Addresses #2154 [NTR-cxg] cortical region-agnostic L2/3-6 intratelencephalic projecting glutamatergic cortical neuron (by layer)

[ghost]

Addresses #2154 [NTR] cortical region-agnostic L2/3-6 intratelencephalic projecting glutamatergic cortical neuron (by layer)

#gogoeditdiff

[ghost]

@anitacaron, any advice on why this is failing QC?

fastobo-validator cl-check.obo
     Parsing `cl-check.obo`
      Failed parsing `cl-check.obo`
             --> cl-check.obo:31176:10
              |
        31176 | xref: An intratelencephalic-projecting glutamatergic neuron with a soma found in cortical layer 5. {xref="PMID:37292694", xref="PMID:37609206"}␊
              |          ^---
              |
              = expected EOL or QuotedString
make: *** [cl.Makefile:190: obocheck] Error 1

[anitacaron]

I checked on Protégé, and you're using database_cross_reference instead of definition annotation 😃
The two new terms with issue are CL:4030064 and CL:4030065.

[ghost]

I checked on Protégé, and you're using database_cross_reference instead of definition annotation 😃

Thank you for spotting that!

[ghost]

#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/2023-10-13/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/2023-10-13/cl-simple.owl
• Loaded from: file:/__w/cell-ontology/cell-ontology/src/ontology/cl-simple-pr.owl/cl-simple.owl

Ontology imports

Ontology annotations

CL_4030059 http://purl.obolibrary.org/obo/CL_4030059

Added

• CL_4030059 date "2023-10-10T14:10:21Z"^^dateTime

• CL_4030059 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"

• CL_4030059 has_related_synonym "L2/3 IT"

  • has_synonym_type abbreviation

  • database_cross_reference "PMID:34004146"

• CL_4030059 label "L2/3 intratelencephalic projecting glutamatergic neuron"

• CL_4030059 contributor 0000-0003-4389-9821

• Class: CL_4030059

• CL_4030059 SubClassOf L2/3-6 intratelencephalic projecting glutamatergic neuron

CL_4030060 http://purl.obolibrary.org/obo/CL_4030060

Added

• CL_4030060 definition "An intratelencephalic-projecting glutamatergic neuron with a soma found in cortical layer 2."

  • database_cross_reference "PMID:34004146"

• CL_4030060 date "2023-10-10T14:10:36Z"^^dateTime

• CL_4030060 label "L2 intratelencephalic projecting glutamatergic neuron"

• CL_4030060 contributor 0000-0003-4389-9821

• CL_4030060 has_related_synonym "L2 IT"

  • has_synonym_type abbreviation

  • database_cross_reference "PMID:34004146"

• Class: CL_4030060

• CL_4030060 SubClassOf L2/3-6 intratelencephalic projecting glutamatergic neuron

CL_4030061 http://purl.obolibrary.org/obo/CL_4030061

Added

• CL_4030061 label "L3 intratelencephalic projecting glutamatergic neuron"

• CL_4030061 contributor 0000-0003-4389-9821

• CL_4030061 has_related_synonym "L3 IT"

  • has_synonym_type abbreviation

  • database_cross_reference "PMID:34004146"

• CL_4030061 definition "An intratelencephalic-projecting glutamatergic neuron with a soma found in cortical layer 3."

  • database_cross_reference "PMID:34004146"

• CL_4030061 date "2023-10-10T14:10:47Z"^^dateTime

• Class: CL_4030061

• CL_4030061 SubClassOf L2/3-6 intratelencephalic projecting glutamatergic neuron

CL_4030062 http://purl.obolibrary.org/obo/CL_4030062

Added

• CL_4030062 has_related_synonym "L4/5 IT"

  • has_synonym_type abbreviation

  • database_cross_reference "PMID:34004146"

• CL_4030062 contributor 0000-0003-4389-9821

• CL_4030062 date "2023-10-10T14:11:04Z"^^dateTime

• CL_4030062 label "L4/5 intratelencephalic projecting glutamatergic neuron"

• CL_4030062 definition "An intratelencephalic-projecting glutamatergic with a soma located in cortical layer 4/5."

