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/2025-02-24/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/2025-02-24/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 IAO_0000115 "Any epithelial cell that is part of some gingival epithelium."

  • hasDbXref "FBC:Autogenerated"

• gingival epithelial cell EquivalentTo epithelial cell and (BFO_0000050 some UBERON_0001949)

Added

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

  • hasDbXref "FBC:Autogenerated"

• gingival epithelial cell EquivalentTo stratified squamous epithelial cell and (BFO_0000050 some UBERON_0001949)

• gingival epithelial cell SubClassOf stratified squamous epithelial cell

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

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

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

Removed

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

Added

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

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

Added

• kidney loop of Henle short descending thin limb 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 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 has characteristic 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

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

Added

• stratified squamous epithelial cell SubClassOf squamous epithelial cell

[Caroline-99]

#gogoeditdiff

[dosumis]

Looks like peridermal cells are squamous:

From Perplexity search

Peridermal cells in the context of embryology are squamous. During embryogenesis, the immature ectoderm initially consists of cuboidal epithelial cells, which stratify to form a superficial layer of flattened, squamous-like peridermal cells. These cells are described as flattened and endothelial-like, covering the developing epithelia as a single layer throughout much of embryonic development before being shed or replaced by terminally differentiated keratinocytes later in development123.

This squamous morphology allows peridermal cells to act as a protective barrier, preventing pathological adhesions between epithelial surfaces during critical stages of development24.

Everything else looks good to me

[Caroline-99]

Looks like peridermal cells are squamous:

From Perplexity search

Peridermal cells in the context of embryology are squamous. During embryogenesis, the immature ectoderm initially consists of cuboidal epithelial cells, which stratify to form a superficial layer of flattened, squamous-like peridermal cells. These cells are described as flattened and endothelial-like, covering the developing epithelia as a single layer throughout much of embryonic development before being shed or replaced by terminally differentiated keratinocytes later in development123.
This squamous morphology allows peridermal cells to act as a protective barrier, preventing pathological adhesions between epithelial surfaces during critical stages of development24.

Everything else looks good to me

I have checked the references provided by perplexity and updated periderm cell's logical defs. I have also double checked the references for kidney loop of Henle short descending thin limb epithelial cell