Enterocyte refactor renaming

[JABelfiore]

No description provided.

[dosumis]

#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/2025-03-12/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/2025-03-12/cl-base.owl
• Loaded from: file:/__w/cell-ontology/cell-ontology/src/ontology/cl-base-pr.owl/cl-base.owl

Ontology imports

Ontology annotations

enterocyte http://purl.obolibrary.org/obo/CL_0000584

Removed

• enterocyte IAO_0000115 "An epithelial cell that has its apical plasma membrane folded into microvilli to provide ample surface for the absorption of nutrients from the intestinal lumen."

  • hasDbXref "SANBI:mhl"

• enterocyte hasNarrowSynonym "differentiated enterocyte"

  • hasDbXref "https://orcid.org/0000-0001-9610-7627"

  • hasDbXref "PMID:33290721"

Added

• enterocyte IAO_0000115 "An epithelial cell that has its apical plasma membrane folded into microvilli to provide ample surface for the absorption of nutrients from the intestinal lumen. This covers both the large and small intestine."
  • hasDbXref "SANBI:mhl"

enterocyte of epithelium of intestinal villus http://purl.obolibrary.org/obo/CL_1000335

Added

• enterocyte of epithelium of intestinal villus hasExactSynonym "late small intestine enterocyte"

• enterocyte of epithelium of intestinal villus hasExactSynonym "mature small intestine enterocyte"

immature colonocyte http://purl.obolibrary.org/obo/CL_4047018

Removed

• immature colonocyte label "early colonocyte"@en

• immature colonocyte EquivalentTo immature small intestine enterocyte and (BFO_0000050 some UBERON_0000397)

• immature colonocyte SubClassOf immature small intestine enterocyte

Added

• immature colonocyte label "immature colonocyte"@en

• immature colonocyte hasExactSynonym "early colonocyte"

immature small intestine enterocyte http://purl.obolibrary.org/obo/CL_4047019

Removed

• immature small intestine enterocyte label "early enterocyte"@en

Added

• immature small intestine enterocyte label "immature small intestine enterocyte"@en

• immature small intestine enterocyte hasExactSynonym "early enterocyte"

immature small intestine entrocyte http://purl.obolibrary.org/obo/CL_0008050

Added

• immature small intestine entrocyte label "immature small intestine entrocyte"

• immature small intestine entrocyte date "2025-03-11T18:54:02Z"^^dateTime

• immature small intestine entrocyte contributor 0000-0002-7073-9172

• Class: immature small intestine entrocyte

• immature small intestine entrocyte SubClassOf small intestine enterocyte

mature colonocyte http://purl.obolibrary.org/obo/CL_0008052

Added

• mature colonocyte date "2025-03-11T18:55:58Z"^^dateTime

• mature colonocyte label "mature colonocyte"

• mature colonocyte contributor 0000-0002-7073-9172

• Class: mature colonocyte

• mature colonocyte SubClassOf colonocyte

• mature colonocyte SubClassOf RO_0002207 some immature colonocyte

mature small intestince enterocyte http://purl.obolibrary.org/obo/CL_0008051

Added

• mature small intestince enterocyte date "2025-03-11T18:54:17Z"^^dateTime

• mature small intestince enterocyte label "mature small intestince enterocyte"

• mature small intestince enterocyte contributor 0000-0002-7073-9172

• Class: mature small intestince enterocyte

• mature small intestince enterocyte SubClassOf RO_0002207 some immature small intestine enterocyte

• mature small intestince enterocyte SubClassOf small intestine enterocyte

small intestine enterocyte http://purl.obolibrary.org/obo/CL_1000334

Removed

• small intestine enterocyte label "enterocyte of epithelium of small intestine"

Added

• small intestine enterocyte hasExactSynonym "enterocyte of epithelium of small intestine"

• small intestine enterocyte label "small intestine enterocyte"