  • database_cross_reference "PMID:34004146"

• Class: CL_4030062

• CL_4030062 SubClassOf L2/3-6 intratelencephalic projecting glutamatergic neuron

CL_4030063 http://purl.obolibrary.org/obo/CL_4030063

Added

• CL_4030063 label "L4 intratelencephalic projecting glutamatergic neuron"

• CL_4030063 date "2023-10-10T14:11:25Z"^^dateTime

• CL_4030063 contributor 0000-0003-4389-9821

• CL_4030063 definition "An intratelencephalic-projecting glutamatergic neuron with a soma found in cortical layer 4."

  • database_cross_reference "PMID:37292694"

• CL_4030063 has_related_synonym "L4 IT"

  • database_cross_reference "PMID:37292694"

  • has_synonym_type abbreviation

• Class: CL_4030063

• CL_4030063 SubClassOf L2/3-6 intratelencephalic projecting glutamatergic neuron

CL_4030064 http://purl.obolibrary.org/obo/CL_4030064

Added

• CL_4030064 date "2023-10-10T14:11:59Z"^^dateTime

• CL_4030064 label "L5 intratelencephalic projecting glutamatergic neuron"

• CL_4030064 has_related_synonym "L5 IT"

  • synonym_type_property abbreviation

  • database_cross_reference "PMID:37292694"

• CL_4030064 contributor 0000-0003-4389-9821

• CL_4030064 definition "An intratelencephalic-projecting glutamatergic neuron with a soma found in cortical layer 5."

  • database_cross_reference "PMID:37609206"

  • database_cross_reference "PMID:37292694"

• Class: CL_4030064

• CL_4030064 SubClassOf L2/3-6 intratelencephalic projecting glutamatergic neuron

CL_4030065 http://purl.obolibrary.org/obo/CL_4030065

Added

• CL_4030065 definition "An intratelencephalic-projecting glutamatergic neuron with a soma found in cortical layer 6."

  • database_cross_reference "PMID:37609206"

  • database_cross_reference "PMID:37292694"

• CL_4030065 date "2023-10-10T14:12:23Z"^^dateTime

• CL_4030065 contributor 0000-0003-4389-9821

• CL_4030065 has_related_synonym "L6 IT"

  • database_cross_reference "PMID:37292694"

  • has_synonym_type abbreviation

• CL_4030065 label "L6 intratelencephalic projecting glutamatergic neuron"

• Class: CL_4030065

• CL_4030065 SubClassOf L2/3-6 intratelencephalic projecting glutamatergic neuron

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 SubClassOf L2/3-6 intratelencephalic projecting glutamatergic neuron

Added

• L2/3 intratelencephalic projecting glutamatergic neuron of the primary motor cortex SubClassOf CL_4030059

L4/5 intratelencephalic projecting glutamatergic neuron of the primary motor cortex http://purl.obolibrary.org/obo/CL_4023048

Removed

• L4/5 intratelencephalic projecting glutamatergic neuron of the primary motor cortex SubClassOf L2/3-6 intratelencephalic projecting glutamatergic neuron

Added

• L4/5 intratelencephalic projecting glutamatergic neuron of the primary motor cortex SubClassOf CL_4030062

L5 intratelencephalic projecting glutamatergic neuron of the primary motor cortex http://purl.obolibrary.org/obo/CL_4023049

Removed

• L5 intratelencephalic projecting glutamatergic neuron of the primary motor cortex SubClassOf L2/3-6 intratelencephalic projecting glutamatergic neuron

Added

• L5 intratelencephalic projecting glutamatergic neuron of the primary motor cortex SubClassOf CL_4030064

L6 intratelencephalic projecting glutamatergic neuron of the primary motor cortex http://purl.obolibrary.org/obo/CL_4023050

