Fixes #2925 Conjunctiva goblet cell

[Caroline-99]

Fixes #2925

• Improved textual and logical definition
• Added references

I am trying to find GO links for this term - In literature, Conjunctiva goblet cell is involved in delivering soluble antigen to dendritic cells through goblet cell-associated antigen passages (included in the textual definition) . Would this term positive regulation of peptide antigen transport be appropriate ?

[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/2025-02-03/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/2025-02-03/cl-base.owl
• Loaded from: file:/__w/cell-ontology/cell-ontology/src/ontology/cl-base-pr.owl/cl-base.owl

Ontology imports

Ontology annotations

UBERON_0006763 http://purl.obolibrary.org/obo/UBERON_0006763

Added

• Class: UBERON_0006763

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

Removed

• conjunctiva goblet cell IAO_0000115 "Any goblet cell that is part of a conjunctiva."

  • hasDbXref "GOC:TermGenie"

• conjunctiva goblet cell id "CL:2000084"

• conjunctiva goblet cell EquivalentTo goblet cell and (BFO_0000050 some UBERON_0001811)

Added

• conjunctiva goblet cell hasRelatedSynonym "CGCs"

  • hasDbXref "PMID:31734511"

  • hasSynonymType OMO_0003000

• conjunctiva goblet cell IAO_0000115 "A goblet cell that is part of the conjunctival epithelium, characterized by apical accumulation of mucin granules (MUC5AC in humans; Muc5ac/Muc5b in mice). These gel-forming mucins support tear film stability, ocular lubrication, and pathogen defence. The conjunctival goblet cell forms tight junctions with neighbouring epithelial cells via species-specific claudins (claudin-10 in humans, claudin-2 in mice) and regulates immune homeostasis by facilitating soluble antigen transport to dendritic cells through goblet cell-associated antigen passages (GAPs) (Barbosa et al., 2017). The transcription factor SPDEF is essential for its differentiation."

  • hasDbXref "PMID:28475124"

  • hasDbXref "PMID:27091323"

  • hasDbXref "PMID:31734511"

  • hasDbXref "GOC:TermGenie"

• conjunctiva goblet cell EquivalentTo goblet cell and (BFO_0000050 some UBERON_0006763)

• conjunctiva goblet cell SubClassOf squamous epithelial cell

• conjunctiva goblet cell SubClassOf BFO_0000050 some UBERON_0006763

[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

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

Removed

• conjunctiva goblet cell definition "Any goblet cell that is part of a conjunctiva."

  • has cross-reference "GOC:TermGenie"

• conjunctiva goblet cell id "CL:2000084"

• conjunctiva goblet cell EquivalentTo goblet cell and (part of some conjunctiva)

Added

• conjunctiva goblet cell has_related_synonym "CGCs"

  • has cross-reference "PMID:31734511"

  • has_synonym_type abbreviation

• conjunctiva goblet cell definition "A goblet cell that is part of the conjunctival epithelium, characterized by apical accumulation of mucin granules (MUC5AC in humans; Muc5ac/Muc5b in mice). These gel-forming mucins support tear film stability, ocular lubrication, and pathogen defence. The conjunctival goblet cell forms tight junctions with neighbouring epithelial cells via species-specific claudins (claudin-10 in humans, claudin-2 in mice) and regulates immune homeostasis by facilitating soluble antigen transport to dendritic cells through goblet cell-associated antigen passages (GAPs) (Barbosa et al., 2017). The transcription factor SPDEF is essential for its differentiation."

  • has cross-reference "PMID:31734511"

  • has cross-reference "PMID:28475124"

  • has cross-reference "PMID:27091323"

  • has cross-reference "GOC:TermGenie"

• conjunctiva goblet cell EquivalentTo goblet cell and (part of some epithelium of conjunctiva)

[aleixpuigb]

Please, see inline comments