Fixes #2671 - Clean up squamous epithelial cell and subclasses

[Caroline-99]

Fixes #2671 -

Squamous epithelial cell and subclasses

[Caroline-99]

#gogoeditdiff

[github-actions]

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

Ontology comparison

Left

• Ontology IRI: http://purl.obolibrary.org/obo/cl/cl-base.owl
• Version IRI: http://purl.obolibrary.org/obo/cl/releases/2025-02-12/cl-base.owl
• Loaded from: file:/__w/cell-ontology/cell-ontology/src/ontology/cl-base-master.owl/cl-base.owl

Right

• Ontology IRI: http://purl.obolibrary.org/obo/cl/cl-base.owl
• Version IRI: http://purl.obolibrary.org/obo/cl/releases/2025-02-12/cl-base.owl
• Loaded from: file:/__w/cell-ontology/cell-ontology/src/ontology/cl-base-pr.owl/cl-base.owl

Ontology imports

Ontology annotations

Caenorhabditis hypodermal cell http://purl.obolibrary.org/obo/CL_0000411

Removed

• Caenorhabditis hypodermal cell SubClassOf squamous epithelial cell

Added

• Caenorhabditis hypodermal cell SubClassOf epithelial cell

PATO_0001872 http://purl.obolibrary.org/obo/PATO_0001872

Added

• Class: PATO_0001872

UBERON_0003055 http://purl.obolibrary.org/obo/UBERON_0003055

Added

• Class: UBERON_0003055

UBERON_0006914 http://purl.obolibrary.org/obo/UBERON_0006914

Removed

• Class: UBERON_0006914

conjunctiva goblet cell http://purl.obolibrary.org/obo/CL_2000084

Removed

• conjunctiva goblet cell SubClassOf squamous epithelial cell

gingival epithelial cell http://purl.obolibrary.org/obo/CL_0002621

Removed

• gingival epithelial cell SubClassOf oral mucosa squamous cell

Added

• gingival epithelial cell SubClassOf epithelial cell of alimentary canal

kidney loop of Henle short descending thin limb epithelial cell http://purl.obolibrary.org/obo/CL_4030012

Removed

• kidney loop of Henle short descending thin limb epithelial cell SubClassOf squamous epithelial cell

obsolete neuronal brush cell http://purl.obolibrary.org/obo/CL_0000555

Removed

• obsolete neuronal brush cell comment "[Obsolete] neuronal brush cell #2634"

parietal epithelial cell http://purl.obolibrary.org/obo/CL_1000452

Removed

• parietal epithelial cell SubClassOf squamous epithelial cell

peridermal cell http://purl.obolibrary.org/obo/CL_0000078

Removed

• peridermal cell SubClassOf squamous epithelial cell

Added

• peridermal cell IAO_0000115 "Any epithelial cell that is part of some periderm."

  • hasDbXref "FBC:Autogenerated"

• peridermal cell EquivalentTo epithelial cell and (BFO_0000050 some UBERON_0003055)

• peridermal cell SubClassOf epidermal cell

• peridermal cell SubClassOf BFO_0000050 some UBERON_0003055

pulmonary alveolar epithelial cell http://purl.obolibrary.org/obo/CL_0000322

Removed

• pulmonary alveolar epithelial cell SubClassOf squamous epithelial cell

pulmonary alveolar type 1 cell http://purl.obolibrary.org/obo/CL_0002062

Added

• pulmonary alveolar type 1 cell SubClassOf squamous epithelial cell

pulmonary alveolar type 2 cell http://purl.obolibrary.org/obo/CL_0002063

Added

• pulmonary alveolar type 2 cell SubClassOf RO_0000053 some PATO_0001872

squamous epithelial cell http://purl.obolibrary.org/obo/CL_0000076

Removed

• squamous epithelial cell IAO_0000115 "Any epithelial cell that is part of some squamous epithelium."

  • hasDbXref "FBC:Autogenerated"

• squamous epithelial cell EquivalentTo epithelial cell and (BFO_0000050 some UBERON_0006914)

• squamous epithelial cell SubClassOf BFO_0000050 some UBERON_0006914

stratified squamous epithelial cell http://purl.obolibrary.org/obo/CL_0000240

Removed

• stratified squamous epithelial cell SubClassOf squamous epithelial cell

type A synovial cell http://purl.obolibrary.org/obo/CL_0002302

Removed

• type A synovial cell SubClassOf squamous epithelial cell

type B synovial cell http://purl.obolibrary.org/obo/CL_0002301

Removed

• type B synovial cell SubClassOf squamous epithelial cell

[github-actions]

Here's a diff of your edit file (unreasoned)

Ontology comparison

Left

• Ontology IRI: http://purl.obolibrary.org/obo/cl-edit.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-edit.owl
• Version IRI: None
• Loaded from: file:/__w/cell-ontology/cell-ontology/branch/src/ontology/cl-edit.owl

Ontology imports

Ontology annotations

Caenorhabditis hypodermal cell http://purl.obolibrary.org/obo/CL_0000411

Removed

• Caenorhabditis hypodermal cell SubClassOf squamous epithelial cell

Added

• Caenorhabditis hypodermal cell SubClassOf epithelial cell

cuboid http://purl.obolibrary.org/obo/PATO_0001872

Added

• Class: cuboid

peridermal cell http://purl.obolibrary.org/obo/CL_0000078

Removed

• peridermal cell SubClassOf squamous epithelial cell

Added

• peridermal cell EquivalentTo epithelial cell and (part of some periderm)

pulmonary alveolar type 1 cell http://purl.obolibrary.org/obo/CL_0002062

Added

• pulmonary alveolar type 1 cell SubClassOf squamous epithelial cell

pulmonary alveolar type 2 cell http://purl.obolibrary.org/obo/CL_0002063

Removed

• pulmonary alveolar type 2 cell SubClassOf squamous epithelial cell

Added

• pulmonary alveolar type 2 cell SubClassOf bearer of some cuboid

squamous epithelial cell http://purl.obolibrary.org/obo/CL_0000076

Removed

• squamous epithelial cell EquivalentTo epithelial cell and (part of some squamous epithelium)

Added

• squamous epithelial cell SubClassOf epithelial cell