Removed

• L6 intratelencephalic projecting glutamatergic neuron of the primary motor cortex SubClassOf L2/3-6 intratelencephalic projecting glutamatergic neuron

Added

• L6 intratelencephalic projecting glutamatergic neuron of the primary motor cortex SubClassOf CL_4030065

[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

CL_4030059 http://purl.obolibrary.org/obo/CL_4030059

Added

• CL_4030059 date "2023-10-10T14:10:21Z"^^dateTime

• CL_4030059 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"

• CL_4030059 has_related_synonym "L2/3 IT"

  • has_synonym_type abbreviation

  • database_cross_reference "PMID:34004146"

• CL_4030059 label "L2/3 intratelencephalic projecting glutamatergic neuron"

• CL_4030059 contributor 0000-0003-4389-9821

• Class: CL_4030059

• CL_4030059 EquivalentTo L2/3-6 intratelencephalic projecting glutamatergic neuron and (has soma location some cortical layer II/III)

CL_4030060 http://purl.obolibrary.org/obo/CL_4030060

Added

• CL_4030060 has_related_synonym "L2 IT"

  • has_synonym_type abbreviation

  • database_cross_reference "PMID:34004146"

• CL_4030060 definition "An intratelencephalic-projecting glutamatergic neuron with a soma found in cortical layer 2."

  • database_cross_reference "PMID:34004146"

• CL_4030060 date "2023-10-10T14:10:36Z"^^dateTime

• CL_4030060 label "L2 intratelencephalic projecting glutamatergic neuron"

• CL_4030060 contributor 0000-0003-4389-9821

• Class: CL_4030060

• CL_4030060 EquivalentTo L2/3-6 intratelencephalic projecting glutamatergic neuron and (has soma location some cortical layer II)

CL_4030061 http://purl.obolibrary.org/obo/CL_4030061

Added

• CL_4030061 label "L3 intratelencephalic projecting glutamatergic neuron"

• CL_4030061 contributor 0000-0003-4389-9821

• CL_4030061 has_related_synonym "L3 IT"

  • has_synonym_type abbreviation

  • database_cross_reference "PMID:34004146"

• CL_4030061 definition "An intratelencephalic-projecting glutamatergic neuron with a soma found in cortical layer 3."

  • database_cross_reference "PMID:34004146"

• CL_4030061 date "2023-10-10T14:10:47Z"^^dateTime

• Class: CL_4030061

• CL_4030061 EquivalentTo L2/3-6 intratelencephalic projecting glutamatergic neuron and (has soma location some cortical layer III)

CL_4030062 http://purl.obolibrary.org/obo/CL_4030062

Added

• CL_4030062 contributor 0000-0003-4389-9821

• CL_4030062 date "2023-10-10T14:11:04Z"^^dateTime

• CL_4030062 label "L4/5 intratelencephalic projecting glutamatergic neuron"

• CL_4030062 definition "An intratelencephalic-projecting glutamatergic with a soma located in cortical layer 4/5."

  • database_cross_reference "PMID:34004146"

• CL_4030062 has_related_synonym "L4/5 IT"

  • has_synonym_type abbreviation

  • database_cross_reference "PMID:34004146"

• Class: CL_4030062

• CL_4030062 EquivalentTo L2/3-6 intratelencephalic projecting glutamatergic neuron and (has soma location some cortical layer IV/V)

CL_4030063 http://purl.obolibrary.org/obo/CL_4030063

Added

• CL_4030063 label "L4 intratelencephalic projecting glutamatergic neuron"

• CL_4030063 date "2023-10-10T14:11:25Z"^^dateTime

• CL_4030063 definition "An intratelencephalic-projecting glutamatergic neuron with a soma found in cortical layer 4."