[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

early colonocyte http://purl.obolibrary.org/obo/CL_4047018

Removed

• early colonocyte label "early colonocyte"@en

• early colonocyte EquivalentTo early enterocyte and (part of some colonic epithelium)

Added

• early colonocyte label "immature colonocyte"@en

• early colonocyte has_exact_synonym "early colonocyte"

• early colonocyte SubClassOf colonocyte

early enterocyte http://purl.obolibrary.org/obo/CL_4047019

Removed

• early enterocyte label "early enterocyte"@en

Added

• early enterocyte label "immature small intestine enterocyte"@en

• early enterocyte has_exact_synonym "early enterocyte"

enterocyte http://purl.obolibrary.org/obo/CL_0000584

Removed

• enterocyte definition "An epithelial cell that has its apical plasma membrane folded into microvilli to provide ample surface for the absorption of nutrients from the intestinal lumen."

  • database_cross_reference "SANBI:mhl"

• enterocyte has_narrow_synonym "differentiated enterocyte"

  • database_cross_reference "https://orcid.org/0000-0001-9610-7627"

  • database_cross_reference "PMID:33290721"

Added

• enterocyte definition "An epithelial cell that has its apical plasma membrane folded into microvilli to provide ample surface for the absorption of nutrients from the intestinal lumen. This covers both the large and small intestine."
  • database_cross_reference "SANBI:mhl"

enterocyte of epithelium of intestinal villus http://purl.obolibrary.org/obo/CL_1000335

Added

• enterocyte of epithelium of intestinal villus has_exact_synonym "late small intestine enterocyte"

• enterocyte of epithelium of intestinal villus has_exact_synonym "mature small intestine enterocyte"

enterocyte of epithelium of small intestine http://purl.obolibrary.org/obo/CL_1000334

Removed

• enterocyte of epithelium of small intestine label "enterocyte of epithelium of small intestine"

Added

• enterocyte of epithelium of small intestine has_exact_synonym "enterocyte of epithelium of small intestine"

• enterocyte of epithelium of small intestine label "small intestine enterocyte"

immature small intestine entrocyte http://purl.obolibrary.org/obo/CL_0008050

Added

• immature small intestine entrocyte label "immature small intestine entrocyte"

• immature small intestine entrocyte date "2025-03-11T18:54:02Z"^^dateTime

• immature small intestine entrocyte contributor 0000-0002-7073-9172

• Class: immature small intestine entrocyte

• immature small intestine entrocyte SubClassOf enterocyte of epithelium of small intestine

mature colonocyte http://purl.obolibrary.org/obo/CL_0008052

Added

• mature colonocyte date "2025-03-11T18:55:58Z"^^dateTime

• mature colonocyte label "mature colonocyte"

• mature colonocyte contributor 0000-0002-7073-9172

• Class: mature colonocyte

• mature colonocyte SubClassOf colonocyte

• mature colonocyte SubClassOf directly develops from some early colonocyte

mature small intestince enterocyte http://purl.obolibrary.org/obo/CL_0008051

Added

• mature small intestince enterocyte date "2025-03-11T18:54:17Z"^^dateTime

• mature small intestince enterocyte label "mature small intestince enterocyte"

• mature small intestince enterocyte contributor 0000-0002-7073-9172

• Class: mature small intestince enterocyte

• mature small intestince enterocyte SubClassOf directly develops from some early enterocyte

• mature small intestince enterocyte SubClassOf enterocyte of epithelium of small intestine

[dosumis]

#gogoeditdiff

[github-actions]

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[dosumis]

#gogoeditdiff

[dosumis]

Remaining issues:

1. General definition of enterocyte refers to mature state. Ditto colonocyte.
2. Defs needed for mature colonocyte + immature and mature small intestine enterocyte
3. EC def of immature small intestine enterocyte is dubious
4. Species neutral terminology: Can we make enterocyte neutral, or should we aim to use 'gut absorptive cell'? A: making either species neutral requires deleting taxon restriction on mucosa to chordata (in Uberon). Suggest push to second ticket.