Fixes #2429 merge 'epithelial cell of alveolus of lung'

[aleixpuigb]

Fixes #2429 merge 'epithelial cell of alveolus of lung' into 'pulmonary alveolar epithelial cell'.
Also adds SubclassOf 'squamous epithelial cell' to 'pulmonary alveolar type 1' cell.
'pulmonary alveolar epithelial cell' is classified as 'squamous epithelial cell' because the alveolar epithelium in uberon is categorized as squamous, although pulmoanry alveolar cells type 2 are not squamous. Getting fixed in obophenotype/uberon#3350

[aleixpuigb]

#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/2024-09-02/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/2024-09-02/cl-simple.owl
• Loaded from: file:/__w/cell-ontology/cell-ontology/src/ontology/cl-simple-pr.owl/cl-simple.owl

Ontology imports

Ontology annotations

epithelial cell of alveolus of lung http://purl.obolibrary.org/obo/CL_0010003

Removed

• epithelial cell of alveolus of lung definition "An epithelial cell that is part_of a alveolus of lung."

• epithelial cell of alveolus of lung comment "May be merged with pneumocyte in future"

• epithelial cell of alveolus of lung label "epithelial cell of alveolus of lung"

• epithelial cell of alveolus of lung SubClassOf epithelial cell

Added

• epithelial cell of alveolus of lung term tracker item 2429

• epithelial cell of alveolus of lung label "obsolete epithelial cell of alveolus of lung"

• epithelial cell of alveolus of lung deprecated true

• epithelial cell of alveolus of lung comment "This cell type is exactly the same as 'pulmonary alveolar epithelial cell'."

• epithelial cell of alveolus of lung term replaced by pulmonary alveolar epithelial cell

• epithelial cell of alveolus of lung definition "OBSOLETE. An epithelial cell that is part_of a alveolus of lung."

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

Removed

• pulmonary alveolar epithelial cell SubClassOf epithelial cell of alveolus of lung

Added

• pulmonary alveolar epithelial cell contributor 0000-0001-6677-8489

• pulmonary alveolar epithelial cell has exact synonym "alveolus of lung epithelial cell"

• pulmonary alveolar epithelial cell has exact synonym "epithelial cell of alveolus of lung"

• pulmonary alveolar epithelial cell date "2024-09-02T08:27:21Z"^^dateTime

• pulmonary alveolar epithelial cell database_cross_reference "MESH:D056809"

[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

obsolete epithelial cell of alveolus of lung http://purl.obolibrary.org/obo/CL_0010003

Removed

• obsolete epithelial cell of alveolus of lung definition "An epithelial cell that is part_of a alveolus of lung."

• obsolete epithelial cell of alveolus of lung comment "May be merged with pneumocyte in future"

• obsolete epithelial cell of alveolus of lung label "epithelial cell of alveolus of lung"

• obsolete epithelial cell of alveolus of lung EquivalentTo epithelial cell and (part of some alveolus of lung)

Added

• obsolete epithelial cell of alveolus of lung term tracker item 2429

• obsolete epithelial cell of alveolus of lung label "obsolete epithelial cell of alveolus of lung"

• obsolete epithelial cell of alveolus of lung deprecated true

• obsolete epithelial cell of alveolus of lung comment "This cell type is exactly the same as 'pulmonary alveolar epithelial cell'."

• obsolete epithelial cell of alveolus of lung term replaced by pulmonary alveolar epithelial cell

• obsolete epithelial cell of alveolus of lung definition "OBSOLETE. An epithelial cell that is part_of a alveolus of lung."

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

Removed

• pulmonary alveolar epithelial cell SubClassOf part of some pulmonary alveolus epithelium

• pulmonary alveolar epithelial cell SubClassOf epithelial cell

Added

• pulmonary alveolar epithelial cell contributor 0000-0001-6677-8489

• pulmonary alveolar epithelial cell has exact synonym "alveolus of lung epithelial cell"

• pulmonary alveolar epithelial cell has exact synonym "epithelial cell of alveolus of lung"

• pulmonary alveolar epithelial cell date "2024-09-02T08:27:21Z"^^dateTime

• pulmonary alveolar epithelial cell database_cross_reference "MESH:D056809"

• pulmonary alveolar epithelial cell EquivalentTo epithelial cell and (part of some pulmonary alveolus epithelium)

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

Added

• pulmonary alveolar type 2 cell SubClassOf squamous epithelial cell