  • database_cross_reference "PMID:37292694"

• CL_4030063 has_related_synonym "L4 IT"

  • database_cross_reference "PMID:37292694"

  • has_synonym_type abbreviation

• CL_4030063 contributor 0000-0003-4389-9821

• Class: CL_4030063

• CL_4030063 EquivalentTo L2/3-6 intratelencephalic projecting glutamatergic neuron and (has soma location some cortical layer IV)

CL_4030064 http://purl.obolibrary.org/obo/CL_4030064

Added

• CL_4030064 date "2023-10-10T14:11:59Z"^^dateTime

• CL_4030064 label "L5 intratelencephalic projecting glutamatergic neuron"

• CL_4030064 has_related_synonym "L5 IT"

  • synonym_type_property abbreviation

  • database_cross_reference "PMID:37292694"

• CL_4030064 contributor 0000-0003-4389-9821

• CL_4030064 definition "An intratelencephalic-projecting glutamatergic neuron with a soma found in cortical layer 5."

  • database_cross_reference "PMID:37609206"

  • database_cross_reference "PMID:37292694"

• Class: CL_4030064

• CL_4030064 EquivalentTo L2/3-6 intratelencephalic projecting glutamatergic neuron and (has soma location some cortical layer V)

CL_4030065 http://purl.obolibrary.org/obo/CL_4030065

Added

• CL_4030065 definition "An intratelencephalic-projecting glutamatergic neuron with a soma found in cortical layer 6."

  • database_cross_reference "PMID:37609206"

  • database_cross_reference "PMID:37292694"

• CL_4030065 label "L6 intratelencephalic projecting glutamatergic neuron"

• CL_4030065 date "2023-10-10T14:12:23Z"^^dateTime

• CL_4030065 contributor 0000-0003-4389-9821

• CL_4030065 has_related_synonym "L6 IT"

  • database_cross_reference "PMID:37292694"

  • has_synonym_type abbreviation

• Class: CL_4030065

• CL_4030065 EquivalentTo L2/3-6 intratelencephalic projecting glutamatergic neuron and (has soma location some cortical layer VI)

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 EquivalentTo L2/3-6 intratelencephalic projecting glutamatergic neuron and (has soma location some primary motor cortex) and (has soma location some cortical layer II/III)

Added

• L2/3 intratelencephalic projecting glutamatergic neuron of the primary motor cortex EquivalentTo CL_4030059 and (has soma location some primary motor cortex)

L4/5 intratelencephalic projecting glutamatergic neuron of the primary motor cortex http://purl.obolibrary.org/obo/CL_4023048

Removed

• L4/5 intratelencephalic projecting glutamatergic neuron of the primary motor cortex EquivalentTo L2/3-6 intratelencephalic projecting glutamatergic neuron and (has soma location some primary motor cortex) and (has soma location some cortical layer IV/V)

Added

• L4/5 intratelencephalic projecting glutamatergic neuron of the primary motor cortex EquivalentTo CL_4030062 and (has soma location some primary motor cortex)

L5 intratelencephalic projecting glutamatergic neuron of the primary motor cortex http://purl.obolibrary.org/obo/CL_4023049

Removed

• L5 intratelencephalic projecting glutamatergic neuron of the primary motor cortex EquivalentTo L2/3-6 intratelencephalic projecting glutamatergic neuron and (has soma location some primary motor cortex) and (has soma location some cortical layer V)

Added

• L5 intratelencephalic projecting glutamatergic neuron of the primary motor cortex EquivalentTo CL_4030064 and (has soma location some primary motor cortex)

L6 intratelencephalic projecting glutamatergic neuron of the primary motor cortex http://purl.obolibrary.org/obo/CL_4023050

Removed

• L6 intratelencephalic projecting glutamatergic neuron of the primary motor cortex EquivalentTo L2/3-6 intratelencephalic projecting glutamatergic neuron and (has soma location some primary motor cortex) and (has soma location some cortical layer VI)

Added

• L6 intratelencephalic projecting glutamatergic neuron of the primary motor cortex EquivalentTo CL_4030065 and (has soma location some primary motor cortex)

[aleixpuigb]

No breaking changes noted.