • database_cross_reference "PMID:38168772"

  • database_cross_reference "MESH:D011689"

  • database_cross_reference "PMID:14568361"

  • database_cross_reference "PMID:12907269"

  • database_cross_reference "PMID:31424738"

• Purkinje cell comment "Neurodegenerative disorders affecting Purkinje cells disrupt motor functions. Some of the neurodegenerative disorders that causes loss and degeration of Purkinje cells are Spinocerebellar ataxias (SCAs) (Josef P Kapfhammer and Etsuko Shimobayashi 2023), Friedreich's ataxia (FRDA) (Kevin C Kemp et al., 2016), Fetal alcohol syndrome (Laurent Servais et al., 2016), Dandy-Walker malformation (Alexander Atamian et al., 2024)."

  • database_cross_reference "PMID:37426070"

  • database_cross_reference "https://doi.org/10.1016/j.stem.2023.11.013"

  • database_cross_reference "PMID:27215193"

  • database_cross_reference "PMID:17535929"

• Purkinje cell has exact synonym "PC"

  • database_cross_reference "PMID:38168772"

  • has_synonym_type abbreviation

• Purkinje cell has exact synonym "Purkinje neuron"

  • database_cross_reference "PMID:28821816"

• Purkinje cell has exact synonym "PN"

  • has_synonym_type abbreviation

  • database_cross_reference "PMID:28821816"

[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

Purkinje cell http://purl.obolibrary.org/obo/CL_0000121

Removed

• Purkinje cell has exact synonym "cerebellum Purkinje cell"

• Purkinje cell has exact synonym "Purkinje's cell"

• Purkinje cell definition "The output neuron of the cerebellar cortex."

  • database_cross_reference "MESH:D011689"

• Purkinje cell has exact synonym "cerebellar Purkinje cell"

• Purkinje cell has exact synonym "Purkinje neuron"

Added

• Purkinje cell has exact synonym "cerebellar Purkinje cell"

  • database_cross_reference "https://doi.org/10.1016/j.proghi.2004.07.002"

• Purkinje cell definition "An inhibitory neuron and the sole output neuron of the cerebellar cortex, the Purkinje cell's soma is located between the granular and molecular layers of the cerebellum. It is one of the largest neural cells in the mammalian brain, ranging from 50 to 80 micrometres in diameter. Purkinje cells have planar, fan-shaped dendrites that branch extensively with little overlap. This cell type receives synaptic input from parallel fibres, which modulate high-frequency spike activity known as "simple spikes," and climbing fibres, which modulate infrequent calcium spike activity known as "complex spikes". Purkinje cells are involved in motor coordination, particularly in correcting movements in progress."

  • database_cross_reference "PMID:33288911"

  • database_cross_reference "PMID:38168772"

  • database_cross_reference "MESH:D011689"

  • database_cross_reference "PMID:14568361"

  • database_cross_reference "PMID:12907269"

  • database_cross_reference "PMID:31424738"

• Purkinje cell comment "Neurodegenerative disorders affecting Purkinje cells disrupt motor functions. Some of the neurodegenerative disorders that causes loss and degeration of Purkinje cells are Spinocerebellar ataxias (SCAs) (Josef P Kapfhammer and Etsuko Shimobayashi 2023), Friedreich's ataxia (FRDA) (Kevin C Kemp et al., 2016), Fetal alcohol syndrome (Laurent Servais et al., 2016), Dandy-Walker malformation (Alexander Atamian et al., 2024)."

  • database_cross_reference "PMID:37426070"

  • database_cross_reference "https://doi.org/10.1016/j.stem.2023.11.013"

  • database_cross_reference "PMID:27215193"

  • database_cross_reference "PMID:17535929"

• Purkinje cell has exact synonym "PC"

  • database_cross_reference "PMID:38168772"

  • has_synonym_type abbreviation

• Purkinje cell has exact synonym "Purkinje neuron"

  • database_cross_reference "PMID:28821816"

• Purkinje cell has exact synonym "PN"

  • has_synonym_type abbreviation

  • database_cross_reference "PMID:28821816"

[JABelfiore]

Definition references

Definition references are all great, all claims in the statement are covered by references :)

PMID:12907269 - confirms cell size, confirms complex spikes and calcium involvement

PMID:14568361 - confirms cell location, confirms dendrite shape and branching

PMID:31424738 - confirms sole output neurons of the cerebellar cortex, confirms spike modulation and definitions of simple and complex spikes

PMID:33288911 - confirms cell location, confirms spike modulation, confirms involvement in movement success

PMID:38168772 - confirms dendrite shape, confirms spike modulation

Comment text

Comment text looks great, just slightly altered wording of the second sentence slightly. Changed fetal (US English) to foetal (UK English)(even though I know the paper you are referencing is US spelling!)

Suggested comment amend:

Neurodegenerative disorders affecting Purkinje cells disrupt motor functions. Neurodegenerative disorders that causes loss and degeneration of Purkinje cells include: spinocerebellar ataxias (SCAs) (Josef P Kapfhammer and Etsuko Shimobayashi, 2023), Friedreich's ataxia (FRDA) (Kevin C Kemp et al., 2016), foetal alcohol syndrome (Laurent Servais et al., 2016), and Dandy-Walker malformation (Alexander Atamian et al., 2024).

Comment references

Comment references are all great, all claims in the statement are covered by references :)

PMID:17535929 - confirms FAS, confirms disrupts motor functions, confirms contributes to ataxia

PMID:27215193 - confirms FRDA

PMID:37426070 - confirms SCAs

https://doi.org/10.1016/j.stem.2023.11.013 - confirms dandy-walker malformation

Synonym references

Synonym references are all correct :)

PMID:38168772 hasExactSynonym "PC" - confirms synonym

PMID:28821816 hasExactSynonym "PN"- confirms synonym

PMID:28821816 "Purkinje neuron"- confirms synonym

https://doi.org/10.1016/j.proghi.2004.07.002 "cerebellar Purkinje cell" - confirms synonym

[aleixpuigb]

Acronyms are related synonyms and should have the annotation property 'abbreviation' (this is included).
CL uses US english, please use the US english version 'fetal'.

[AvolaAmg]

Hi there, thanks for the reviews!!
I am sticking with fetal, also the 'abbreviation' as an annotation property is present.